G4MolecularConfiguration Class Reference

#include <G4MolecularConfiguration.hh>

Classes
struct	G4MolecularConfigurationManager

Public Member Functions
const G4MoleculeDefinition *	GetDefinition () const
const G4String &	GetName () const
G4int	GetAtomsNumber () const
G4MolecularConfiguration *	ExciteMolecule (G4int)
G4MolecularConfiguration *	IonizeMolecule (G4int)
G4MolecularConfiguration *	AddElectron (G4int orbit, G4int n=1)
G4MolecularConfiguration *	RemoveElectron (G4int, G4int number=1)
G4MolecularConfiguration *	MoveOneElectron (G4int, G4int)
G4double	GetNbElectrons () const
void	PrintState () const
const std::vector< const G4MolecularDecayChannel * > *	GetDecayChannel () const
G4int	GetMoleculeID () const
void	SetDiffusionCoefficient (G4double)
G4double	GetDiffusionCoefficient () 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

Static Public Member Functions
static G4MolecularConfiguration *	GetMolecularConfiguration (const G4MoleculeDefinition *, const G4ElectronOccupancy &electronOccupancy)
static G4MolecularConfiguration *	GetMolecularConfiguration (const G4MoleculeDefinition *)
static void	DeleteManager ()

Protected Member Functions
	G4MolecularConfiguration (const G4MoleculeDefinition *, const G4ElectronOccupancy &)
	G4MolecularConfiguration (const G4MolecularConfiguration &)
G4MolecularConfiguration &	operator= (G4MolecularConfiguration &right)
	~G4MolecularConfiguration ()
G4MolecularConfiguration *	ChangeConfiguration (const G4ElectronOccupancy &newElectronOccupancy)

Static Protected Member Functions
static G4MolecularConfigurationManager *	GetManager ()

Protected Attributes
const G4MoleculeDefinition *	fMoleculeDefinition
const G4ElectronOccupancy *	fElectronOccupancy
G4double	fDynDiffusionCoefficient
G4double	fDynVanDerVaalsRadius
G4double	fDynDecayTime
G4double	fDynMass
G4int	fDynCharge
G4String	fName

Static Protected Attributes
static G4MolecularConfigurationManager *	fgManager = 0

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 59 of file G4MolecularConfiguration.hh.

Constructor & Destructor Documentation

G4MolecularConfiguration() [1/2]

G4MolecularConfiguration::G4MolecularConfiguration ( const G4MoleculeDefinition *  moleculeDef, const G4ElectronOccupancy &  elecOcc  )

protected

Definition at line 111 of file G4MolecularConfiguration.cc.

{
    fMoleculeDefinition = moleculeDef ;
    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();
    fDynMass = fMoleculeDefinition->GetMass() ;
 
    fDynDiffusionCoefficient = fMoleculeDefinition->GetDiffusionCoefficient() ;
    fDynVanDerVaalsRadius = fMoleculeDefinition->GetVanDerVaalsRadius() ;
    fDynDecayTime = fMoleculeDefinition->GetDecayTime() ;
}

G4MolecularConfiguration() [2/2]

G4MolecularConfiguration::G4MolecularConfiguration ( const G4MolecularConfiguration &  )

protected

~G4MolecularConfiguration()

G4MolecularConfiguration::~G4MolecularConfiguration ( )

protected

Definition at line 128 of file G4MolecularConfiguration.cc.

{
    if(fElectronOccupancy)
    {
        delete fElectronOccupancy;
        fElectronOccupancy = 0;
    }
}

Member Function Documentation

AddElectron()

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 189 of file G4MolecularConfiguration.cc.

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

Referenced by G4Molecule::AddElectron(), and MoveOneElectron().

ChangeConfiguration()

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

protected

Definition at line 137 of file G4MolecularConfiguration.cc.

{
    G4MolecularConfiguration* output = fgManager->fTable[fMoleculeDefinition][newElectronOccupancy] ;
    if(! output)
    {
        output = new G4MolecularConfiguration(fMoleculeDefinition, newElectronOccupancy);
    }
    return output ;
}

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

DeleteManager()

void G4MolecularConfiguration::DeleteManager ( )

static

Definition at line 103 of file G4MolecularConfiguration.cc.

{
    if(fgManager) delete fgManager;
    fgManager = 0;
}

ExciteMolecule()

G4MolecularConfiguration * G4MolecularConfiguration::ExciteMolecule

(

G4int

ExcitedLevel

)

Method used in Geant4-DNA to excite water molecules

Definition at line 156 of file G4MolecularConfiguration.cc.

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

Referenced by G4Molecule::ExciteMolecule().

GetAtomsNumber()

G4int G4MolecularConfiguration::GetAtomsNumber

(

)

const

Returns the nomber of atoms compouning the molecule

Definition at line 248 of file G4MolecularConfiguration.cc.

{
    return fMoleculeDefinition->GetAtomsNumber();
}

Referenced by G4Molecule::GetAtomsNumber().

GetCharge()

G4int G4MolecularConfiguration::GetCharge ( ) const

inline

Returns the charge of molecule.

Definition at line 275 of file G4MolecularConfiguration.hh.

{
    return fDynCharge ;
}

Referenced by G4Molecule::GetCharge().

GetDecayChannel()

const vector< const G4MolecularDecayChannel * > * G4MolecularConfiguration::GetDecayChannel

(

)

const

Definition at line 274 of file G4MolecularConfiguration.cc.

{
    return fMoleculeDefinition-> GetDecayChannels(fElectronOccupancy);
}

Referenced by G4Molecule::GetDecayChannel().

GetDecayTime()

G4double G4MolecularConfiguration::GetDecayTime ( ) const

inline

Returns the decay time of the molecule.

Definition at line 260 of file G4MolecularConfiguration.hh.

{
    return fDynDecayTime;
}

Referenced by G4Molecule::GetDecayTime().

GetDefinition()

const G4MoleculeDefinition * G4MolecularConfiguration::GetDefinition ( ) const

inline

Definition at line 235 of file G4MolecularConfiguration.hh.

{
    return fMoleculeDefinition;
}

Referenced by G4Molecule::BuildTrack(), G4Molecule::GetDefinition(), and G4Molecule::SetElectronOccupancy().

GetDiffusionCoefficient()

G4double G4MolecularConfiguration::GetDiffusionCoefficient ( ) const

inline

Returns the diffusion coefficient D.

Definition at line 250 of file G4MolecularConfiguration.hh.

{
    return fDynDiffusionCoefficient;
}

Referenced by G4Molecule::GetDiffusionCoefficient().

GetElectronOccupancy()

const G4ElectronOccupancy * G4MolecularConfiguration::GetElectronOccupancy ( ) const

inline

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

Definition at line 240 of file G4MolecularConfiguration.hh.

{
    return fElectronOccupancy ;
}

Referenced by G4Molecule::GetElectronOccupancy().

GetManager()

G4MolecularConfiguration::G4MolecularConfigurationManager * G4MolecularConfiguration::GetManager ( )

staticprotected

Definition at line 46 of file G4MolecularConfiguration.cc.

{
    if(!fgManager)
    {
        fgManager = new G4MolecularConfiguration::G4MolecularConfigurationManager;
    }
 
    return fgManager;
}

Referenced by GetMolecularConfiguration().

GetMass()

G4double G4MolecularConfiguration::GetMass ( ) const

inline

Returns the total mass of the molecule.

Definition at line 285 of file G4MolecularConfiguration.hh.

{
    return fDynMass;
}

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

GetMolecularConfiguration() [1/2]

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

static

Definition at line 75 of file G4MolecularConfiguration.cc.

{
    const G4ElectronOccupancy& elecOcc = *molDef->GetGroundStateElectronOccupancy();
    if(GetManager()->fTable[molDef][elecOcc])
    {
        return GetManager()->fTable[molDef][elecOcc];
    }
    else
    {
        G4MolecularConfiguration* newConf = new G4MolecularConfiguration(molDef, elecOcc);
        return newConf ;
    }
}

GetMolecularConfiguration() [2/2]

G4MolecularConfiguration * G4MolecularConfiguration::GetMolecularConfiguration ( const G4MoleculeDefinition *  molDef, const G4ElectronOccupancy &  electronOccupancy  )

static

Definition at line 89 of file G4MolecularConfiguration.cc.

{
    if(GetManager()->fTable[molDef][elecOcc])
    {
        return GetManager()->fTable[molDef][elecOcc];
    }
    else
    {
        G4MolecularConfiguration* newConf = new G4MolecularConfiguration(molDef, elecOcc);
        return newConf ;
    }
}

Referenced by G4MoleculeDefinition::AddeConfToExcitedState(), G4Molecule::G4Molecule(), and G4Molecule::SetElectronOccupancy().

GetMoleculeID()

G4int G4MolecularConfiguration::GetMoleculeID

(

)

const

Definition at line 279 of file G4MolecularConfiguration.cc.

{
    if(fMoleculeDefinition)
        return fMoleculeDefinition->GetPDGEncoding();
    else
        G4Exception("G4Molecule::GetMoleculeID","",FatalErrorInArgument, "You should first enter a molecule defintion");
 
    return INT_MAX;
}

Referenced by G4Molecule::GetMoleculeID().

GetName()

const G4String & G4MolecularConfiguration::GetName

(

)

const

Returns the name of the molecule

Definition at line 235 of file G4MolecularConfiguration.cc.

{
    if(fName.isNull())
    {
        fName = fMoleculeDefinition->GetName();
        fName+= "^";
        fName+= "{";
        fName+= G4UIcommand::ConvertToString(fDynCharge);
        fName+= "}";
    }
    return fName;
}

Referenced by G4Molecule::GetName(), IonizeMolecule(), MoveOneElectron(), PrintState(), and RemoveElectron().

GetNbElectrons()

G4double G4MolecularConfiguration::GetNbElectrons

(

)

const

Returns the number of electron.

Definition at line 253 of file G4MolecularConfiguration.cc.

{
    return fElectronOccupancy->GetTotalOccupancy();
}

Referenced by G4Molecule::GetNbElectrons().

GetVanDerVaalsRadius()

G4double G4MolecularConfiguration::GetVanDerVaalsRadius ( ) const

inline

Definition at line 270 of file G4MolecularConfiguration.hh.

{
    return fDynVanDerVaalsRadius;
}

Referenced by G4Molecule::GetVanDerVaalsRadius().

IonizeMolecule()

G4MolecularConfiguration * G4MolecularConfiguration::IonizeMolecule

(

G4int

IonizedLevel

)

Method used in Geant4-DNA to ionize water molecules

Definition at line 168 of file G4MolecularConfiguration.cc.

{
    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("G4Molecule::IonizeMolecule","",FatalErrorInArgument, errMsg);
        PrintState();
    }
 
    // PrintState();
 
    return ChangeConfiguration(newElectronOccupancy);
}

Referenced by G4Molecule::IonizeMolecule().

MoveOneElectron()

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

Move one electron from an orbit to another.

Definition at line 215 of file G4MolecularConfiguration.cc.

{
    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("G4Molecule::MoveOneElectron","",FatalErrorInArgument, errMsg);
        PrintState();
    }
 
    return ChangeConfiguration(newElectronOccupancy);
}

Referenced by G4Molecule::MoveOneElectron().

operator=()

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

protected

Definition at line 147 of file G4MolecularConfiguration.cc.

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

PrintState()

void G4MolecularConfiguration::PrintState

(

)

const

Show the electronic state of the molecule.

Definition at line 258 of file G4MolecularConfiguration.cc.

{
    G4cout<<"--------------Print electronic state of "<<GetName()<<"---------------"<<G4endl;
    fElectronOccupancy->DumpInfo();
    if(fElectronOccupancy==fMoleculeDefinition->GetGroundStateElectronOccupancy())
    {
        G4cout<<"At ground state"<<G4endl;
    }
    else
    {
        if(fMoleculeDefinition->GetDecayTable())
            G4cout<<"Transition :"<<(fMoleculeDefinition->GetDecayTable())->GetExcitedState(fElectronOccupancy)<<G4endl;
    }
}

Referenced by IonizeMolecule(), MoveOneElectron(), G4Molecule::PrintState(), and RemoveElectron().

RemoveElectron()

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

Remove n electrons to a given orbit.

Definition at line 196 of file G4MolecularConfiguration.cc.

{
    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("G4Molecule::RemoveElectron","",JustWarning, errMsg);
        PrintState();
    }
 
    return ChangeConfiguration(newElectronOccupancy);
}

Referenced by MoveOneElectron(), and G4Molecule::RemoveElectron().

SetDecayTime()

void G4MolecularConfiguration::SetDecayTime ( G4double  dynDecayTime )

inline

Set the decay time of the molecule.

Definition at line 255 of file G4MolecularConfiguration.hh.

{
    fDynDecayTime = dynDecayTime;
}

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

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.

Definition at line 245 of file G4MolecularConfiguration.hh.

{
    fDynDiffusionCoefficient = dynDiffusionCoefficient ;
}

Referenced by G4Molecule::SetDiffusionCoefficient().

SetMass()

void G4MolecularConfiguration::SetMass ( G4double  aMass )

inline

Set the total mass of the molecule.

Definition at line 280 of file G4MolecularConfiguration.hh.

{
    fDynMass = aMass ;
}

Referenced by G4Molecule::SetMass().

SetVanDerVaalsRadius()

void G4MolecularConfiguration::SetVanDerVaalsRadius ( G4double  dynVanDerVaalsRadius )

inline

The Van Der Valls Radius of the molecule

Definition at line 265 of file G4MolecularConfiguration.hh.

{
    fDynVanDerVaalsRadius = dynVanDerVaalsRadius ;
}

Referenced by G4Molecule::SetVanDerVaalsRadius().

Member Data Documentation

fDynCharge

G4int G4MolecularConfiguration::fDynCharge

protected

Definition at line 190 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), GetCharge(), and GetName().

fDynDecayTime

G4double G4MolecularConfiguration::fDynDecayTime

protected

Definition at line 188 of file G4MolecularConfiguration.hh.

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

fDynDiffusionCoefficient

G4double G4MolecularConfiguration::fDynDiffusionCoefficient

protected

Definition at line 186 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), GetDiffusionCoefficient(), and SetDiffusionCoefficient().

fDynMass

G4double G4MolecularConfiguration::fDynMass

protected

Definition at line 189 of file G4MolecularConfiguration.hh.

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

fDynVanDerVaalsRadius

G4double G4MolecularConfiguration::fDynVanDerVaalsRadius

protected

Definition at line 187 of file G4MolecularConfiguration.hh.

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

fElectronOccupancy

const G4ElectronOccupancy* G4MolecularConfiguration::fElectronOccupancy

protected

Definition at line 171 of file G4MolecularConfiguration.hh.

Referenced by AddElectron(), ExciteMolecule(), G4MolecularConfiguration(), GetDecayChannel(), GetElectronOccupancy(), GetNbElectrons(), IonizeMolecule(), MoveOneElectron(), PrintState(), RemoveElectron(), and ~G4MolecularConfiguration().

fgManager

G4MolecularConfiguration::G4MolecularConfigurationManager * G4MolecularConfiguration::fgManager = 0

staticprotected

Definition at line 182 of file G4MolecularConfiguration.hh.

Referenced by ChangeConfiguration(), DeleteManager(), G4MolecularConfiguration(), and GetManager().

fMoleculeDefinition

const G4MoleculeDefinition* G4MolecularConfiguration::fMoleculeDefinition

protected

Definition at line 170 of file G4MolecularConfiguration.hh.

Referenced by ChangeConfiguration(), G4MolecularConfiguration(), GetAtomsNumber(), GetDecayChannel(), GetDefinition(), GetMoleculeID(), GetName(), and PrintState().

fName

G4String G4MolecularConfiguration::fName

mutableprotected

Definition at line 191 of file G4MolecularConfiguration.hh.

Referenced by GetName().

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

• G4MolecularConfiguration.hh
• G4MolecularConfiguration.cc