WARNING: THIS CLASS IS A PROTOTYPE G4DNAChemistryManager is called from the physics models. More...

#include <G4DNAChemistryManager.hh>

Inheritance diagram for G4DNAChemistryManager:

Collaboration diagram for G4DNAChemistryManager:

Public Member Functions
G4bool	IsChemistryActivated ()

void	SetChemistryActivation (G4bool)

virtual G4bool	Notify (G4ApplicationState requestedState)

virtual void	SetNewValue (G4UIcommand *, G4String)

void	Initialize ()

void	SetChemistryList (G4VUserChemistryList *)

void	Deregister (G4VUserChemistryList *)

void	ForceMasterReinitialization ()

void	TagThreadForReinitialization ()

void	Run ()

void	Clear ()

void	Gun (G4ITGun *, bool physicsTableToBuild=true)

void	ForceThreadReinitialization ()

void	ForceRebuildingPhysicsTable ()

void	WriteInto (const G4String &, std::ios_base::openmode mode=std::ios_base::out)
	Tells the chemMan to write into a file the position and electronic state of the water molecule and the position thermalized or not of the solvated electron. More...

void	AddEmptyLineInOuputFile ()

void	CloseFile ()
	Close the file specified with WriteInto. More...

void	CreateWaterMolecule (ElectronicModification, G4int, const G4Track *)
	Method used by DNA physics model to create a water molecule. More...

void	CreateSolvatedElectron (const G4Track , G4ThreeVector finalPosition=0)
	On the same idea as the previous method but for solvated electron. More...

void	PushMolecule (G4Molecule *&molecule, double time, const G4ThreeVector &position, int parentID)
	WARNING : In case chemistry is not activated, PushMolecule will take care of deleting the transfered molecule. More...

void	PushMoleculeAtParentTimeAndPlace (G4Molecule &molecule, const G4Track )
	WARNING : In case chemistry is not activated, PushMoleculeAtParentTimeAndPlace will take care of deleting the transfered molecule. More...

void	SetVerbose (G4int verbose)

Public Member Functions inherited from G4UImessenger
	G4UImessenger ()

	G4UImessenger (const G4String &path, const G4String &dsc, G4bool commandsToBeBroadcasted=true)

virtual	~G4UImessenger ()

virtual G4String	GetCurrentValue (G4UIcommand *command)

G4bool	operator== (const G4UImessenger &messenger) const

G4bool	CommandsShouldBeInMaster () const

Public Member Functions inherited from G4VStateDependent
	G4VStateDependent (G4bool bottom=false)

virtual	~G4VStateDependent ()

G4int	operator== (const G4VStateDependent &right) const

G4int	operator!= (const G4VStateDependent &right) const

Static Public Member Functions
static G4DNAChemistryManager *	Instance ()

static G4DNAChemistryManager *	GetInstanceIfExists ()

static void	DeleteInstance ()
	You should rather use DeleteInstance than the destructor of this class. More...

static G4bool	IsActivated ()

static void	Activated (G4bool flag=true)

Protected Member Functions
virtual	~G4DNAChemistryManager ()

G4DNAWaterExcitationStructure *	GetExcitationLevel ()

G4DNAWaterIonisationStructure *	GetIonisationLevel ()

void	InitializeFile ()

void	InitializeMaster ()

void	InitializeThread ()

	G4DNAChemistryManager ()

Protected Member Functions inherited from G4UImessenger
G4String	ItoS (G4int i)

G4String	DtoS (G4double a)

G4String	BtoS (G4bool b)

G4int	StoI (G4String s)

G4double	StoD (G4String s)

G4bool	StoB (G4String s)

void	AddUIcommand (G4UIcommand *newCommand)

void	CreateDirectory (const G4String &path, const G4String &dsc, G4bool commandsToBeBroadcasted=true)

template<typename T >
T *	CreateCommand (const G4String &cname, const G4String &dsc)

Static Private Attributes
static G4DNAChemistryManager *	fgInstance

static G4ThreadLocal std::ofstream *	fpgOutput_tl = 0

static G4ThreadLocal G4bool *	fpgThreadInitialized_tl = 0

Additional Inherited Members
Protected Attributes inherited from G4UImessenger
G4UIdirectory *	baseDir

G4String	baseDirName

G4bool	commandsShouldBeInMaster

Detailed Description

WARNING: THIS CLASS IS A PROTOTYPE G4DNAChemistryManager is called from the physics models.

It creates the water molecules and the solvated electrons and and send them to G4ITStepManager to be treated in the chemistry stage. For this, the fActiveChemistry flag needs to be on. It is also possible to give already molecule's pointers already built. G4DNAChemistryManager will then be in charge of creating the track and loading it to the IT system. The user can also ask to create a file containing a information about the creation of water molecules and solvated electrons.

Definition at line 87 of file G4DNAChemistryManager.hh.

Constructor & Destructor Documentation

G4DNAChemistryManager::~G4DNAChemistryManager ( )

protectedvirtual

Definition at line 126 of file G4DNAChemistryManager.cc.

References Clear(), and fgInstance.

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G4DNAChemistryManager::G4DNAChemistryManager ( )

protected

Definition at line 68 of file G4DNAChemistryManager.cc.

References fActiveChemistry, fBuildPhysicsTable, fFileInitialized, fForceThreadReinitialization, fGeometryClosed, fMasterInitialized, fpActivateChem, fpChemDNADirectory, fpExcitationLevel, fPhysicsTableBuilt, fpIonisationLevel, fpRunChem, fpUserChemistryList, fVerbose, and fWriteFile.

Referenced by Instance().

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Member Function Documentation

void G4DNAChemistryManager::Activated ( G4bool flag = true )

static

Definition at line 436 of file G4DNAChemistryManager.cc.

References fActiveChemistry, and Instance().

Referenced by SetChemistryList(), and SetNewValue().

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void G4DNAChemistryManager::AddEmptyLineInOuputFile ( )

Definition at line 466 of file G4DNAChemistryManager.cc.

References fpgOutput_tl, fWriteFile, and G4endl.

void G4DNAChemistryManager::Clear ( )

Definition at line 138 of file G4DNAChemistryManager.cc.

References G4MoleculeCounter::DeleteInstance(), G4DNAMolecularReactionTable::DeleteInstance(), G4MolecularConfiguration::DeleteManager(), fpActivateChem, fpChemDNADirectory, fpExcitationLevel, fpIonisationLevel, fpRunChem, fpUserChemistryList, and G4VUserChemistryList::IsPhysicsConstructor().

Referenced by Notify(), and ~G4DNAChemistryManager().

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void G4DNAChemistryManager::CloseFile ( )

Close the file specified with WriteInto.

Definition at line 474 of file G4DNAChemistryManager.cc.

References fpgOutput_tl, fVerbose, G4cout, and G4endl.

Referenced by Run().

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void G4DNAChemistryManager::CreateSolvatedElectron	(	const G4Track *	theIncomingTrack,
		G4ThreeVector *	finalPosition = `0`
	)

On the same idea as the previous method but for solvated electron.

This method should be used by the physics model of the ElectronSolvatation process.

Definition at line 574 of file G4DNAChemistryManager.cc.

References G4Molecule::BuildTrack(), G4Electron_aq::Definition(), eV, fActiveChemistry, fAlive, fFileInitialized, fpgOutput_tl, fWriteFile, G4endl, G4Track::GetKineticEnergy(), G4Track::GetPosition(), G4Track::GetTrackID(), InitializeFile(), G4VITTrackHolder::Instance(), nanometer, picosecond, and G4VITTrackHolder::Push().

Referenced by G4DNATransformElectronModel::SampleSecondaries(), and G4DNAOneStepSolvatationModel::SampleSecondaries().

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void G4DNAChemistryManager::CreateWaterMolecule	(	ElectronicModification	modification,
		G4int	electronicLevel,
		const G4Track *	theIncomingTrack
	)

Method used by DNA physics model to create a water molecule.

The ElectronicModification is a flag telling wheter the molecule is ionized or excited, the electronic level is calculated by the model and the IncomingTrack is the track responsible for the creation of this molecule, for instance an electron.

Definition at line 508 of file G4DNAChemistryManager.cc.

References G4Molecule::BuildTrack(), G4H2O::Definition(), eDissociativeAttachment, eExcitedMolecule, eIonizedMolecule, G4INCL::KinematicsUtils::energy(), eV, G4DNAWaterExcitationStructure::ExcitationEnergy(), fActiveChemistry, fFileInitialized, fpgOutput_tl, fStopButAlive, fWriteFile, G4endl, GetExcitationLevel(), GetIonisationLevel(), G4Track::GetPosition(), G4Track::GetTrackID(), InitializeFile(), G4VITTrackHolder::Instance(), G4DNAWaterIonisationStructure::IonisationEnergy(), left, nanometer, picosecond, G4VITTrackHolder::Push(), and right.

Referenced by G4DNABornExcitationModel::SampleSecondaries(), G4DNAMillerGreenExcitationModel::SampleSecondaries(), G4DNAMeltonAttachmentModel::SampleSecondaries(), G4DNARuddIonisationModel::SampleSecondaries(), G4DNARuddIonisationExtendedModel::SampleSecondaries(), and G4DNABornIonisationModel::SampleSecondaries().

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void G4DNAChemistryManager::DeleteInstance ( )

static

You should rather use DeleteInstance than the destructor of this class.

Definition at line 190 of file G4DNAChemistryManager.cc.

References chemManExistence, fgInstance, G4cout, G4endl, and G4TemplateAutoLock< M, L, U >::unlock().

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void G4DNAChemistryManager::Deregister ( G4VUserChemistryList * chemistryList )

inline

Definition at line 247 of file G4DNAChemistryManager.hh.

References fpUserChemistryList.

Referenced by G4VUserChemistryList::~G4VUserChemistryList().

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void G4DNAChemistryManager::ForceMasterReinitialization ( )

inline

Definition at line 252 of file G4DNAChemistryManager.hh.

References fMasterInitialized, and InitializeMaster().

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void G4DNAChemistryManager::ForceRebuildingPhysicsTable ( )

inline

Definition at line 236 of file G4DNAChemistryManager.hh.

References fPhysicsTableBuilt.

void G4DNAChemistryManager::ForceThreadReinitialization ( )

inline

Definition at line 258 of file G4DNAChemistryManager.hh.

References fForceThreadReinitialization.

G4DNAWaterExcitationStructure * G4DNAChemistryManager::GetExcitationLevel ( )

protected

Definition at line 489 of file G4DNAChemistryManager.cc.

References fpExcitationLevel.

Referenced by CreateWaterMolecule().

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G4DNAChemistryManager * G4DNAChemistryManager::GetInstanceIfExists ( )

static

Definition at line 121 of file G4DNAChemistryManager.cc.

References fgInstance.

Referenced by G4VUserChemistryList::~G4VUserChemistryList().

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G4DNAWaterIonisationStructure * G4DNAChemistryManager::GetIonisationLevel ( )

protected

Definition at line 499 of file G4DNAChemistryManager.cc.

References fpIonisationLevel.

Referenced by CreateWaterMolecule().

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void G4DNAChemistryManager::Gun	(	G4ITGun *	gun,
		bool	physicsTableToBuild = `true`
	)

Definition at line 268 of file G4DNAChemistryManager.cc.

References fBuildPhysicsTable, G4Scheduler::Instance(), and G4Scheduler::SetGun().

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void G4DNAChemistryManager::Initialize ( )

Definition at line 274 of file G4DNAChemistryManager.cc.

References InitializeMaster(), InitializeThread(), G4Threading::IsMultithreadedApplication(), and G4Threading::IsWorkerThread().

Referenced by G4EmDNAChemistry::ConstructProcess().

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void G4DNAChemistryManager::InitializeFile ( )

protected

Definition at line 402 of file G4DNAChemistryManager.cc.

References fFileInitialized, fpgOutput_tl, fVerbose, fWriteFile, G4cout, G4endl, and left.

Referenced by CreateSolvatedElectron(), CreateWaterMolecule(), InitializeThread(), PushMolecule(), and PushMoleculeAtParentTimeAndPlace().

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void G4DNAChemistryManager::InitializeMaster ( )

protected

Definition at line 310 of file G4DNAChemistryManager.cc.

References G4VUserChemistryList::ConstructDissociationChannels(), G4VUserChemistryList::ConstructReactionTable(), fActiveChemistry, FatalException, fMasterInitialized, fpUserChemistryList, fVerbose, G4cout, G4endl, G4Exception(), G4DNAMolecularReactionTable::GetReactionTable(), and G4Scheduler::Instance().

Referenced by ForceMasterReinitialization(), and Initialize().

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void G4DNAChemistryManager::InitializeThread ( )

protected

Definition at line 343 of file G4DNAChemistryManager.cc.

References G4VUserChemistryList::BuildPhysicsTable(), G4GeometryManager::CloseGeometry(), G4VUserChemistryList::ConstructTimeStepModel(), FatalException, fBuildPhysicsTable, fForceThreadReinitialization, fGeometryClosed, fpgThreadInitialized_tl, fPhysicsTableBuilt, fpUserChemistryList, fVerbose, G4cout, G4endl, G4Exception(), G4GeometryManager::GetInstance(), G4DNAMolecularReactionTable::GetReactionTable(), G4Scheduler::Initialize(), InitializeFile(), G4MoleculeCounter::InitializeInstance(), G4Scheduler::Instance(), and G4GeometryManager::OpenGeometry().

Referenced by Initialize(), and Run().

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G4DNAChemistryManager * G4DNAChemistryManager::Instance ( void )

static

Definition at line 106 of file G4DNAChemistryManager.cc.

References chemManExistence, fgInstance, G4DNAChemistryManager(), and G4TemplateAutoLock< M, L, U >::unlock().

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G4bool G4DNAChemistryManager::IsActivated ( )

static

Definition at line 431 of file G4DNAChemistryManager.cc.

References fActiveChemistry, and Instance().

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G4bool G4DNAChemistryManager::IsChemistryActivated ( )

Definition at line 441 of file G4DNAChemistryManager.cc.

References fActiveChemistry.

G4bool G4DNAChemistryManager::Notify ( G4ApplicationState requestedState )

virtual

Implements G4VStateDependent.

Definition at line 210 of file G4DNAChemistryManager.cc.

References Clear(), fGeometryClosed, fVerbose, G4cout, G4endl, G4State_GeomClosed, and G4State_Quit.

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void G4DNAChemistryManager::PushMolecule	(	G4Molecule *&	molecule,
		double	time,
		const G4ThreeVector &	position,
		int	parentID
	)

WARNING : In case chemistry is not activated, PushMolecule will take care of deleting the transfered molecule.

Before calling this method, it is also possible to check if the chemistry is activated through IsChemistryActived(). This method will create the track corresponding to the transfered molecule and will be in charge of loading the new track to the system.

Definition at line 621 of file G4DNAChemistryManager.cc.

References G4Molecule::BuildTrack(), fActiveChemistry, fAlive, fFileInitialized, fpgOutput_tl, fWriteFile, G4endl, G4Molecule::GetName(), InitializeFile(), G4VITTrackHolder::Instance(), nanometer, and G4VITTrackHolder::Push().

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void G4DNAChemistryManager::PushMoleculeAtParentTimeAndPlace	(	G4Molecule *&	molecule,
		const G4Track *	theIncomingTrack
	)

WARNING : In case chemistry is not activated, PushMoleculeAtParentTimeAndPlace will take care of deleting the transfered molecule.

Before calling this method, it is also possible to check if the chemistry is activated through IsChemistryActived(). This method will create the track corresponding to the transfered molecule and will be in charge of loading the new track to the system.

Definition at line 653 of file G4DNAChemistryManager.cc.

References G4Molecule::BuildTrack(), eV, fActiveChemistry, fAlive, fFileInitialized, fpgOutput_tl, fWriteFile, G4endl, G4Track::GetGlobalTime(), G4Track::GetKineticEnergy(), G4Molecule::GetName(), G4Track::GetPosition(), G4Track::GetTrackID(), InitializeFile(), G4VITTrackHolder::Instance(), nanometer, and G4VITTrackHolder::Push().

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void G4DNAChemistryManager::Run ( )

Definition at line 241 of file G4DNAChemistryManager.cc.

References CloseFile(), fActiveChemistry, FatalException, fMasterInitialized, fpgThreadInitialized_tl, G4Exception(), InitializeThread(), G4Scheduler::Instance(), and G4Scheduler::Process().

Referenced by StackingAction::NewStage(), and SetNewValue().

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void G4DNAChemistryManager::SetChemistryActivation ( G4bool flag )

Definition at line 446 of file G4DNAChemistryManager.cc.

References fActiveChemistry.

void G4DNAChemistryManager::SetChemistryList ( G4VUserChemistryList * chemistryList )

inline

Definition at line 241 of file G4DNAChemistryManager.hh.

References Activated(), and fpUserChemistryList.

Referenced by G4EmDNAChemistry::G4EmDNAChemistry().

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void G4DNAChemistryManager::SetNewValue	(	G4UIcommand *	command,
		G4String	value
	)

virtual

Reimplemented from G4UImessenger.

Definition at line 229 of file G4DNAChemistryManager.cc.

References Activated(), fpActivateChem, fpRunChem, G4UIcmdWithABool::GetNewBoolValue(), and Run().

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void G4DNAChemistryManager::SetVerbose ( G4int verbose )

inline

Definition at line 195 of file G4DNAChemistryManager.hh.

References fVerbose.

void G4DNAChemistryManager::TagThreadForReinitialization ( )

inline

Definition at line 264 of file G4DNAChemistryManager.hh.

References fpgThreadInitialized_tl.

void G4DNAChemistryManager::WriteInto	(	const G4String &	,
		std::ios_base::openmode	mode = `std::ios_base::out`
	)

Tells the chemMan to write into a file the position and electronic state of the water molecule and the position thermalized or not of the solvated electron.

Definition at line 451 of file G4DNAChemistryManager.cc.

References G4String::data(), fFileInitialized, fpgOutput_tl, fVerbose, fWriteFile, G4cout, and G4endl.

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Member Data Documentation

bool G4DNAChemistryManager::fActiveChemistry

private

Definition at line 216 of file G4DNAChemistryManager.hh.

Referenced by Activated(), CreateSolvatedElectron(), CreateWaterMolecule(), G4DNAChemistryManager(), InitializeMaster(), IsActivated(), IsChemistryActivated(), PushMolecule(), PushMoleculeAtParentTimeAndPlace(), Run(), and SetChemistryActivation().

G4bool G4DNAChemistryManager::fBuildPhysicsTable

private

Definition at line 228 of file G4DNAChemistryManager.hh.

Referenced by G4DNAChemistryManager(), Gun(), and InitializeThread().

G4bool G4DNAChemistryManager::fFileInitialized

private

Definition at line 217 of file G4DNAChemistryManager.hh.

Referenced by CreateSolvatedElectron(), CreateWaterMolecule(), G4DNAChemistryManager(), InitializeFile(), PushMolecule(), PushMoleculeAtParentTimeAndPlace(), and WriteInto().

G4bool G4DNAChemistryManager::fForceThreadReinitialization

private

Definition at line 222 of file G4DNAChemistryManager.hh.

Referenced by ForceThreadReinitialization(), G4DNAChemistryManager(), and InitializeThread().

G4bool G4DNAChemistryManager::fGeometryClosed

private

Definition at line 231 of file G4DNAChemistryManager.hh.

Referenced by G4DNAChemistryManager(), InitializeThread(), and Notify().

G4DNAChemistryManager * G4DNAChemistryManager::fgInstance

staticprivate

Definition at line 214 of file G4DNAChemistryManager.hh.

Referenced by DeleteInstance(), GetInstanceIfExists(), Instance(), and ~G4DNAChemistryManager().

G4bool G4DNAChemistryManager::fMasterInitialized

private

Definition at line 221 of file G4DNAChemistryManager.hh.

Referenced by ForceMasterReinitialization(), G4DNAChemistryManager(), InitializeMaster(), and Run().

G4UIcmdWithABool* G4DNAChemistryManager::fpActivateChem

private

Definition at line 211 of file G4DNAChemistryManager.hh.

Referenced by Clear(), G4DNAChemistryManager(), and SetNewValue().

G4UIdirectory* G4DNAChemistryManager::fpChemDNADirectory

private

Definition at line 210 of file G4DNAChemistryManager.hh.

Referenced by Clear(), and G4DNAChemistryManager().

G4DNAWaterExcitationStructure* G4DNAChemistryManager::fpExcitationLevel

private

Definition at line 224 of file G4DNAChemistryManager.hh.

Referenced by Clear(), G4DNAChemistryManager(), and GetExcitationLevel().

G4ThreadLocal std::ofstream * G4DNAChemistryManager::fpgOutput_tl = 0

staticprivate

Definition at line 219 of file G4DNAChemistryManager.hh.

Referenced by AddEmptyLineInOuputFile(), CloseFile(), CreateSolvatedElectron(), CreateWaterMolecule(), InitializeFile(), PushMolecule(), PushMoleculeAtParentTimeAndPlace(), and WriteInto().

G4ThreadLocal G4bool * G4DNAChemistryManager::fpgThreadInitialized_tl = 0

staticprivate

Definition at line 220 of file G4DNAChemistryManager.hh.

Referenced by InitializeThread(), Run(), and TagThreadForReinitialization().

G4bool G4DNAChemistryManager::fPhysicsTableBuilt

private

Definition at line 229 of file G4DNAChemistryManager.hh.

Referenced by ForceRebuildingPhysicsTable(), G4DNAChemistryManager(), and InitializeThread().

G4DNAWaterIonisationStructure* G4DNAChemistryManager::fpIonisationLevel

private

Definition at line 225 of file G4DNAChemistryManager.hh.

Referenced by Clear(), G4DNAChemistryManager(), and GetIonisationLevel().

G4UIcmdWithoutParameter* G4DNAChemistryManager::fpRunChem

private

Definition at line 212 of file G4DNAChemistryManager.hh.

Referenced by Clear(), G4DNAChemistryManager(), and SetNewValue().

G4VUserChemistryList* G4DNAChemistryManager::fpUserChemistryList

private

Definition at line 227 of file G4DNAChemistryManager.hh.

Referenced by Clear(), Deregister(), G4DNAChemistryManager(), InitializeMaster(), InitializeThread(), and SetChemistryList().

G4int G4DNAChemistryManager::fVerbose

private

Definition at line 233 of file G4DNAChemistryManager.hh.

Referenced by CloseFile(), G4DNAChemistryManager(), InitializeFile(), InitializeMaster(), InitializeThread(), Notify(), SetVerbose(), and WriteInto().

G4bool G4DNAChemistryManager::fWriteFile

private

Definition at line 218 of file G4DNAChemistryManager.hh.

Referenced by AddEmptyLineInOuputFile(), CreateSolvatedElectron(), CreateWaterMolecule(), G4DNAChemistryManager(), InitializeFile(), PushMolecule(), PushMoleculeAtParentTimeAndPlace(), and WriteInto().

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

source/source/processes/electromagnetic/dna/utils/include/G4DNAChemistryManager.hh
source/source/processes/electromagnetic/dna/utils/src/G4DNAChemistryManager.cc

Private Attributes
G4UIdirectory *	fpChemDNADirectory

G4UIcmdWithABool *	fpActivateChem

G4UIcmdWithoutParameter *	fpRunChem

bool	fActiveChemistry

G4bool	fFileInitialized

G4bool	fWriteFile

G4bool	fMasterInitialized

G4bool	fForceThreadReinitialization

G4DNAWaterExcitationStructure *	fpExcitationLevel

G4DNAWaterIonisationStructure *	fpIonisationLevel

G4VUserChemistryList *	fpUserChemistryList

G4bool	fBuildPhysicsTable

G4bool	fPhysicsTableBuilt

G4bool	fGeometryClosed

G4int	fVerbose

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation