G4MolecularConfiguration Class Reference

#include <G4MolecularConfiguration.hh>

Classes
class	G4MolecularConfigurationManager

Public Types
using	G4DiffCoeffParam = std::function<double (const G4Material *, double, const G4MolecularConfiguration *)>

Public Member Functions
void	AddDiffCoeffParameterization (const G4DiffCoeffParam &)
const G4MoleculeDefinition *	GetDefinition () const
const G4String &	GetName () const
const G4String &	GetFormatedName () const
G4int	GetAtomsNumber () const
G4MolecularConfiguration *	ExciteMolecule (G4int) const
G4MolecularConfiguration *	IonizeMolecule (G4int) const
G4MolecularConfiguration *	AddElectron (G4int orbit, G4int n=1) const
G4MolecularConfiguration *	RemoveElectron (G4int, G4int number=1) const
G4MolecularConfiguration *	MoveOneElectron (G4int, G4int) const
G4double	GetNbElectrons () const
void	PrintState () const
const std::vector< const G4MolecularDissociationChannel * > *	GetDissociationChannels () const
G4int	GetFakeParticleID () const
G4int	GetMoleculeID () const
void	SetDiffusionCoefficient (G4double)
G4double	GetDiffusionCoefficient () const
G4double	GetDiffusionCoefficient (const G4Material *, double temperature) const
void	SetDecayTime (G4double)
G4double	GetDecayTime () const
void	SetVanDerVaalsRadius (G4double)
G4double	GetVanDerVaalsRadius () const
const G4ElectronOccupancy *	GetElectronOccupancy () const
G4int	GetCharge () const
void	SetMass (G4double)
G4double	GetMass () const
void	SetLabel (const G4String &)
const G4String &	GetLabel () const
void	Finalize ()
void	UnFinalize ()
void	SetUserID (const G4String &userID)
const G4String &	GetUserID () const
void	Serialize (std::ostream &)
void	Unserialize (std::istream &)

Static Public Member Functions
static G4MolecularConfiguration *	GetOrCreateMolecularConfiguration (const G4MoleculeDefinition *)
static G4MolecularConfiguration *	GetOrCreateMolecularConfiguration (const G4MoleculeDefinition *, const G4ElectronOccupancy &eOcc)
static G4MolecularConfiguration *	GetOrCreateMolecularConfiguration (const G4MoleculeDefinition *, int charge)
static G4MolecularConfiguration *	CreateMolecularConfiguration (const G4String &userIdentifier, const G4MoleculeDefinition *, bool &wasAlreadyCreated)
static G4MolecularConfiguration *	CreateMolecularConfiguration (const G4String &userIdentifier, const G4MoleculeDefinition *, const G4String &label, const G4ElectronOccupancy &eOcc, bool &wasAlreadyCreated)
static G4MolecularConfiguration *	CreateMolecularConfiguration (const G4String &userIdentifier, const G4MoleculeDefinition *, int charge, const G4String &label, bool &wasAlreadyCreated)
static G4MolecularConfiguration *	CreateMolecularConfiguration (const G4String &userIdentifier, const G4MoleculeDefinition *, const G4String &label, bool &wasAlreadyCreated)
static G4MolecularConfiguration *	GetMolecularConfiguration (const G4MoleculeDefinition *, const G4String &label)
static G4MolecularConfiguration *	GetMolecularConfiguration (int moleculeID)
static G4MolecularConfiguration *	GetMolecularConfiguration (const G4String &userID)
static int	GetNumberOfSpecies ()
static std::map< G4String, G4MolecularConfiguration * > &	GetUserIDTable ()
static void	DeleteManager ()
static double	DiffCoeffWater (double temperature_K)
static void	FinalizeAll ()
static void	PrintAll ()
static void	SetGlobalTemperature (G4double)
static G4double	GetGlobalTemperature ()
static G4MolecularConfiguration *	Load (std::istream &)

Protected Member Functions
	G4MolecularConfiguration (const G4MoleculeDefinition *, const G4ElectronOccupancy &, const G4String &label="")
	G4MolecularConfiguration (const G4MoleculeDefinition *, int charge)
	G4MolecularConfiguration (const G4MoleculeDefinition *, const G4String &label, int charge)
	G4MolecularConfiguration (std::istream &)
	G4MolecularConfiguration (const G4MolecularConfiguration &)
G4MolecularConfiguration &	operator= (G4MolecularConfiguration &right)
	~G4MolecularConfiguration ()
G4MolecularConfiguration *	ChangeConfiguration (const G4ElectronOccupancy &newElectronOccupancy) const
G4MolecularConfiguration *	ChangeConfiguration (int charge) const
void	CheckElectronOccupancy (const char *line) const
void	MakeExceptionIfFinalized ()
void	CreateDefaultDiffCoeffParam ()

Static Protected Member Functions
static void	ScaleAllDiffusionCoefficientsOnWater (double temperature_K)
static G4MolecularConfigurationManager *	GetManager ()
static double	ReturnDefaultDiffCoeff (const G4Material *, double, const G4MolecularConfiguration *molConf)

Protected Attributes
const G4MoleculeDefinition *	fMoleculeDefinition
const G4ElectronOccupancy *	fElectronOccupancy
G4String *	fLabel
G4double	fDynDiffusionCoefficient
G4double	fDynVanDerVaalsRadius
G4double	fDynDecayTime
G4double	fDynMass
G4int	fDynCharge
G4int	fMoleculeID
G4String	fFormatedName
G4String	fName
G4String	fUserIdentifier
G4bool	fIsFinalized
G4DiffCoeffParam	fDiffParam

Static Protected Attributes
static G4MolecularConfigurationManager *	fgManager = nullptr
static double	fgTemperature = 298

Detailed Description

The pointer G4MolecularConfiguration will be shared by all the molecules having the same molecule definition and the same electron occupancy BE CAREFUlL !!! : If you change the mass for instance of a OH^-, this will affect all the OH^- molecule diffusing around

Definition at line 97 of file G4MolecularConfiguration.hh.

Member Typedef Documentation

G4DiffCoeffParam

using G4MolecularConfiguration::G4DiffCoeffParam = std::function<double (const G4Material *, double, const G4MolecularConfiguration *)>

Definition at line 101 of file G4MolecularConfiguration.hh.

Constructor & Destructor Documentation

G4MolecularConfiguration() [1/5]

G4MolecularConfiguration::G4MolecularConfiguration ( const G4MoleculeDefinition * moleculeDef, const G4ElectronOccupancy & elecOcc, const G4String & label = "" )

protected

Definition at line 412 of file G4MolecularConfiguration.cc.

{
  fMoleculeDefinition = moleculeDef;
 
  fMoleculeID = GetManager()->Insert(moleculeDef,
                                     elecOcc,
                                     this);
  fElectronOccupancy = GetManager()->FindCommonElectronOccupancy(moleculeDef,
                                                                 elecOcc);
 
  /*
   fgManager->fTable[fMoleculeDefinition][elecOcc] = this;
   std::map<G4ElectronOccupancy, G4MolecularConfiguration*, comparator>::iterator it ;
   it = fgManager->fTable[moleculeDef].find(elecOcc);
   fElectronOccupancy = &(it->first);
   */
 
  fDynCharge = fMoleculeDefinition->GetNbElectrons()
      - fElectronOccupancy->GetTotalOccupancy()
               + moleculeDef->GetCharge();
  fDynMass = fMoleculeDefinition->GetMass();
 
  fDynDiffusionCoefficient = fMoleculeDefinition->GetDiffusionCoefficient();
  fDynVanDerVaalsRadius = fMoleculeDefinition->GetVanDerVaalsRadius();
  fDynDecayTime = fMoleculeDefinition->GetDecayTime();
 
  fName = fMoleculeDefinition->GetName();
  fName += "^";
  fName += G4UIcommand::ConvertToString(fDynCharge);
 
  fFormatedName = fMoleculeDefinition->GetFormatedName();
  fFormatedName += "^";
  fFormatedName += "{";
  fFormatedName += G4UIcommand::ConvertToString(fDynCharge);
  fFormatedName += "}";
 
  fLabel = nullptr; // let it here
 
  if(!label.empty())
  {
    SetLabel(label);
  }
 
  fDiffParam = &G4MolecularConfiguration::ReturnDefaultDiffCoeff;
 
  fIsFinalized = false;
}

Referenced by AddElectron(), G4MolecularConfiguration::G4MolecularConfigurationManager::AddUserID(), ChangeConfiguration(), ChangeConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration::G4MolecularConfigurationManager::GetOrCreateMolecularConfiguration(), G4MolecularConfiguration::G4MolecularConfigurationManager::GetOrCreateMolecularConfiguration(), GetOrCreateMolecularConfiguration(), GetOrCreateMolecularConfiguration(), G4MolecularConfiguration::G4MolecularConfigurationManager::Insert(), G4MolecularConfiguration::G4MolecularConfigurationManager::Insert(), G4MolecularConfiguration::G4MolecularConfigurationManager::Insert(), Load(), operator=(), G4MolecularConfiguration::G4MolecularConfigurationManager::RecordNewlyLabeledConfiguration(), G4MolecularConfiguration::G4MolecularConfigurationManager::RemoveMolecularConfigurationFromTable(), ReturnDefaultDiffCoeff(), and ScaleAllDiffusionCoefficientsOnWater().

G4MolecularConfiguration() [2/5]

G4MolecularConfiguration::G4MolecularConfiguration ( const G4MoleculeDefinition * moleculeDef, int charge )

protected

Definition at line 465 of file G4MolecularConfiguration.cc.

{
  fMoleculeDefinition = moleculeDef;
 
  fMoleculeID = GetManager()->Insert(moleculeDef,
                                     charge,
                                     this);
  fElectronOccupancy = nullptr;
 
  fDynCharge = charge;
  fDynMass = fMoleculeDefinition->GetMass();
 
  fDynDiffusionCoefficient = fMoleculeDefinition->GetDiffusionCoefficient();
  fDynVanDerVaalsRadius = fMoleculeDefinition->GetVanDerVaalsRadius();
  fDynDecayTime = fMoleculeDefinition->GetDecayTime();
 
  fName = fMoleculeDefinition->GetName();
  fName += "^";
  fName += G4UIcommand::ConvertToString(fDynCharge);
 
  fFormatedName = fMoleculeDefinition->GetFormatedName();
  fFormatedName += "^";
  fFormatedName += "{";
  fFormatedName += G4UIcommand::ConvertToString(fDynCharge);
  fFormatedName += "}";
 
  fLabel = nullptr;
 
  fDiffParam = &G4MolecularConfiguration::ReturnDefaultDiffCoeff;
 
  fIsFinalized = false;
}

G4MolecularConfiguration() [3/5]

G4MolecularConfiguration::G4MolecularConfiguration ( const G4MoleculeDefinition * moleculeDef, const G4String & label, int charge )

protected

Definition at line 77 of file G4MolecularConfiguration.cc.

{
  fMoleculeDefinition = moleculeDef;
 
  fLabel = new G4String(label);
 
  fMoleculeID = GetManager()->Insert(moleculeDef,
                                     label,
                                     this);
  fElectronOccupancy = nullptr;
 
  fDynCharge = charge;
 
  fDynMass = fMoleculeDefinition->GetMass();
 
  fDynDiffusionCoefficient = fMoleculeDefinition->GetDiffusionCoefficient();
  fDynVanDerVaalsRadius = fMoleculeDefinition->GetVanDerVaalsRadius();
  fDynDecayTime = fMoleculeDefinition->GetDecayTime();
 
  fName = fMoleculeDefinition->GetName();
  fName += "^";
  fName += G4UIcommand::ConvertToString(fDynCharge);
 
  fFormatedName = fMoleculeDefinition->GetFormatedName();
  fFormatedName += "^";
  fFormatedName += "{";
  fFormatedName += G4UIcommand::ConvertToString(fDynCharge);
  fFormatedName += "}";
 
  fDiffParam = &G4MolecularConfiguration::ReturnDefaultDiffCoeff;
  fIsFinalized = false;
}

G4MolecularConfiguration() [4/5]

G4MolecularConfiguration::G4MolecularConfiguration ( std::istream & in )

protected

Definition at line 1379 of file G4MolecularConfiguration.cc.

{
  fLabel = nullptr; // TODO: for now not serialized
  Unserialize(in);
  fMoleculeDefinition = nullptr;
  fElectronOccupancy = nullptr;
  if(fElectronOccupancy != nullptr)
  {
    GetManager()->Insert(fMoleculeDefinition, *fElectronOccupancy, this);
    fElectronOccupancy =
        GetManager()->FindCommonElectronOccupancy(fMoleculeDefinition,
                                                  *fElectronOccupancy);
 
    if(fLabel != nullptr)
    {
      GetManager()->RecordNewlyLabeledConfiguration(this);
    }
  }
  else if(fLabel != nullptr)
  {
    fMoleculeID = GetManager()->Insert(fMoleculeDefinition, *fLabel, this);
  }
  else if(fDynCharge != 0)
  {
    fMoleculeID = GetManager()->Insert(fMoleculeDefinition, fDynCharge, this);
  }
}

G4MolecularConfiguration() [5/5]

G4MolecularConfiguration::G4MolecularConfiguration ( const G4MolecularConfiguration & )

protected

~G4MolecularConfiguration()

G4MolecularConfiguration::~G4MolecularConfiguration ( )

protected

Definition at line 502 of file G4MolecularConfiguration.cc.

{
  if (fgManager != nullptr) fgManager->RemoveMolecularConfigurationFromTable(this);
}

Member Function Documentation

AddDiffCoeffParameterization()

void G4MolecularConfiguration::AddDiffCoeffParameterization ( const G4DiffCoeffParam & para )

inline

Definition at line 572 of file G4MolecularConfiguration.hh.

{
  fDiffParam = para;
}

AddElectron()

G4MolecularConfiguration * G4MolecularConfiguration::AddElectron	(	G4int	orbit,
		G4int	n = 1 ) const

Add n electrons to a given orbit. Note : You can add as many electrons to a given orbit, the result may be unrealist.

Definition at line 602 of file G4MolecularConfiguration.cc.

{
//  MakeExceptionIfFinalized();
  CheckElectronOccupancy(__func__);
  G4ElectronOccupancy newElectronOccupancy(*fElectronOccupancy);
  newElectronOccupancy.AddElectron(orbit, number);
  return ChangeConfiguration(newElectronOccupancy);
}

ChangeConfiguration() [1/2]

G4MolecularConfiguration * G4MolecularConfiguration::ChangeConfiguration ( const G4ElectronOccupancy & newElectronOccupancy ) const

protected

Definition at line 510 of file G4MolecularConfiguration.cc.

{
  G4MolecularConfiguration* output =
      GetManager()->GetMolecularConfiguration(fMoleculeDefinition,
                                              newElectronOccupancy);
 
  if (output == nullptr)
  {
    output = new G4MolecularConfiguration(fMoleculeDefinition,
                                          newElectronOccupancy);
  }
  return output;
}

Referenced by AddElectron(), ExciteMolecule(), IonizeMolecule(), MoveOneElectron(), and RemoveElectron().

ChangeConfiguration() [2/2]

G4MolecularConfiguration * G4MolecularConfiguration::ChangeConfiguration ( int charge ) const

protected

Definition at line 528 of file G4MolecularConfiguration.cc.

{
  G4MolecularConfiguration* output =
      GetManager()->GetMolecularConfiguration(fMoleculeDefinition, charge);
 
  if (output == nullptr)
  {
    output = new G4MolecularConfiguration(fMoleculeDefinition, charge);
  }
  return output;
}

CheckElectronOccupancy()

void G4MolecularConfiguration::CheckElectronOccupancy ( const char * line ) const

protected

Definition at line 774 of file G4MolecularConfiguration.cc.

{
  if (fElectronOccupancy == nullptr)
  {
    G4String functionName(function);
    G4ExceptionDescription description;
    description
        << "No G4ElectronOccupancy was defined for molecule definition : "
        << fMoleculeDefinition->GetName()
        << ". The definition was probably defined using the charge state, "
            "rather than electron state.";
 
    G4Exception(functionName, "", FatalErrorInArgument, description);
  }
}

Referenced by AddElectron(), ExciteMolecule(), GetNbElectrons(), IonizeMolecule(), MoveOneElectron(), and RemoveElectron().

CreateDefaultDiffCoeffParam()

void G4MolecularConfiguration::CreateDefaultDiffCoeffParam ( )

protected

Definition at line 1451 of file G4MolecularConfiguration.cc.

{
  if(!static_cast<bool>(fDiffParam))
  {
    fDiffParam = &G4MolecularConfiguration::ReturnDefaultDiffCoeff;
  }
}

Referenced by Finalize().

CreateMolecularConfiguration() [1/4]

G4MolecularConfiguration * G4MolecularConfiguration::CreateMolecularConfiguration ( const G4String & userIdentifier, const G4MoleculeDefinition * molDef, bool & wasAlreadyCreated )

static

Definition at line 1045 of file G4MolecularConfiguration.cc.

{
  wasAlreadyCreated = false;
  G4MolecularConfiguration* preRegisteredMolConf =
      GetManager()->GetMolecularConfiguration(userIdentifier);
 
  if(preRegisteredMolConf != nullptr)
  {
    if(preRegisteredMolConf->GetDefinition() == molDef)
    {
      wasAlreadyCreated = true;
      return preRegisteredMolConf;
    }
  }
 
  if(molDef->GetGroundStateElectronOccupancy() != nullptr)
  {
    const G4ElectronOccupancy& elecOcc = *molDef
        ->GetGroundStateElectronOccupancy();
    G4MolecularConfiguration* molConf =
        GetManager()->GetMolecularConfiguration(molDef, elecOcc);
 
    if(molConf != nullptr)
    {
      if(molConf->fUserIdentifier.empty())
      {
        molConf->fUserIdentifier = userIdentifier;
      }
      else if(molConf->fUserIdentifier != userIdentifier)
      {
        G4ExceptionDescription errMsg;
        errMsg << "A molecular configuration for the definition named "
               << molDef->GetName() << " has already been created "
               "and recorded with a different user ID "
               << molConf->fUserIdentifier;
        G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
                    "DOUBLE_CREATION",
                    FatalErrorInArgument,
                    errMsg);
      }
// TODO exception
      G4ExceptionDescription errMsg;
      errMsg << "A molecular configuration for the definition named "
             << molDef->GetName() << " has already been created.";
      G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
                  "DOUBLE_CREATION",
                  JustWarning,
                  errMsg);
      wasAlreadyCreated = true;
      return molConf;
    }
    
    // G4cout << "Create molConf for " << molDef->GetName() << G4endl;
    auto  newConf = new G4MolecularConfiguration(molDef,
                                                                    elecOcc);
    newConf->fUserIdentifier = userIdentifier;
 
    GetManager()->AddUserID(userIdentifier, newConf);
 
//      G4MoleculeTable::Instance()->RecordMolecularConfiguration(userIdentifier,
//                                                                newConf);
    return newConf;
  }
  
  return CreateMolecularConfiguration(userIdentifier,
                                      molDef,
                                      molDef->GetName(),
                                      molDef->GetCharge(),
                                      wasAlreadyCreated);
}

Referenced by G4MoleculeTable::CreateConfiguration(), G4MoleculeTable::CreateConfiguration(), G4MoleculeTable::CreateConfiguration(), G4MoleculeTable::CreateConfiguration(), CreateMolecularConfiguration(), G4MoleculeDefinition::NewConfiguration(), G4MoleculeDefinition::NewConfigurationWithElectronOccupancy(), and G4MoleculeTableMessenger::SetNewValue().

CreateMolecularConfiguration() [2/4]

G4MolecularConfiguration * G4MolecularConfiguration::CreateMolecularConfiguration ( const G4String & userIdentifier, const G4MoleculeDefinition * molDef, const G4String & label, bool & wasAlreadyCreated )

static

Definition at line 1122 of file G4MolecularConfiguration.cc.

{
  assert(label != "");
  wasAlreadyCreated = false;
 
  G4MolecularConfiguration* molConf =
      GetManager()->GetMolecularConfiguration(molDef, label);
  if(molConf != nullptr)
  {
    if((molConf->fLabel != nullptr)
       && *molConf->fLabel == label)
    {
      wasAlreadyCreated = true;
      return molConf;
    }
    if(molConf->fLabel == nullptr)
    {
      wasAlreadyCreated = true;
      molConf->SetLabel(label);
      return molConf;
    }
    if(molConf->fLabel->empty())
    {
      wasAlreadyCreated = true;
      molConf->SetLabel(label);
      return molConf;
    }
 
    molConf->PrintState();
    G4ExceptionDescription errMsg ;
    errMsg << "A molecular configuration for the definition named "
           << molDef->GetName()
           << " has already been created "
              "with user ID "
           << molConf->fUserIdentifier << " and label "
           << molConf->GetLabel();
    G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
                "DOUBLE_CREATION",
                FatalErrorInArgument,
                errMsg);
    // KILL APP
  }
  else
  {
    auto  newConf =
      new G4MolecularConfiguration(molDef,
                                   label,
                                   molDef->GetCharge());
    newConf->fUserIdentifier = userIdentifier;
 
    GetManager()->AddUserID(userIdentifier, newConf);
 
//    G4MoleculeTable::Instance()->
//        RecordMolecularConfiguration(userIdentifier, newConf);
    return newConf;
  }
  return molConf;
}

CreateMolecularConfiguration() [3/4]

G4MolecularConfiguration * G4MolecularConfiguration::CreateMolecularConfiguration ( const G4String & userIdentifier, const G4MoleculeDefinition * molDef, const G4String & label, const G4ElectronOccupancy & eOcc, bool & wasAlreadyCreated )

static

Definition at line 1188 of file G4MolecularConfiguration.cc.

{
  assert(label != "");
  wasAlreadyCreated = false;
 
  G4MolecularConfiguration* molConf =
      GetManager()->GetMolecularConfiguration(molDef, eOcc);
 
  if(molConf != nullptr)
  {
    if(molConf->GetElectronOccupancy() != nullptr)
    {
      if(*molConf->GetElectronOccupancy() == eOcc)
      {
        if((molConf->fLabel != nullptr) && *molConf->fLabel == label)
        {
          wasAlreadyCreated = true;
          return molConf;
        }
        if(molConf->fLabel == nullptr)
        {
          wasAlreadyCreated = true;
          molConf->SetLabel(label);
          return molConf;
        }
        if(molConf->fLabel->empty())
        {
          wasAlreadyCreated = true;
          molConf->SetLabel(label);
          return molConf;
        }
      }
    }
 
 
    molConf->PrintState();
    G4ExceptionDescription errMsg ;
    errMsg << "A molecular configuration for the definition named "
           << molDef->GetName()
           << " has already been created "
              "with user ID "
           << molConf->fUserIdentifier
           << " and possible different electronic state";
    G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
                "DOUBLE_CREATION",
                FatalErrorInArgument,
                errMsg);
  }
  else
  {
    auto  newConf =
      new G4MolecularConfiguration(molDef,
                                   eOcc,
                                   label);
    newConf->fUserIdentifier = userIdentifier;
 
    GetManager()->AddUserID(userIdentifier, newConf);
 
//    G4MoleculeTable::Instance()->
//        RecordMolecularConfiguration(userIdentifier, newConf);
    return newConf;
  }
  return molConf;
}

CreateMolecularConfiguration() [4/4]

G4MolecularConfiguration * G4MolecularConfiguration::CreateMolecularConfiguration ( const G4String & userIdentifier, const G4MoleculeDefinition * molDef, int charge, const G4String & label, bool & wasAlreadyCreated )

static

Definition at line 955 of file G4MolecularConfiguration.cc.

{
  wasAlreadyCreated = false;
  G4MolecularConfiguration* molConf =
      GetManager()->GetMolecularConfiguration(molDef, charge);
 
  if (molConf != nullptr)
  {
    if(molConf->fLabel == nullptr)
    {
      molConf->SetLabel(label);
      G4ExceptionDescription wMsg ;
      wMsg << "The molecular configuration for the definition named "
             << molDef->GetName()
             << " with charge " << charge << " has already been created "
                 "but with NO label";
      G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
                  "DOUBLE_CREATION",
                  JustWarning,
                  wMsg);
    }
    else if(molConf->fLabel->empty() )
    {
      molConf->SetLabel(label);
    }
    else if(*(molConf->fLabel) != label)
    {
      G4ExceptionDescription errMsg ;
      errMsg << "The molecular configuration for the definition named "
             << molDef->GetName()
             << " with charge " << charge << " has already been created "
                 "but with a different label :"
             << molConf->GetLabel();
      G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
                  "DOUBLE_CREATION",
                  FatalErrorInArgument,
                  errMsg);
      // KILL APP
    }
 
    if(molConf->fUserIdentifier.empty())
    {
      molConf->fUserIdentifier = userIdentifier;
 
      G4ExceptionDescription wMsg ;
      wMsg << "The molecular configuration for the definition named "
             << molDef->GetName()
             << " with label " << label << " has already been created.";
      G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
                  "DOUBLE_CREATION",
                  JustWarning,
                  wMsg);
    }
    else if(molConf->fUserIdentifier != userIdentifier)
    {
      G4ExceptionDescription errMsg ;
      errMsg << "The molecular configuration for the definition named "
             << molDef->GetName()
             << " with label " << label << " has already been created "
                 "BUT with a different user ID :"
             << molConf->fUserIdentifier;
      G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
                  "DOUBLE_CREATION",
                  FatalErrorInArgument,
                  errMsg);
      // KILL APP
    }
 
    wasAlreadyCreated = true;
    return molConf;
  }
  
  auto  newConf =
      new G4MolecularConfiguration(molDef, label, charge);
  newConf->fUserIdentifier = userIdentifier;
 
  GetManager()->AddUserID(userIdentifier, newConf);
 
//    G4MoleculeTable::Instance()->RecordMolecularConfiguration(userIdentifier,
//                                                              newConf);
  return newConf;
}

DeleteManager()

void G4MolecularConfiguration::DeleteManager ( )

static

Definition at line 402 of file G4MolecularConfiguration.cc.

{
  G4AutoLock lock(&MolecularConfigurationManager::fManagerCreationMutex);
  delete fgManager;
  fgManager = nullptr;
  lock.unlock();
}

Referenced by G4DNAChemistryManager::Clear().

DiffCoeffWater()

double G4MolecularConfiguration::DiffCoeffWater ( double temperature_K )

static

Definition at line 1418 of file G4MolecularConfiguration.cc.

{
  return pow(10, 4.311
             - 2.722e3/temperature_K
             + 8.565e5/(temperature_K *temperature_K)
             - 1.181e8/(temperature_K*temperature_K*temperature_K ))*1e-9*m2/s;
}

Referenced by ScaleAllDiffusionCoefficientsOnWater(), and G4DNAMolecularReactionData::ScaledParameterization().

ExciteMolecule()

G4MolecularConfiguration * G4MolecularConfiguration::ExciteMolecule

(

G4int

ExcitedLevel

)

const

Method used in Geant4-DNA to excite water molecules

Definition at line 554 of file G4MolecularConfiguration.cc.

{
//  MakeExceptionIfFinalized();
  CheckElectronOccupancy(__func__);
  G4ElectronOccupancy newElectronOccupancy(*fElectronOccupancy);
 
  newElectronOccupancy.RemoveElectron(ExcitedLevel, 1);
  newElectronOccupancy.AddElectron(5, 1);
 
  return ChangeConfiguration(newElectronOccupancy);
}

Finalize()

void G4MolecularConfiguration::Finalize ( )

inline

Definition at line 561 of file G4MolecularConfiguration.hh.

{
  CreateDefaultDiffCoeffParam();
  fIsFinalized = true;
}

FinalizeAll()

void G4MolecularConfiguration::FinalizeAll ( )

static

Definition at line 1497 of file G4MolecularConfiguration.cc.

{
  const std::vector<G4MolecularConfiguration*>& species =
      GetManager()->GetAllSpecies();
 
  for(auto specie : species)
  {
    specie->Finalize();
  }
 
}

Referenced by G4MoleculeTable::Finalize().

GetAtomsNumber()

G4int G4MolecularConfiguration::GetAtomsNumber

(

)

const

Returns the nomber of atoms compouning the molecule

Definition at line 687 of file G4MolecularConfiguration.cc.

{
  return fMoleculeDefinition->GetAtomsNumber();
}

GetCharge()

G4int G4MolecularConfiguration::GetCharge ( ) const

inline

Returns the charge of molecule.

Definition at line 518 of file G4MolecularConfiguration.hh.

{
  return fDynCharge;
}

GetDecayTime()

G4double G4MolecularConfiguration::GetDecayTime ( ) const

inline

Returns the decay time of the molecule.

Definition at line 502 of file G4MolecularConfiguration.hh.

{
  return fDynDecayTime;
}

GetDefinition()

const G4MoleculeDefinition * G4MolecularConfiguration::GetDefinition ( ) const

inline

Definition at line 475 of file G4MolecularConfiguration.hh.

{
  return fMoleculeDefinition;
}

Referenced by CreateMolecularConfiguration(), G4DNAWaterDissociationDisplacer::GetProductsDisplacement(), and G4MolecularConfiguration::G4MolecularConfigurationManager::RemoveMolecularConfigurationFromTable().

GetDiffusionCoefficient() [1/2]

G4double G4MolecularConfiguration::GetDiffusionCoefficient ( ) const

inline

Returns the diffusion coefficient D.

Definition at line 491 of file G4MolecularConfiguration.hh.

{
  return fDynDiffusionCoefficient;
}

Referenced by G4ChemReboundTransportation::calculateDistanceFromTimeStep(), G4DNAIRT::GetIndependentReactionTime(), G4DNAGillespieDirectMethod::PropensityFunction(), G4DNAIRT::Sampling(), and ScaleAllDiffusionCoefficientsOnWater().

GetDiffusionCoefficient() [2/2]

G4double G4MolecularConfiguration::GetDiffusionCoefficient ( const G4Material * material, double temperature ) const

inline

Definition at line 579 of file G4MolecularConfiguration.hh.

{
  return fDiffParam(material, temperature, this);
}

GetDissociationChannels()

const vector< const G4MolecularDissociationChannel * > * G4MolecularConfiguration::GetDissociationChannels

(

)

const

Definition at line 740 of file G4MolecularConfiguration.cc.

{
  // if (fElectronOccupancy == 0) return 0;
  return fMoleculeDefinition->GetDecayChannels(this);
}

GetElectronOccupancy()

const G4ElectronOccupancy * G4MolecularConfiguration::GetElectronOccupancy ( ) const

inline

Returns the object ElectronOccupancy describing the electronic configuration of the molecule.

Definition at line 480 of file G4MolecularConfiguration.hh.

{
  return fElectronOccupancy;
}

Referenced by CreateMolecularConfiguration(), and G4MolecularConfiguration::G4MolecularConfigurationManager::RemoveMolecularConfigurationFromTable().

GetFakeParticleID()

G4int G4MolecularConfiguration::GetFakeParticleID

(

)

const

Definition at line 748 of file G4MolecularConfiguration.cc.

{
  if(fMoleculeDefinition != nullptr) return fMoleculeDefinition->GetPDGEncoding();
  G4Exception("G4MolecularConfiguration::GetMoleculeID",
                   "",
                   FatalErrorInArgument,
                   "You should first enter a molecule definition");
 
  return INT_MAX;
}

GetFormatedName()

const G4String & G4MolecularConfiguration::GetFormatedName

(

)

const

Returns the formated name of the molecule

Definition at line 680 of file G4MolecularConfiguration.cc.

{
  return fFormatedName;
}

GetGlobalTemperature()

G4double G4MolecularConfiguration::GetGlobalTemperature ( )

static

Definition at line 1469 of file G4MolecularConfiguration.cc.

{
  return fgTemperature;
}

Referenced by G4DNAChemistryManager::GetCurrentValue(), and G4Molecule::GetDiffusionVelocity().

GetLabel()

const G4String & G4MolecularConfiguration::GetLabel ( ) const

inline

Definition at line 553 of file G4MolecularConfiguration.hh.

{
  if(fLabel == nullptr)
    fLabel = new G4String();
 
  return (*fLabel);
}

Referenced by CreateMolecularConfiguration(), CreateMolecularConfiguration(), and PrintState().

GetManager()

G4MolecularConfiguration::G4MolecularConfigurationManager * G4MolecularConfiguration::GetManager ( )

staticprotected

Definition at line 128 of file G4MolecularConfiguration.cc.

{
  if (fgManager == nullptr)
  {
    G4AutoLock lock(&MolecularConfigurationManager::fManagerCreationMutex);
    if (fgManager == nullptr) // double check for MT
    {
      fgManager = new G4MolecularConfiguration::
          G4MolecularConfigurationManager();
    }
    lock.unlock();
  }
 
  return fgManager;
}

Referenced by ChangeConfiguration(), ChangeConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), FinalizeAll(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetMolecularConfiguration(), GetMolecularConfiguration(), GetMolecularConfiguration(), GetNumberOfSpecies(), GetOrCreateMolecularConfiguration(), GetOrCreateMolecularConfiguration(), GetOrCreateMolecularConfiguration(), GetUserIDTable(), PrintAll(), and SetUserID().

GetMass()

G4double G4MolecularConfiguration::GetMass ( ) const

inline

Returns the total mass of the molecule.

Definition at line 529 of file G4MolecularConfiguration.hh.

{
  return fDynMass;
}

GetMolecularConfiguration() [1/3]

G4MolecularConfiguration * G4MolecularConfiguration::GetMolecularConfiguration ( const G4MoleculeDefinition * molDef, const G4String & label )

static

Definition at line 938 of file G4MolecularConfiguration.cc.

{
  return GetManager()->GetMolecularConfiguration(molDef, label);
}

Referenced by G4MoleculeDefinition::AddDecayChannel(), G4Molecule::ChangeConfigurationToLabel(), G4MoleculeTable::GetConfiguration(), G4MoleculeTable::GetConfiguration(), G4MoleculeDefinition::GetConfigurationWithLabel(), and G4MoleculeTableMessenger::SetNewValue().

GetMolecularConfiguration() [2/3]

G4MolecularConfiguration * G4MolecularConfiguration::GetMolecularConfiguration ( const G4String & userID )

static

Definition at line 1490 of file G4MolecularConfiguration.cc.

{
  return GetManager()->GetMolecularConfiguration(userID);
}

GetMolecularConfiguration() [3/3]

G4MolecularConfiguration * G4MolecularConfiguration::GetMolecularConfiguration ( int moleculeID )

static

Definition at line 947 of file G4MolecularConfiguration.cc.

{
  return GetManager()->GetMolecularConfiguration(moleculeID);
}

GetMoleculeID()

G4int G4MolecularConfiguration::GetMoleculeID ( ) const

inline

Definition at line 534 of file G4MolecularConfiguration.hh.

{
  return fMoleculeID;
}

Referenced by G4DNAIRTMoleculeEncounterStepper::CalculateStep(), and G4DNAMoleculeEncounterStepper::CalculateStep().

GetName()

const G4String & G4MolecularConfiguration::GetName

(

)

const

Returns the name of the molecule

Definition at line 673 of file G4MolecularConfiguration.cc.

{
  return fName;
}

Referenced by G4DNAScavengerMaterial::AddAMoleculeAtTime(), G4DNAMolecularReactionTable::CanReactWith(), G4DNAScavengerMaterial::GetNMoleculesAtTime(), G4DNAMolecularReactionTable::GetReactionData(), G4DNAMolecularReactionTable::GetReactionData(), G4DiffusionControlledReactionModel::GetReactionRadius(), G4DNAMolecularReactionTable::GetReativesNData(), IonizeMolecule(), MakeExceptionIfFinalized(), MoveOneElectron(), PrintState(), G4DNAMolecularReactionTable::PrintTable(), G4DNAScavengerMaterial::RemoveAMoleculeAtTime(), RemoveElectron(), G4DNAIRT::Sampling(), G4ChemEquilibrium::SetEquilibrium(), G4DNAScavengerProcess::SetReaction(), and G4DNAUpdateSystemModel::UpdateSystem().

GetNbElectrons()

G4double G4MolecularConfiguration::GetNbElectrons

(

)

const

Returns the number of electron.

Definition at line 694 of file G4MolecularConfiguration.cc.

{
  CheckElectronOccupancy(__func__);
  return fElectronOccupancy->GetTotalOccupancy();
}

GetNumberOfSpecies()

int G4MolecularConfiguration::GetNumberOfSpecies ( )

static

Definition at line 64 of file G4MolecularConfiguration.cc.

{
  return GetManager()->GetNumberOfCreatedSpecies();
}

Referenced by G4MoleculeTable::GetNumberOfDefinedSpecies().

GetOrCreateMolecularConfiguration() [1/3]

G4MolecularConfiguration * G4MolecularConfiguration::GetOrCreateMolecularConfiguration ( const G4MoleculeDefinition * molDef )

static

Definition at line 321 of file G4MolecularConfiguration.cc.

{
  if (molDef->GetGroundStateElectronOccupancy() != nullptr)
  {
    const G4ElectronOccupancy& elecOcc =
        *molDef->GetGroundStateElectronOccupancy();
    G4MolecularConfiguration* molConf =
        GetManager()->GetMolecularConfiguration(molDef, elecOcc);
 
    if (molConf != nullptr)
    {
      return molConf;
    }
    
    auto  newConf =
        new G4MolecularConfiguration(molDef,
                                     elecOcc);
    newConf->SetUserID(molDef->GetName());
    return newConf;
  }
  
  G4MolecularConfiguration* molConf =
      GetManager()->GetMolecularConfiguration(molDef, molDef->GetCharge());
  if(molConf != nullptr)
  {
    return molConf;
  }
    
  auto  newConf =
      new G4MolecularConfiguration(molDef, molDef->GetCharge());
  newConf->SetUserID(molDef->GetName());
  return newConf;
}

Referenced by G4Molecule::G4Molecule(), G4Molecule::G4Molecule(), G4Molecule::G4Molecule(), G4Molecule::G4Molecule(), G4MoleculeTable::PrepareMolecularConfiguration(), G4Molecule::SetElectronOccupancy(), and G4MoleculeTableMessenger::SetNewValue().

GetOrCreateMolecularConfiguration() [2/3]

G4MolecularConfiguration * G4MolecularConfiguration::GetOrCreateMolecularConfiguration ( const G4MoleculeDefinition * molDef, const G4ElectronOccupancy & eOcc )

static

Definition at line 359 of file G4MolecularConfiguration.cc.

{
  return GetManager()->GetOrCreateMolecularConfiguration(molDef, elecOcc);
 
//  G4MolecularConfiguration* molConf =
//      GetManager()->GetMolecularConfiguration(molDef, elecOcc);
//
//  if (molConf)
//  {
//    return molConf;
//  }
//  else
//  {
//    G4MolecularConfiguration* newConf =
//        new G4MolecularConfiguration(molDef, elecOcc);
//    return newConf;
//  }
}

GetOrCreateMolecularConfiguration() [3/3]

G4MolecularConfiguration * G4MolecularConfiguration::GetOrCreateMolecularConfiguration ( const G4MoleculeDefinition * molDef, int charge )

static

Definition at line 383 of file G4MolecularConfiguration.cc.

{
  G4MolecularConfiguration* molConf =
      GetManager()->GetMolecularConfiguration(molDef, charge);
 
  if(molConf != nullptr)
  {
    return molConf;
  }
  
  auto  newConf =
      new G4MolecularConfiguration(molDef, charge);
  return newConf;
}

GetUserID()

const G4String & G4MolecularConfiguration::GetUserID ( ) const

inline

Definition at line 567 of file G4MolecularConfiguration.hh.

{
  return fUserIdentifier;
}

Referenced by G4MoleculeReactionCounterIndex::FormattedReactionString().

GetUserIDTable()

std::map< G4String, G4MolecularConfiguration * > & G4MolecularConfiguration::GetUserIDTable ( )

inlinestatic

Definition at line 166 of file G4MolecularConfiguration.hh.

  {
    return GetManager()->GetUserIDTable();
  }

Referenced by G4MoleculeTable::GetConfigurationIterator().

GetVanDerVaalsRadius()

G4double G4MolecularConfiguration::GetVanDerVaalsRadius ( ) const

inline

Definition at line 513 of file G4MolecularConfiguration.hh.

{
  return fDynVanDerVaalsRadius;
}

IonizeMolecule()

G4MolecularConfiguration * G4MolecularConfiguration::IonizeMolecule

(

G4int

IonizedLevel

)

const

Method used in Geant4-DNA to ionize water molecules

Definition at line 571 of file G4MolecularConfiguration.cc.

{
//  MakeExceptionIfFinalized();
  CheckElectronOccupancy(__func__);
  G4ElectronOccupancy newElectronOccupancy(*fElectronOccupancy);
 
  if (newElectronOccupancy.GetOccupancy(IonizedLevel) != 0)
  {
    newElectronOccupancy.RemoveElectron(IonizedLevel, 1);
  }
  else
  {
    G4String errMsg = "There is no electron on the orbit "
        + G4UIcommand::ConvertToString(IonizedLevel)
        + " you want to free. The molecule's name you want to ionized is "
        + GetName();
    G4Exception("G4MolecularConfiguration::IonizeMolecule",
                "",
                FatalErrorInArgument,
                errMsg);
    PrintState();
  }
 
  // DEBUG
  // PrintState();
 
  return ChangeConfiguration(newElectronOccupancy);
}

Load()

G4MolecularConfiguration * G4MolecularConfiguration::Load ( std::istream & in )

static

Definition at line 1372 of file G4MolecularConfiguration.cc.

{
  return new G4MolecularConfiguration(in);
}

MakeExceptionIfFinalized()

void G4MolecularConfiguration::MakeExceptionIfFinalized ( )

protected

Definition at line 112 of file G4MolecularConfiguration.cc.

{
  if(fIsFinalized)
  {
    G4ExceptionDescription errMsg;
    errMsg << "This molecular configuration " << GetName()
           << " is already finalized. Therefore its "
           " properties cannot be changed.";
    G4Exception("G4MolecularConfiguration::MakeExceptionIfFinalized",
                "CONF_FINALIZED",FatalException,errMsg);
  }
}

Referenced by SetDecayTime(), SetDiffusionCoefficient(), SetMass(), and SetVanDerVaalsRadius().

MoveOneElectron()

G4MolecularConfiguration * G4MolecularConfiguration::MoveOneElectron	(	G4int	orbitToFree,
		G4int	orbitToFill ) const

Move one electron from an orbit to another.

Definition at line 644 of file G4MolecularConfiguration.cc.

{
//  MakeExceptionIfFinalized();
  CheckElectronOccupancy(__func__);
  G4ElectronOccupancy newElectronOccupancy(*fElectronOccupancy);
 
  if (newElectronOccupancy.GetOccupancy(orbitToFree) >= 1)
  {
    newElectronOccupancy.RemoveElectron(orbitToFree, 1);
    newElectronOccupancy.AddElectron(orbitToFill, 1);
  }
  else
  {
    G4String errMsg = "There is no electron on the orbit "
        + G4UIcommand::ConvertToString(orbitToFree)
        + " you want to free. The molecule's name is " + GetName();
    G4Exception("G4MolecularConfiguration::MoveOneElectron",
                "",
                FatalErrorInArgument,
                errMsg);
    PrintState();
  }
 
  return ChangeConfiguration(newElectronOccupancy);
}

operator=()

G4MolecularConfiguration & G4MolecularConfiguration::operator= ( G4MolecularConfiguration & right )

protected

Definition at line 543 of file G4MolecularConfiguration.cc.

{
//  if (&right == this) return *this;
  return *this;
}

PrintAll()

void G4MolecularConfiguration::PrintAll ( )

static

Definition at line 1509 of file G4MolecularConfiguration.cc.

{
  const std::vector<G4MolecularConfiguration*>& species =
    GetManager()->GetAllSpecies();
  G4cout<<G4endl;
  G4cout<<"Molecular Config"<<std::setw(25)<<" | Diffusion Coefficient (m2 / s) "<<std::setw(20)<<" | Radius (nm) "<<G4endl;
  G4cout<<"__________________________________________"
            "___________________________________"<<G4endl;
  for(auto specie : species)
  {
    G4cout<<specie->GetName()
           <<std::setw(G4int(30 - specie->GetName().length()))
           <<right<<specie->GetDiffusionCoefficient() * 1.0e3<<std::setw(30)
           <<specie->GetVanDerVaalsRadius()/CLHEP::nm<<G4endl;
    G4cout<<"__________________________________________"
              "___________________________________"<<G4endl;
  }
 
}

Referenced by G4MoleculeTableMessenger::SetNewValue().

PrintState()

void G4MolecularConfiguration::PrintState

(

)

const

Display the electronic state of the molecule.

Definition at line 702 of file G4MolecularConfiguration.cc.

{
  G4cout << "-------------- Start Printing State " << GetName()
         << " ---------------" << G4endl;
 
  if (fElectronOccupancy != nullptr)
  {
    G4cout << "--------------Print electronic state of " << GetName()
           << "---------------" << G4endl;
    fElectronOccupancy->DumpInfo();
    if(fElectronOccupancy==fMoleculeDefinition->GetGroundStateElectronOccupancy())
    {
      G4cout<<"At ground state"<<G4endl;
    }
  }
  else
  {
    G4cout << "--- No electron occupancy set up ---" << G4endl;
  }
 
  G4cout << "Charge :"
         << fDynCharge
         << G4endl;
 
  if(fLabel != nullptr)
  {
    G4cout << "Label :"
           << GetLabel()
           << G4endl;
  }
  G4cout  << "-------------- End Of State " << GetName()
          << " -----------------------" << G4endl;
}

Referenced by CreateMolecularConfiguration(), CreateMolecularConfiguration(), IonizeMolecule(), MoveOneElectron(), and RemoveElectron().

RemoveElectron()

G4MolecularConfiguration * G4MolecularConfiguration::RemoveElectron	(	G4int	orbit,
		G4int	number = 1 ) const

Remove n electrons to a given orbit.

Definition at line 615 of file G4MolecularConfiguration.cc.

{
//  MakeExceptionIfFinalized();
  CheckElectronOccupancy(__func__);
  G4ElectronOccupancy newElectronOccupancy(*fElectronOccupancy);
 
  if (newElectronOccupancy.GetOccupancy(orbit) != 0)
  {
    newElectronOccupancy.RemoveElectron(orbit, number);
  }
  else
  {
    G4String errMsg = "There is already no electron into the orbit "
        + G4UIcommand::ConvertToString(orbit)
        + " you want to free. The molecule's name is " + GetName();
    G4Exception("G4MolecularConfiguration::RemoveElectron",
                "",
                JustWarning,
                errMsg);
    PrintState();
  }
 
  return ChangeConfiguration(newElectronOccupancy);
}

ReturnDefaultDiffCoeff()

double G4MolecularConfiguration::ReturnDefaultDiffCoeff ( const G4Material * , double , const G4MolecularConfiguration * molConf )

staticprotected

Definition at line 69 of file G4MolecularConfiguration.cc.

{
  return molConf->fDynDiffusionCoefficient;
}

Referenced by CreateDefaultDiffCoeffParam(), G4MolecularConfiguration(), G4MolecularConfiguration(), and G4MolecularConfiguration().

ScaleAllDiffusionCoefficientsOnWater()

void G4MolecularConfiguration::ScaleAllDiffusionCoefficientsOnWater ( double temperature_K )

staticprotected

Definition at line 1429 of file G4MolecularConfiguration.cc.

{
  double D_water_0 = DiffCoeffWater(fgTemperature);
  double D_water_f = DiffCoeffWater(temperature_K);
 
  G4cout << "Scaling factor = " << D_water_f/D_water_0 << G4endl;
 
  G4ConfigurationIterator it =
      G4MoleculeTable::Instance()->GetConfigurationIterator();
 
  while(it())
  {
    G4MolecularConfiguration* conf = it.value();
    double D_0 = conf->GetDiffusionCoefficient() ;
    double D_f = D_water_f * D_0 /D_water_0;
    conf->SetDiffusionCoefficient(D_f);
  };
}

Referenced by SetGlobalTemperature().

Serialize()

void G4MolecularConfiguration::Serialize

(

std::ostream &

out

)

Definition at line 1322 of file G4MolecularConfiguration.cc.

{
  G4String moleculeName = fMoleculeDefinition->GetName();
  WRITE(out, moleculeName);
 
//  if(fLabel)
//   out << fLabel;
//  else
//    out << "";
  WRITE(out,fDynDiffusionCoefficient);
  WRITE(out,fDynVanDerVaalsRadius);
  WRITE(out,fDynDecayTime);
  WRITE(out,fDynMass);
  WRITE(out,fDynCharge);
  WRITE(out,fMoleculeID);
  WRITE(out,fFormatedName);
  WRITE(out,fName);
  WRITE(out,fIsFinalized);
}

SetDecayTime()

void G4MolecularConfiguration::SetDecayTime ( G4double dynDecayTime )

inline

Set the decay time of the molecule.

Definition at line 496 of file G4MolecularConfiguration.hh.

{
  MakeExceptionIfFinalized();
  fDynDecayTime = dynDecayTime;
}

Referenced by G4MoleculeDefinition::NewConfigurationWithElectronOccupancy().

SetDiffusionCoefficient()

void G4MolecularConfiguration::SetDiffusionCoefficient ( G4double dynDiffusionCoefficient )

inline

Sets the diffusion coefficient D of the molecule used in diffusion processes to calculate the mean square jump distance between two changes of direction. In three dimension : <x^2> = 6 D t where t is the mean jump time between two changes of direction.

Note : Diffusion Coefficient in one medium only For the time being, we will consider only one diffusion coefficient for the all simulation => diffusion in one medium only If the user needs to use the diffusion in different materials, she/he should contact the developers/maintainers of this package

Definition at line 485 of file G4MolecularConfiguration.hh.

{
  MakeExceptionIfFinalized();
  fDynDiffusionCoefficient = dynDiffusionCoefficient;
}

Referenced by G4EmDNAChemistry_option1::ConstructMolecule(), G4MoleculeTable::CreateConfiguration(), and ScaleAllDiffusionCoefficientsOnWater().

SetGlobalTemperature()

void G4MolecularConfiguration::SetGlobalTemperature ( G4double temperature )

static

Definition at line 1461 of file G4MolecularConfiguration.cc.

{
  ScaleAllDiffusionCoefficientsOnWater(temperature);
  fgTemperature = temperature;
}

Referenced by G4DNAChemistryManager::SetGlobalTemperature().

SetLabel()

void G4MolecularConfiguration::SetLabel ( const G4String & label )

inline

Definition at line 539 of file G4MolecularConfiguration.hh.

{
  assert(fLabel == 0 || *fLabel == "");
  if(fLabel == nullptr)
  {
    fLabel = new G4String(label);
  }
  else
  {
    *fLabel = label;
  }
  fgManager->RecordNewlyLabeledConfiguration(this);
}

Referenced by CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), and G4MolecularConfiguration().

SetMass()

void G4MolecularConfiguration::SetMass ( G4double aMass )

inline

Set the total mass of the molecule.

Definition at line 523 of file G4MolecularConfiguration.hh.

{
  MakeExceptionIfFinalized();
  fDynMass = aMass;
}

Referenced by G4ChemDissociationChannels::ConstructMolecule(), and G4ChemDissociationChannels_option1::ConstructMolecule().

SetUserID()

void G4MolecularConfiguration::SetUserID

(

const G4String &

userID

)

Definition at line 1409 of file G4MolecularConfiguration.cc.

{
  fUserIdentifier = userID;
  GetManager()->AddUserID(userID, this);
//  G4MoleculeTable::Instance()->RecordMolecularConfiguration(userID, this);
}

SetVanDerVaalsRadius()

void G4MolecularConfiguration::SetVanDerVaalsRadius ( G4double dynVanDerVaalsRadius )

inline

The Van Der Valls Radius of the molecule

Definition at line 507 of file G4MolecularConfiguration.hh.

{
  MakeExceptionIfFinalized();
  fDynVanDerVaalsRadius = dynVanDerVaalsRadius;
}

Referenced by G4ChemDissociationChannels_option1::ConstructMolecule().

UnFinalize()

void G4MolecularConfiguration::UnFinalize ( )

inline

Definition at line 585 of file G4MolecularConfiguration.hh.

{
  fIsFinalized = false;
}

Unserialize()

void G4MolecularConfiguration::Unserialize

(

std::istream &

in

)

Definition at line 1344 of file G4MolecularConfiguration.cc.

{
  G4String moleculeName;
  READ(in, moleculeName);
  fMoleculeDefinition =
      G4MoleculeTable::Instance()->GetMoleculeDefinition(moleculeName);
 
//  G4String label;
//
//  in.read((char*)(&label), sizeof(label));
//
//  if(label)
//   fLabel = new G4String(label);
//  else
//    fLabel = 0;
  READ(in,fDynDiffusionCoefficient);
  READ(in,fDynVanDerVaalsRadius);
  READ(in,fDynDecayTime);
  READ(in,fDynMass);
  READ(in,fDynCharge);
  READ(in,fMoleculeID);
  READ(in,fFormatedName);
  READ(in,fName);
  READ(in,fIsFinalized);
}

Referenced by G4MolecularConfiguration().

Member Data Documentation

fDiffParam

G4DiffCoeffParam G4MolecularConfiguration::fDiffParam

protected

Definition at line 466 of file G4MolecularConfiguration.hh.

Referenced by AddDiffCoeffParameterization(), CreateDefaultDiffCoeffParam(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), and GetDiffusionCoefficient().

fDynCharge

G4int G4MolecularConfiguration::fDynCharge

protected

Definition at line 459 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetCharge(), PrintState(), Serialize(), and Unserialize().

fDynDecayTime

G4double G4MolecularConfiguration::fDynDecayTime

protected

Definition at line 457 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetDecayTime(), Serialize(), SetDecayTime(), and Unserialize().

fDynDiffusionCoefficient

G4double G4MolecularConfiguration::fDynDiffusionCoefficient

protected

Definition at line 455 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetDiffusionCoefficient(), ReturnDefaultDiffCoeff(), Serialize(), SetDiffusionCoefficient(), and Unserialize().

fDynMass

G4double G4MolecularConfiguration::fDynMass

protected

Definition at line 458 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetMass(), Serialize(), SetMass(), and Unserialize().

fDynVanDerVaalsRadius

G4double G4MolecularConfiguration::fDynVanDerVaalsRadius

protected

Definition at line 456 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetVanDerVaalsRadius(), Serialize(), SetVanDerVaalsRadius(), and Unserialize().

fElectronOccupancy

const G4ElectronOccupancy* G4MolecularConfiguration::fElectronOccupancy

protected

Definition at line 451 of file G4MolecularConfiguration.hh.

Referenced by AddElectron(), CheckElectronOccupancy(), ExciteMolecule(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetElectronOccupancy(), GetNbElectrons(), IonizeMolecule(), MoveOneElectron(), PrintState(), RemoveElectron(), and G4MolecularConfiguration::G4MolecularConfigurationManager::RemoveMolecularConfigurationFromTable().

fFormatedName

G4String G4MolecularConfiguration::fFormatedName

protected

Definition at line 461 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetFormatedName(), Serialize(), and Unserialize().

fgManager

MolecularConfigurationManager * G4MolecularConfiguration::fgManager = nullptr

staticprotected

Definition at line 447 of file G4MolecularConfiguration.hh.

Referenced by DeleteManager(), GetManager(), SetLabel(), ~G4MolecularConfiguration(), and G4MolecularConfiguration::G4MolecularConfigurationManager::~G4MolecularConfigurationManager().

fgTemperature

G4double G4MolecularConfiguration::fgTemperature = 298

staticprotected

Definition at line 467 of file G4MolecularConfiguration.hh.

Referenced by GetGlobalTemperature(), ScaleAllDiffusionCoefficientsOnWater(), and SetGlobalTemperature().

fIsFinalized

G4bool G4MolecularConfiguration::fIsFinalized

protected

Definition at line 464 of file G4MolecularConfiguration.hh.

Referenced by Finalize(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), MakeExceptionIfFinalized(), Serialize(), UnFinalize(), and Unserialize().

fLabel

G4String* G4MolecularConfiguration::fLabel

mutableprotected

Definition at line 453 of file G4MolecularConfiguration.hh.

Referenced by CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetLabel(), PrintState(), G4MolecularConfiguration::G4MolecularConfigurationManager::RecordNewlyLabeledConfiguration(), and SetLabel().

fMoleculeDefinition

const G4MoleculeDefinition* G4MolecularConfiguration::fMoleculeDefinition

protected

Definition at line 450 of file G4MolecularConfiguration.hh.

Referenced by ChangeConfiguration(), ChangeConfiguration(), CheckElectronOccupancy(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetAtomsNumber(), GetDefinition(), GetDissociationChannels(), GetFakeParticleID(), PrintState(), G4MolecularConfiguration::G4MolecularConfigurationManager::RecordNewlyLabeledConfiguration(), Serialize(), and Unserialize().

fMoleculeID

G4int G4MolecularConfiguration::fMoleculeID

protected

Definition at line 460 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetMoleculeID(), Serialize(), and Unserialize().

fName

G4String G4MolecularConfiguration::fName

protected

Definition at line 462 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetName(), Serialize(), and Unserialize().

fUserIdentifier

G4String G4MolecularConfiguration::fUserIdentifier

protected

Definition at line 463 of file G4MolecularConfiguration.hh.

Referenced by CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), GetUserID(), and SetUserID().

---

The documentation for this class was generated from the following files:

• G4MolecularConfiguration.hh
• G4MolecularConfiguration.cc