G4DNAChemistryManager Class Reference

#include <G4DNAChemistryManager.hh>

Public Member Functions
void	WriteInto (const G4String &, std::ios_base::openmode mode=std::ios_base::out)
void	CloseFile ()
G4bool	IsChemistryActived ()
void	SetChemistryActivation (G4bool)
void	CreateWaterMolecule (ElectronicModification, G4int, const G4Track *)
void	CreateSolvatedElectron (const G4Track *, G4ThreeVector *finalPosition=0)
void	PushMolecule (G4Molecule *&molecule, double time, const G4ThreeVector &position, int parentID)
void	PushMoleculeAtParentTimeAndPlace (G4Molecule *&molecule, const G4Track *)
void	AddEmptyLineInOuputFile ()

Static Public Member Functions
static G4DNAChemistryManager *	Instance ()
static void	DeleteInstance ()

Protected Member Functions
G4DNAWaterExcitationStructure *	GetExcitationLevel ()
G4DNAWaterIonisationStructure *	GetIonisationLevel ()
void	InitializeFile ()
	G4DNAChemistryManager ()

Friends
class	std::auto_ptr< G4DNAChemistryManager >

Detailed Description

G4DNAChemistryManager is called from the physics models. It creates the water molecules and the solvated electrons and and send them to synchronous step manager 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 71 of file G4DNAChemistryManager.hh.

Constructor & Destructor Documentation

G4DNAChemistryManager::G4DNAChemistryManager ( )

protected

Definition at line 60 of file G4DNAChemistryManager.cc.

Referenced by Instance().

                                             :
        fActiveChemistry(false)
{
    fExcitationLevel = 0;
    fIonisationLevel = 0;
    fWriteFile       = false;
}

Member Function Documentation

void G4DNAChemistryManager::AddEmptyLineInOuputFile

(

)

Definition at line 335 of file G4DNAChemistryManager.cc.

References G4endl.

{
    if(fWriteFile)
    {
        *fOutput << G4endl;
    }
}

void G4DNAChemistryManager::CloseFile

(

)

Close the file specified with WriteInto

Definition at line 132 of file G4DNAChemistryManager.cc.

{
    if (fOutput->is_open())
    {
        fOutput->close();
    }

    fWriteFile = false;
}

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 225 of file G4DNAChemistryManager.cc.

References G4Molecule::BuildTrack(), G4Electron_aq::Definition(), python.hepunit::eV, fAlive, G4endl, G4Track::GetKineticEnergy(), G4Track::GetPosition(), G4Track::GetTrackID(), G4ITTrackHolder::Instance(), G4ITManager< T >::Instance(), python.hepunit::nanometer, python.hepunit::picosecond, G4ITTrackHolder::PushTrack(), CLHEP::Hep3Vector::x(), CLHEP::Hep3Vector::y(), and CLHEP::Hep3Vector::z().

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

{
    if(fWriteFile)
    {
        *fOutput << setw(11)<< theIncomingTrack->GetTrackID()
                                                << setw(10)<< "e_aq"
                                                << setw(14)<< -1
                                                << std::setprecision(2) << std::fixed
                                                << setw(13)<< theIncomingTrack->GetKineticEnergy()/eV
                                                << std::setprecision(6) << std::scientific
                                                << setw(22)<< (theIncomingTrack->GetPosition().x())/nanometer
                                                << setw(22)<< (theIncomingTrack->GetPosition().y())/nanometer
                                                << setw(22)<< (theIncomingTrack->GetPosition().z())/nanometer  ;

        if(finalPosition != 0)
        {
            *fOutput<< setw(14)<< (finalPosition->x())/nanometer
                    << setw(14)<< (finalPosition->y())/nanometer
                    << setw(14)<< (finalPosition->z())/nanometer ;
        }

        *fOutput << G4endl;
    }

    if(fActiveChemistry)
    {
        G4Molecule* e_aq = new G4Molecule(G4Electron_aq::Definition());
        G4Track * e_aqTrack(0);
        if(finalPosition)
        {
            e_aqTrack  = e_aq->BuildTrack(picosecond,*finalPosition);
        }
        else
        {
            e_aqTrack  = e_aq->BuildTrack(picosecond,theIncomingTrack->GetPosition());
        }
        e_aqTrack -> SetTrackStatus(fAlive);
        e_aqTrack -> SetParentID(theIncomingTrack->GetTrackID());
        G4ITTrackHolder::Instance()->PushTrack(e_aqTrack);
        G4ITManager<G4Molecule>::Instance()->Push(e_aqTrack);
    }
}

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 160 of file G4DNAChemistryManager.cc.

References G4Molecule::BuildTrack(), G4H2O::Definition(), eDissociativeAttachment, eExcitedMolecule, eIonizedMolecule, energy(), python.hepunit::eV, G4DNAWaterExcitationStructure::ExcitationEnergy(), fStopButAlive, G4endl, GetExcitationLevel(), GetIonisationLevel(), G4Track::GetPosition(), G4Track::GetTrackID(), G4ITTrackHolder::Instance(), G4DNAWaterIonisationStructure::IonisationEnergy(), left, python.hepunit::nanometer, python.hepunit::picosecond, G4ITTrackHolder::PushTrack(), right, CLHEP::Hep3Vector::x(), CLHEP::Hep3Vector::y(), and CLHEP::Hep3Vector::z().

Referenced by G4DNAEmfietzoglouExcitationModel::SampleSecondaries(), G4DNAMillerGreenExcitationModel::SampleSecondaries(), G4DNABornExcitationModel::SampleSecondaries(), G4DNAMeltonAttachmentModel::SampleSecondaries(), G4DNARuddIonisationModel::SampleSecondaries(), G4DNARuddIonisationExtendedModel::SampleSecondaries(), and G4DNABornIonisationModel::SampleSecondaries().

{
    if(fWriteFile)
    {
        G4double energy = -1.;

        switch (modification)
        {
        case eDissociativeAttachment:
            energy = -1;
            break;
        case eExcitedMolecule :
            energy = GetExcitationLevel()->ExcitationEnergy(electronicLevel);
            break;
        case eIonizedMolecule :
            energy = GetIonisationLevel()->IonisationEnergy(electronicLevel);
            break;
        }

        *fOutput << setw(11) << left << theIncomingTrack->GetTrackID()
                                                << setw(10) << "H2O"
                                                << left << modification
                                                << internal <<":"
                                                << right <<electronicLevel
                                                << left
                                                << setw(11) << ""
                                                << std::setprecision(2) << std::fixed
                                                << setw(13) << energy/eV
                                                << std::setprecision(6) << std::scientific
                                                << setw(22) << (theIncomingTrack->GetPosition().x())/nanometer
                                                << setw(22) << (theIncomingTrack->GetPosition().y())/nanometer
                                                << setw(22) << (theIncomingTrack->GetPosition().z())/nanometer
                                                << G4endl;
    }

    if(fActiveChemistry)
    {
        G4Molecule * H2O = new G4Molecule (G4H2O::Definition());

        switch (modification)
        {
        case eDissociativeAttachment:
            H2O -> AddElectron(5,1);
            break;
        case eExcitedMolecule :
            H2O -> ExciteMolecule(electronicLevel);
            break;
        case eIonizedMolecule :
            H2O -> IonizeMolecule(electronicLevel);
            break;
        }

        G4Track * H2OTrack = H2O->BuildTrack(1*picosecond,
                theIncomingTrack->GetPosition());

        H2OTrack -> SetParentID(theIncomingTrack->GetTrackID());
        H2OTrack -> SetTrackStatus(fStopButAlive);
        H2OTrack -> SetKineticEnergy(0.);

        G4ITTrackHolder::Instance()->PushTrack(H2OTrack);
    }
}

void G4DNAChemistryManager::DeleteInstance ( )

static

You should rather use DeleteInstance than the destructor of this class

Definition at line 93 of file G4DNAChemistryManager.cc.

References chemManExistence.

{
    G4AutoLock lock(&chemManExistence);
    if(fInstance.get())
    {
        fInstance.reset();
    }
}

G4DNAWaterExcitationStructure * G4DNAChemistryManager::GetExcitationLevel ( )

protected

Definition at line 142 of file G4DNAChemistryManager.cc.

Referenced by CreateWaterMolecule().

{
    if(!fExcitationLevel)
    {
        fExcitationLevel = new G4DNAWaterExcitationStructure;
    }
    return fExcitationLevel;
}

G4DNAWaterIonisationStructure * G4DNAChemistryManager::GetIonisationLevel ( )

protected

Definition at line 151 of file G4DNAChemistryManager.cc.

Referenced by CreateWaterMolecule().

{
    if(!fIonisationLevel)
    {
        fIonisationLevel = new G4DNAWaterIonisationStructure;
    }
    return fIonisationLevel;
}

void G4DNAChemistryManager::InitializeFile ( )

protected

Definition at line 102 of file G4DNAChemistryManager.cc.

References G4endl, and left.

{
    *fOutput << std::setprecision(6) << std::scientific;
    *fOutput << setw(11) << left << "#Parent ID"
            << setw(10) << "Molecule"
            << setw(14) << "Elec Modif"
            << setw(13) << "Energy (eV)"
            << setw(22) << "X pos of parent [nm]"
            << setw(22) << "Y pos of parent [nm]"
            << setw(22) << "Z pos of parent [nm]"
            << setw(14) << "X pos [nm]"
            << setw(14) << "Y pos [nm]"
            << setw(14) << "Z pos [nm]"
            << G4endl
            << setw(21) << "#"
            << setw(13) << "1)io/ex=0/1"
            << G4endl
            << setw(21) << "#"
            << setw(13) << "2)level=0...5"
            << G4endl;
}

G4DNAChemistryManager * G4DNAChemistryManager::Instance ( void  )

static

Definition at line 68 of file G4DNAChemistryManager.cc.

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

Referenced by G4DNAEmfietzoglouExcitationModel::SampleSecondaries(), G4DNAMillerGreenExcitationModel::SampleSecondaries(), G4DNABornExcitationModel::SampleSecondaries(), G4DNAMeltonAttachmentModel::SampleSecondaries(), G4DNARuddIonisationModel::SampleSecondaries(), G4DNARuddIonisationExtendedModel::SampleSecondaries(), G4DNABornIonisationModel::SampleSecondaries(), G4DNATransformElectronModel::SampleSecondaries(), and G4DNAOneStepSolvatationModel::SampleSecondaries().

{
    if (fInstance.get() == 0)
    {
        G4AutoLock lock(&chemManExistence);
        if(fInstance.get() == 0) // MT : double check at initialisation
        {
            fInstance = auto_ptr<G4DNAChemistryManager> (new G4DNAChemistryManager()) ;
        }
        lock.unlock();
    }
    return fInstance.get();
}

G4bool G4DNAChemistryManager::IsChemistryActived ( )

inline

Definition at line 159 of file G4DNAChemistryManager.hh.

{
    return fActiveChemistry;
}

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 271 of file G4DNAChemistryManager.cc.

References G4Molecule::BuildTrack(), fAlive, G4endl, G4Molecule::GetName(), G4ITTrackHolder::Instance(), G4ITManager< T >::Instance(), python.hepunit::nanometer, G4ITTrackHolder::PushTrack(), CLHEP::Hep3Vector::x(), CLHEP::Hep3Vector::y(), and CLHEP::Hep3Vector::z().

{
    if(fWriteFile)
    {
        *fOutput << setw(11)<< parentID
                << setw(10)<< molecule->GetName()
                << setw(14)<< -1
                << std::setprecision(2) << std::fixed
                << setw(13)<< -1
                << std::setprecision(6) << std::scientific
                << setw(22)<< (position.x())/nanometer
                << setw(22)<< (position.y())/nanometer
                << setw(22)<< (position.z())/nanometer;
        *fOutput << G4endl;
    }

    if(fActiveChemistry)
    {
        G4Track* track = molecule->BuildTrack(time,position);
        track -> SetTrackStatus(fAlive);
        track -> SetParentID(parentID);
        G4ITTrackHolder::Instance()->PushTrack(track);
        G4ITManager<G4Molecule>::Instance()->Push(track);
    }
    else
    {
        delete molecule;
        molecule = 0;
    }
}

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 303 of file G4DNAChemistryManager.cc.

References G4Molecule::BuildTrack(), python.hepunit::eV, fAlive, G4endl, G4Track::GetGlobalTime(), G4Track::GetKineticEnergy(), G4Molecule::GetName(), G4Track::GetPosition(), G4Track::GetTrackID(), G4ITTrackHolder::Instance(), G4ITManager< T >::Instance(), python.hepunit::nanometer, G4ITTrackHolder::PushTrack(), CLHEP::Hep3Vector::x(), CLHEP::Hep3Vector::y(), and CLHEP::Hep3Vector::z().

{
    if(fWriteFile)
    {
        *fOutput << setw(11)<< theIncomingTrack->GetTrackID()
                                                << setw(10)<< molecule->GetName()
                                                << setw(14)<< -1
                                                << std::setprecision(2) << std::fixed
                                                << setw(13)<< theIncomingTrack->GetKineticEnergy()/eV
                                                << std::setprecision(6) << std::scientific
                                                << setw(22)<< (theIncomingTrack->GetPosition().x())/nanometer
                                                << setw(22)<< (theIncomingTrack->GetPosition().y())/nanometer
                                                << setw(22)<< (theIncomingTrack->GetPosition().z())/nanometer  ;
        *fOutput << G4endl;
    }

    if(fActiveChemistry)
    {
        G4Track* track = molecule->BuildTrack(theIncomingTrack->GetGlobalTime(),theIncomingTrack->GetPosition());
        track -> SetTrackStatus(fAlive);
        track -> SetParentID(theIncomingTrack->GetTrackID());
        G4ITTrackHolder::Instance()->PushTrack(track);
        G4ITManager<G4Molecule>::Instance()->Push(track);
    }
    else
    {
        delete molecule;
        molecule = 0;
    }
}

void G4DNAChemistryManager::SetChemistryActivation ( G4bool  flag )

inline

Definition at line 164 of file G4DNAChemistryManager.hh.

{
    fActiveChemistry = flag;
}

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 124 of file G4DNAChemistryManager.cc.

References G4String::data().

{
    fOutput =  new std::ofstream();
    fOutput->open(output.data(), mode);
    fWriteFile = true;
}

Friends And Related Function Documentation

friend class std::auto_ptr< G4DNAChemistryManager >

friend

Definition at line 73 of file G4DNAChemistryManager.hh.

---

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

• G4DNAChemistryManager.hh
• G4DNAChemistryManager.cc