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. More...

#include <G4MolecularConfiguration.hh>

Collaboration diagram for G4MolecularConfiguration:

Classes
class	G4MolecularConfigurationManager

Public Types
typedef std::function< double(const G4Material , double, const G4MolecularConfiguration )>	G4DiffCoeffParam

Public Member Functions
void	AddDiffCoeffParameterization (const G4DiffCoeffParam &)

const G4MoleculeDefinition *	GetDefinition () const

const G4String &	GetName () const
	Returns the name of the molecule. More...

const G4String &	GetFormatedName () const
	Returns the formated name of the molecule. More...

G4int	GetAtomsNumber () const
	Returns the nomber of atoms compouning the molecule. More...

G4MolecularConfiguration *	ExciteMolecule (G4int)
	Method used in Geant4-DNA to excite water molecules. More...

G4MolecularConfiguration *	IonizeMolecule (G4int)
	Method used in Geant4-DNA to ionize water molecules. More...

G4MolecularConfiguration *	AddElectron (G4int orbit, G4int n=1)
	Add n electrons to a given orbit. More...

G4MolecularConfiguration *	RemoveElectron (G4int, G4int number=1)
	Remove n electrons to a given orbit. More...

G4MolecularConfiguration *	MoveOneElectron (G4int, G4int)
	Move one electron from an orbit to another. More...

G4double	GetNbElectrons () const
	Returns the number of electron. More...

void	PrintState () const
	Display the electronic state of the molecule. More...

const std::vector< const G4MolecularDissociationChannel * > *	GetDecayChannel () const

G4int	GetFakeParticleID () const

G4int	GetMoleculeID () const

void	SetDiffusionCoefficient (G4double)
	Sets the diffusion coefficient D of the molecule used in diffusion processes to calculate the mean square jump distance between two changes of direction. More...

G4double	GetDiffusionCoefficient () const
	Returns the diffusion coefficient D. More...

G4double	GetDiffusionCoefficient (const G4Material *, double temperature) const

void	SetDecayTime (G4double)
	Set the decay time of the molecule. More...

G4double	GetDecayTime () const
	Returns the decay time of the molecule. More...

void	SetVanDerVaalsRadius (G4double)
	The Van Der Valls Radius of the molecule. More...

G4double	GetVanDerVaalsRadius () const

const G4ElectronOccupancy *	GetElectronOccupancy () const
	Returns the object ElectronOccupancy describing the electronic configuration of the molecule. More...

G4int	GetCharge () const
	Returns the charge of molecule. More...

void	SetMass (G4double)
	Set the total mass of the molecule. More...

G4double	GetMass () const
	Returns the total mass of the molecule. More...

void	SetLabel (const G4String &)

const G4String &	GetLabel () const

void	Finalize ()

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	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)

G4MolecularConfiguration *	ChangeConfiguration (int charge)

void	CheckElectronOccupancy (const char *line) const

void	MakeExceptionIfFinalized ()

void	SetUserID (const G4String &userID)

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 = 0

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 98 of file G4MolecularConfiguration.hh.

Member Typedef Documentation

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

Definition at line 104 of file G4MolecularConfiguration.hh.

Constructor & Destructor Documentation

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

protected

Definition at line 438 of file G4MolecularConfiguration.cc.

References G4UIcommand::ConvertToString(), fName, G4MoleculeDefinition::GetCharge(), G4MoleculeDefinition::GetNbElectrons(), and ReturnDefaultDiffCoeff().

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

protected

Definition at line 491 of file G4MolecularConfiguration.cc.

References G4UIcommand::ConvertToString(), fName, G4MoleculeDefinition::GetMass(), and ReturnDefaultDiffCoeff().

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

protected

Definition at line 80 of file G4MolecularConfiguration.cc.

References G4UIcommand::ConvertToString(), fName, and ReturnDefaultDiffCoeff().

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

protected

Definition at line 1444 of file G4MolecularConfiguration.cc.

G4MolecularConfiguration::G4MolecularConfiguration ( const G4MolecularConfiguration & )

protected

G4MolecularConfiguration::~G4MolecularConfiguration ( )

protected

Definition at line 527 of file G4MolecularConfiguration.cc.

Member Function Documentation

void G4MolecularConfiguration::AddDiffCoeffParameterization ( const G4DiffCoeffParam & para )

inline

Definition at line 586 of file G4MolecularConfiguration.hh.

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

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 636 of file G4MolecularConfiguration.cc.

References G4ElectronOccupancy::AddElectron().

Referenced by G4Molecule::AddElectron().

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

protected

Definition at line 545 of file G4MolecularConfiguration.cc.

References GetMolecularConfiguration().

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G4MolecularConfiguration * G4MolecularConfiguration::ChangeConfiguration ( int charge )

protected

Definition at line 562 of file G4MolecularConfiguration.cc.

References GetMolecularConfiguration().

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

protected

Definition at line 824 of file G4MolecularConfiguration.cc.

References FatalErrorInArgument, and G4Exception().

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void G4MolecularConfiguration::CreateDefaultDiffCoeffParam ( )

protected

Definition at line 1516 of file G4MolecularConfiguration.cc.

References ReturnDefaultDiffCoeff().

Referenced by Finalize().

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

static

Definition at line 1099 of file G4MolecularConfiguration.cc.

References FatalErrorInArgument, fUserIdentifier, G4Exception(), G4MoleculeDefinition::GetCharge(), GetDefinition(), G4MoleculeDefinition::GetGroundStateElectronOccupancy(), GetMolecularConfiguration(), G4MoleculeDefinition::GetName(), and JustWarning.

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

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

static

Definition at line 1246 of file G4MolecularConfiguration.cc.

References FatalErrorInArgument, fLabel, fUserIdentifier, G4Exception(), GetElectronOccupancy(), GetMolecularConfiguration(), G4MoleculeDefinition::GetName(), PrintState(), and SetLabel().

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

static

Definition at line 1006 of file G4MolecularConfiguration.cc.

References FatalErrorInArgument, fLabel, fUserIdentifier, G4Exception(), GetLabel(), GetMolecularConfiguration(), G4MoleculeDefinition::GetName(), JustWarning, and SetLabel().

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

static

Definition at line 1180 of file G4MolecularConfiguration.cc.

References FatalErrorInArgument, fLabel, fUserIdentifier, G4Exception(), G4MoleculeDefinition::GetCharge(), GetLabel(), GetMolecularConfiguration(), G4MoleculeDefinition::GetName(), PrintState(), and SetLabel().

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void G4MolecularConfiguration::DeleteManager ( )

static

Definition at line 427 of file G4MolecularConfiguration.cc.

References G4MolecularConfiguration::G4MolecularConfigurationManager::fManagerCreationMutex, and G4TemplateAutoLock< M, L, U >::unlock().

Referenced by G4DNAChemistryManager::Clear().

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double G4MolecularConfiguration::DiffCoeffWater ( double temperature_K )

static

Definition at line 1483 of file G4MolecularConfiguration.cc.

References e3, m2, and s.

Referenced by G4DNAMolecularReactionData::ScaledParameterization().

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G4MolecularConfiguration * G4MolecularConfiguration::ExciteMolecule ( G4int ExcitedLevel )

Method used in Geant4-DNA to excite water molecules.

Definition at line 588 of file G4MolecularConfiguration.cc.

References G4ElectronOccupancy::AddElectron(), and G4ElectronOccupancy::RemoveElectron().

Referenced by G4Molecule::ExciteMolecule().

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void G4MolecularConfiguration::Finalize ( )

inline

Definition at line 574 of file G4MolecularConfiguration.hh.

References CreateDefaultDiffCoeffParam(), and fIsFinalized.

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void G4MolecularConfiguration::FinalizeAll ( )

static

Definition at line 1560 of file G4MolecularConfiguration.cc.

Referenced by G4MoleculeTable::Finalize().

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G4int G4MolecularConfiguration::GetAtomsNumber ( ) const

Returns the nomber of atoms compouning the molecule.

Definition at line 737 of file G4MolecularConfiguration.cc.

Referenced by G4Molecule::GetAtomsNumber().

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G4int G4MolecularConfiguration::GetCharge ( ) const

inline

Returns the charge of molecule.

Definition at line 531 of file G4MolecularConfiguration.hh.

References fDynCharge.

Referenced by G4Molecule::GetCharge().

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const vector< const G4MolecularDissociationChannel * > * G4MolecularConfiguration::GetDecayChannel ( ) const

Definition at line 790 of file G4MolecularConfiguration.cc.

Referenced by G4Molecule::GetDecayChannel().

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G4double G4MolecularConfiguration::GetDecayTime ( ) const

inline

Returns the decay time of the molecule.

Definition at line 515 of file G4MolecularConfiguration.hh.

References fDynDecayTime.

Referenced by G4Molecule::GetDecayTime().

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const G4MoleculeDefinition * G4MolecularConfiguration::GetDefinition ( ) const

inline

Definition at line 488 of file G4MolecularConfiguration.hh.

References fMoleculeDefinition.

Referenced by G4MoleculeCounter::AddAMoleculeAtTime(), G4Molecule::BuildTrack(), G4Molecule::ChangeConfigurationToLabel(), CreateMolecularConfiguration(), G4Molecule::GetDefinition(), G4DNAWaterDissociationDisplacer::GetProductsDisplacement(), G4MoleculeCounter::RemoveAMoleculeAtTime(), G4MolecularConfiguration::G4MolecularConfigurationManager::RemoveMolecularConfigurationFromTable(), and G4Molecule::SetElectronOccupancy().

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G4double G4MolecularConfiguration::GetDiffusionCoefficient ( ) const

inline

Returns the diffusion coefficient D.

Definition at line 504 of file G4MolecularConfiguration.hh.

References fDynDiffusionCoefficient.

Referenced by G4DNAMolecularReactionData::G4DNAMolecularReactionData(), G4Molecule::GetDiffusionCoefficient(), G4DNAMolecularReaction::MakeReaction(), ScaleAllDiffusionCoefficientsOnWater(), and G4DNAMoleculeEncounterStepper::Utils::Utils().

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

inline

Definition at line 592 of file G4MolecularConfiguration.hh.

References fDiffParam.

const G4ElectronOccupancy * G4MolecularConfiguration::GetElectronOccupancy ( ) const

inline

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

Definition at line 493 of file G4MolecularConfiguration.hh.

References fElectronOccupancy.

Referenced by CreateMolecularConfiguration(), G4Molecule::GetElectronOccupancy(), and G4MolecularConfiguration::G4MolecularConfigurationManager::RemoveMolecularConfigurationFromTable().

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G4int G4MolecularConfiguration::GetFakeParticleID ( ) const

Definition at line 798 of file G4MolecularConfiguration.cc.

References FatalErrorInArgument, G4Exception(), and INT_MAX.

Referenced by G4Molecule::GetFakeParticleID().

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const G4String & G4MolecularConfiguration::GetFormatedName ( ) const

Returns the formated name of the molecule.

Definition at line 722 of file G4MolecularConfiguration.cc.

Referenced by G4Molecule::GetFormatedName().

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G4double G4MolecularConfiguration::GetGlobalTemperature ( )

static

Definition at line 1534 of file G4MolecularConfiguration.cc.

Referenced by G4Molecule::GetDiffusionVelocity().

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const G4String & G4MolecularConfiguration::GetLabel ( ) const

inline

Definition at line 566 of file G4MolecularConfiguration.hh.

Referenced by CreateMolecularConfiguration(), and G4Molecule::GetLabel().

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G4MolecularConfiguration::G4MolecularConfigurationManager * G4MolecularConfiguration::GetManager ( )

staticprotected

Definition at line 131 of file G4MolecularConfiguration.cc.

References G4MolecularConfiguration::G4MolecularConfigurationManager::fManagerCreationMutex, and G4TemplateAutoLock< M, L, U >::unlock().

Referenced by GetUserIDTable().

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G4double G4MolecularConfiguration::GetMass ( ) const

inline

Returns the total mass of the molecule.

Definition at line 542 of file G4MolecularConfiguration.hh.

References fDynMass.

Referenced by G4Molecule::GetDiffusionVelocity(), G4Molecule::GetKineticEnergy(), and G4Molecule::GetMass().

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

static

Definition at line 989 of file G4MolecularConfiguration.cc.

References GetMolecularConfiguration().

Referenced by G4MoleculeDefinition::AddDecayChannel(), ChangeConfiguration(), G4Molecule::ChangeConfigurationToLabel(), CreateMolecularConfiguration(), G4MoleculeTable::GetConfiguration(), G4MoleculeDefinition::GetConfigurationWithLabel(), GetMolecularConfiguration(), and GetOrCreateMolecularConfiguration().

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G4MolecularConfiguration * G4MolecularConfiguration::GetMolecularConfiguration ( int moleculeID )

static

Definition at line 998 of file G4MolecularConfiguration.cc.

References GetMolecularConfiguration().

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

static

Definition at line 1555 of file G4MolecularConfiguration.cc.

References GetMolecularConfiguration().

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G4int G4MolecularConfiguration::GetMoleculeID ( ) const

inline

Definition at line 547 of file G4MolecularConfiguration.hh.

References fMoleculeID.

Referenced by G4DNAMoleculeEncounterStepper::CalculateStep(), and G4Molecule::GetMoleculeID().

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const G4String & G4MolecularConfiguration::GetName ( void ) const

Returns the name of the molecule.

Definition at line 707 of file G4MolecularConfiguration.cc.

References fName.

Referenced by G4MoleculeCounter::AddAMoleculeAtTime(), G4DNAMolecularReactionTable::CanReactWith(), G4DNAMoleculeEncounterStepper::CheckAndRecordResults(), G4MoleculeCounter::Dump(), G4Molecule::GetName(), G4DNAMolecularReactionTable::GetReactionData(), G4DNAMolecularReactionTable::GetReativesNData(), G4DNAMolecularReactionTable::PrintTable(), G4MoleculeCounter::RemoveAMoleculeAtTime(), and G4DNAMolecularReaction::TestReactibility().

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G4double G4MolecularConfiguration::GetNbElectrons ( ) const

Returns the number of electron.

Definition at line 744 of file G4MolecularConfiguration.cc.

Referenced by G4Molecule::GetNbElectrons().

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int G4MolecularConfiguration::GetNumberOfSpecies ( )

static

Definition at line 67 of file G4MolecularConfiguration.cc.

Referenced by G4MoleculeTable::GetNumberOfDefinedSpecies().

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

static

Definition at line 339 of file G4MolecularConfiguration.cc.

References G4MoleculeDefinition::GetCharge(), G4MoleculeDefinition::GetGroundStateElectronOccupancy(), GetMolecularConfiguration(), G4MoleculeDefinition::GetName(), and SetUserID().

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

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

static

Definition at line 383 of file G4MolecularConfiguration.cc.

References GetOrCreateMolecularConfiguration().

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

static

Definition at line 407 of file G4MolecularConfiguration.cc.

References GetMolecularConfiguration().

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const G4String & G4MolecularConfiguration::GetUserID ( ) const

inline

Definition at line 580 of file G4MolecularConfiguration.hh.

References fUserIdentifier.

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

inlinestatic

Definition at line 169 of file G4MolecularConfiguration.hh.

References GetManager(), and G4MolecularConfiguration::G4MolecularConfigurationManager::GetUserIDTable().

Referenced by G4MoleculeTable::GetConfigurationIterator().

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G4double G4MolecularConfiguration::GetVanDerVaalsRadius ( ) const

inline

Definition at line 526 of file G4MolecularConfiguration.hh.

References fDynVanDerVaalsRadius.

Referenced by G4Molecule::GetVanDerVaalsRadius().

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G4MolecularConfiguration * G4MolecularConfiguration::IonizeMolecule ( G4int IonizedLevel )

Method used in Geant4-DNA to ionize water molecules.

Definition at line 605 of file G4MolecularConfiguration.cc.

References G4UIcommand::ConvertToString(), FatalErrorInArgument, G4Exception(), G4ElectronOccupancy::GetOccupancy(), and G4ElectronOccupancy::RemoveElectron().

Referenced by G4Molecule::IonizeMolecule().

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

static

Definition at line 1437 of file G4MolecularConfiguration.cc.

void G4MolecularConfiguration::MakeExceptionIfFinalized ( )

protected

Definition at line 115 of file G4MolecularConfiguration.cc.

References FatalException, and G4Exception().

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

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

Move one electron from an orbit to another.

Definition at line 678 of file G4MolecularConfiguration.cc.

References G4ElectronOccupancy::AddElectron(), G4UIcommand::ConvertToString(), FatalErrorInArgument, G4Exception(), G4ElectronOccupancy::GetOccupancy(), and G4ElectronOccupancy::RemoveElectron().

Referenced by G4Molecule::MoveOneElectron().

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

protected

Definition at line 577 of file G4MolecularConfiguration.cc.

void G4MolecularConfiguration::PrintState ( ) const

Display the electronic state of the molecule.

Definition at line 752 of file G4MolecularConfiguration.cc.

References G4cout, and G4endl.

Referenced by CreateMolecularConfiguration(), G4Molecule::PrintState(), and G4MoleculeCounter::RemoveAMoleculeAtTime().

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

Remove n electrons to a given orbit.

Definition at line 649 of file G4MolecularConfiguration.cc.

References G4UIcommand::ConvertToString(), G4Exception(), G4ElectronOccupancy::GetOccupancy(), JustWarning, and G4ElectronOccupancy::RemoveElectron().

Referenced by G4Molecule::RemoveElectron().

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

staticprotected

Definition at line 72 of file G4MolecularConfiguration.cc.

References fDynDiffusionCoefficient.

Referenced by CreateDefaultDiffCoeffParam(), and G4MolecularConfiguration().

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void G4MolecularConfiguration::ScaleAllDiffusionCoefficientsOnWater ( double temperature_K )

staticprotected

Definition at line 1495 of file G4MolecularConfiguration.cc.

References G4cout, G4endl, G4MoleculeTable::GetConfigurationIterator(), GetDiffusionCoefficient(), G4MoleculeTable::Instance(), SetDiffusionCoefficient(), and G4MoleculeIterator< MOLECULE >::value().

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void G4MolecularConfiguration::Serialize ( std::ostream & out )

Definition at line 1387 of file G4MolecularConfiguration.cc.

References fName, and WRITE().

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void G4MolecularConfiguration::SetDecayTime ( G4double dynDecayTime )

inline

Set the decay time of the molecule.

Definition at line 509 of file G4MolecularConfiguration.hh.

References fDynDecayTime, and MakeExceptionIfFinalized().

Referenced by G4MoleculeDefinition::NewConfigurationWithElectronOccupancy(), and G4Molecule::SetDecayTime().

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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 developpers/mainteners of this package

Definition at line 498 of file G4MolecularConfiguration.hh.

References fDynDiffusionCoefficient, and MakeExceptionIfFinalized().

Referenced by G4MoleculeTable::CreateConfiguration(), ScaleAllDiffusionCoefficientsOnWater(), and G4Molecule::SetDiffusionCoefficient().

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void G4MolecularConfiguration::SetGlobalTemperature ( G4double temperature )

static

Definition at line 1526 of file G4MolecularConfiguration.cc.

Referenced by G4DNAChemistryManager::SetGlobalTemperature().

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void G4MolecularConfiguration::SetLabel ( const G4String & label )

inline

Definition at line 552 of file G4MolecularConfiguration.hh.

References G4MolecularConfiguration::G4MolecularConfigurationManager::RecordNewlyLabeledConfiguration().

Referenced by CreateMolecularConfiguration(), and G4Molecule::SetLabel().

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void G4MolecularConfiguration::SetMass ( G4double aMass )

inline

Set the total mass of the molecule.

Definition at line 536 of file G4MolecularConfiguration.hh.

References fDynMass, and MakeExceptionIfFinalized().

Referenced by G4EmDNAChemistry::ConstructMolecule(), and G4Molecule::SetMass().

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void G4MolecularConfiguration::SetUserID ( const G4String & userID )

protected

Definition at line 1474 of file G4MolecularConfiguration.cc.

Referenced by GetOrCreateMolecularConfiguration().

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void G4MolecularConfiguration::SetVanDerVaalsRadius ( G4double dynVanDerVaalsRadius )

inline

The Van Der Valls Radius of the molecule.

Definition at line 520 of file G4MolecularConfiguration.hh.

References fDynVanDerVaalsRadius, and MakeExceptionIfFinalized().

Referenced by G4Molecule::SetVanDerVaalsRadius().

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

Definition at line 1409 of file G4MolecularConfiguration.cc.

References fName, G4MoleculeTable::GetMoleculeDefinition(), G4MoleculeTable::Instance(), and READ().

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Member Data Documentation

G4DiffCoeffParam G4MolecularConfiguration::fDiffParam

protected

Definition at line 479 of file G4MolecularConfiguration.hh.

Referenced by GetDiffusionCoefficient().

G4int G4MolecularConfiguration::fDynCharge

protected

Definition at line 472 of file G4MolecularConfiguration.hh.

Referenced by GetCharge().

G4double G4MolecularConfiguration::fDynDecayTime

protected

Definition at line 470 of file G4MolecularConfiguration.hh.

Referenced by GetDecayTime(), and SetDecayTime().

G4double G4MolecularConfiguration::fDynDiffusionCoefficient

protected

Definition at line 468 of file G4MolecularConfiguration.hh.

Referenced by GetDiffusionCoefficient(), ReturnDefaultDiffCoeff(), and SetDiffusionCoefficient().

G4double G4MolecularConfiguration::fDynMass

protected

Definition at line 471 of file G4MolecularConfiguration.hh.

Referenced by GetMass(), and SetMass().

G4double G4MolecularConfiguration::fDynVanDerVaalsRadius

protected

Definition at line 469 of file G4MolecularConfiguration.hh.

Referenced by GetVanDerVaalsRadius(), and SetVanDerVaalsRadius().

const G4ElectronOccupancy* G4MolecularConfiguration::fElectronOccupancy

protected

Definition at line 464 of file G4MolecularConfiguration.hh.

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

G4String G4MolecularConfiguration::fFormatedName

protected

Definition at line 474 of file G4MolecularConfiguration.hh.

MolecularConfigurationManager * G4MolecularConfiguration::fgManager = 0

staticprotected

Definition at line 460 of file G4MolecularConfiguration.hh.

G4double G4MolecularConfiguration::fgTemperature = 298

staticprotected

Definition at line 480 of file G4MolecularConfiguration.hh.

G4bool G4MolecularConfiguration::fIsFinalized

protected

Definition at line 477 of file G4MolecularConfiguration.hh.

Referenced by Finalize().

G4String* G4MolecularConfiguration::fLabel

mutableprotected

Definition at line 466 of file G4MolecularConfiguration.hh.

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

const G4MoleculeDefinition* G4MolecularConfiguration::fMoleculeDefinition

protected

Definition at line 463 of file G4MolecularConfiguration.hh.

Referenced by GetDefinition(), and G4MolecularConfiguration::G4MolecularConfigurationManager::RecordNewlyLabeledConfiguration().

G4int G4MolecularConfiguration::fMoleculeID

protected

Definition at line 473 of file G4MolecularConfiguration.hh.

Referenced by GetMoleculeID().

G4String G4MolecularConfiguration::fName

protected

Definition at line 475 of file G4MolecularConfiguration.hh.

G4String G4MolecularConfiguration::fUserIdentifier

protected

Definition at line 476 of file G4MolecularConfiguration.hh.

Referenced by CreateMolecularConfiguration(), and GetUserID().

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

geant4.10.02/source/processes/electromagnetic/dna/molecules/management/include/G4MolecularConfiguration.hh
geant4.10.02/source/processes/electromagnetic/dna/molecules/management/src/G4MolecularConfiguration.cc

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