#include <G4MolecularConfiguration.hh>

Data Structures
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 G4ThreadLocal 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::G4MolecularConfiguration	(	const G4MoleculeDefinition *	moleculeDef,
		const G4ElectronOccupancy &	elecOcc
	)

protected

Definition at line 113 of file G4MolecularConfiguration.cc.

References G4MoleculeDefinition::GetNbElectrons().

 {
     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::G4MolecularConfiguration ( const G4MolecularConfiguration & )

protected

G4MolecularConfiguration::~G4MolecularConfiguration ( )

protected

Definition at line 130 of file G4MolecularConfiguration.cc.

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

Member Function Documentation

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 191 of file G4MolecularConfiguration.cc.

References G4ElectronOccupancy::AddElectron().

Referenced by G4Molecule::AddElectron().

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

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

protected

Definition at line 139 of file G4MolecularConfiguration.cc.

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

void G4MolecularConfiguration::DeleteManager ( )

static

Definition at line 105 of file G4MolecularConfiguration.cc.

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

G4MolecularConfiguration * G4MolecularConfiguration::ExciteMolecule ( G4int ExcitedLevel )

Method used in Geant4-DNA to excite water molecules

Definition at line 158 of file G4MolecularConfiguration.cc.

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

Referenced by G4Molecule::ExciteMolecule().

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

G4int G4MolecularConfiguration::GetAtomsNumber ( ) const

Returns the nomber of atoms compouning the molecule

Definition at line 250 of file G4MolecularConfiguration.cc.

Referenced by G4Molecule::GetAtomsNumber().

 {
     return fMoleculeDefinition->GetAtomsNumber();
 }

G4int G4MolecularConfiguration::GetCharge ( ) const

inline

Returns the charge of molecule.

Definition at line 283 of file G4MolecularConfiguration.hh.

References fDynCharge.

Referenced by G4Molecule::GetCharge().

 {
     return fDynCharge ;
 }

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

Definition at line 276 of file G4MolecularConfiguration.cc.

Referenced by G4Molecule::GetDecayChannel().

 {
     return fMoleculeDefinition-> GetDecayChannels(fElectronOccupancy);
 }

G4double G4MolecularConfiguration::GetDecayTime ( ) const

inline

Returns the decay time of the molecule.

Definition at line 268 of file G4MolecularConfiguration.hh.

References fDynDecayTime.

Referenced by G4Molecule::GetDecayTime().

 {
     return fDynDecayTime;
 }

const G4MoleculeDefinition * G4MolecularConfiguration::GetDefinition ( ) const

inline

Definition at line 243 of file G4MolecularConfiguration.hh.

References fMoleculeDefinition.

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

 {
     return fMoleculeDefinition;
 }

G4double G4MolecularConfiguration::GetDiffusionCoefficient ( ) const

inline

Returns the diffusion coefficient D.

Definition at line 258 of file G4MolecularConfiguration.hh.

References fDynDiffusionCoefficient.

Referenced by G4Molecule::GetDiffusionCoefficient().

 {
     return fDynDiffusionCoefficient;
 }

const G4ElectronOccupancy * G4MolecularConfiguration::GetElectronOccupancy ( ) const

inline

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

Definition at line 248 of file G4MolecularConfiguration.hh.

References fElectronOccupancy.

Referenced by G4Molecule::GetElectronOccupancy().

 {
     return fElectronOccupancy ;
 }

G4MolecularConfiguration::G4MolecularConfigurationManager * G4MolecularConfiguration::GetManager ( )

staticprotected

Definition at line 48 of file G4MolecularConfiguration.cc.

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

G4double G4MolecularConfiguration::GetMass ( ) const

inline

Returns the total mass of the molecule.

Definition at line 293 of file G4MolecularConfiguration.hh.

References fDynMass.

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

 {
     return fDynMass;
 }

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

static

Definition at line 91 of file G4MolecularConfiguration.cc.

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

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

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

static

Definition at line 77 of file G4MolecularConfiguration.cc.

References G4MoleculeDefinition::GetGroundStateElectronOccupancy().

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

G4int G4MolecularConfiguration::GetMoleculeID ( ) const

Definition at line 281 of file G4MolecularConfiguration.cc.

References FatalErrorInArgument, G4Exception(), and INT_MAX.

Referenced by G4Molecule::GetMoleculeID().

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

const G4String & G4MolecularConfiguration::GetName ( void ) const

Returns the name of the molecule

Definition at line 237 of file G4MolecularConfiguration.cc.

References G4UIcommand::ConvertToString(), fName, and G4String::isNull().

Referenced by G4Molecule::GetName().

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

G4double G4MolecularConfiguration::GetNbElectrons ( ) const

Returns the number of electron.

Definition at line 255 of file G4MolecularConfiguration.cc.

Referenced by G4Molecule::GetNbElectrons().

 {
     return fElectronOccupancy->GetTotalOccupancy();
 }

G4double G4MolecularConfiguration::GetVanDerVaalsRadius ( ) const

inline

Definition at line 278 of file G4MolecularConfiguration.hh.

References fDynVanDerVaalsRadius.

Referenced by G4Molecule::GetVanDerVaalsRadius().

 {
     return fDynVanDerVaalsRadius;
 }

G4MolecularConfiguration * G4MolecularConfiguration::IonizeMolecule ( G4int IonizedLevel )

Method used in Geant4-DNA to ionize water molecules

Definition at line 170 of file G4MolecularConfiguration.cc.

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

Referenced by G4Molecule::IonizeMolecule().

 {
     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);
 }

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

Move one electron from an orbit to another.

Definition at line 217 of file G4MolecularConfiguration.cc.

References G4UIcommand::ConvertToString(), FatalErrorInArgument, and G4Exception().

Referenced by G4Molecule::MoveOneElectron().

 {
     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);
 }

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

protected

Definition at line 149 of file G4MolecularConfiguration.cc.

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

void G4MolecularConfiguration::PrintState ( ) const

Display the electronic state of the molecule.

Definition at line 260 of file G4MolecularConfiguration.cc.

References G4cout, and G4endl.

Referenced by G4Molecule::PrintState().

 {
     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;
     }
 }

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

Remove n electrons to a given orbit.

Definition at line 198 of file G4MolecularConfiguration.cc.

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

Referenced by G4Molecule::RemoveElectron().

 {
     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);
 }

void G4MolecularConfiguration::SetDecayTime ( G4double dynDecayTime )

inline

Set the decay time of the molecule.

Definition at line 263 of file G4MolecularConfiguration.hh.

References fDynDecayTime.

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

 {
     fDynDecayTime = dynDecayTime;
 }

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 253 of file G4MolecularConfiguration.hh.

References fDynDiffusionCoefficient.

Referenced by G4Molecule::SetDiffusionCoefficient().

 {
     fDynDiffusionCoefficient = dynDiffusionCoefficient ;
 }

void G4MolecularConfiguration::SetMass ( G4double aMass )

inline

Set the total mass of the molecule.

Definition at line 288 of file G4MolecularConfiguration.hh.

References fDynMass.

Referenced by G4Molecule::SetMass().

 {
     fDynMass = aMass ;
 }

void G4MolecularConfiguration::SetVanDerVaalsRadius ( G4double dynVanDerVaalsRadius )

inline

The Van Der Valls Radius of the molecule

Definition at line 273 of file G4MolecularConfiguration.hh.

References fDynVanDerVaalsRadius.

Referenced by G4Molecule::SetVanDerVaalsRadius().

 {
     fDynVanDerVaalsRadius = dynVanDerVaalsRadius ;
 }

Field Documentation

G4int G4MolecularConfiguration::fDynCharge

protected

Definition at line 198 of file G4MolecularConfiguration.hh.

Referenced by GetCharge().

G4double G4MolecularConfiguration::fDynDecayTime

protected

Definition at line 196 of file G4MolecularConfiguration.hh.

Referenced by GetDecayTime(), and SetDecayTime().

G4double G4MolecularConfiguration::fDynDiffusionCoefficient

protected

Definition at line 194 of file G4MolecularConfiguration.hh.

Referenced by GetDiffusionCoefficient(), and SetDiffusionCoefficient().

G4double G4MolecularConfiguration::fDynMass

protected

Definition at line 197 of file G4MolecularConfiguration.hh.

Referenced by GetMass(), and SetMass().

G4double G4MolecularConfiguration::fDynVanDerVaalsRadius

protected

Definition at line 195 of file G4MolecularConfiguration.hh.

Referenced by GetVanDerVaalsRadius(), and SetVanDerVaalsRadius().

const G4ElectronOccupancy* G4MolecularConfiguration::fElectronOccupancy

protected

Definition at line 177 of file G4MolecularConfiguration.hh.

Referenced by GetElectronOccupancy().

G4ThreadLocal MolecularConfigurationManager * G4MolecularConfiguration::fgManager = 0

staticprotected

Definition at line 190 of file G4MolecularConfiguration.hh.

const G4MoleculeDefinition* G4MolecularConfiguration::fMoleculeDefinition

protected

Definition at line 176 of file G4MolecularConfiguration.hh.

Referenced by GetDefinition().

G4String G4MolecularConfiguration::fName

mutableprotected

Definition at line 199 of file G4MolecularConfiguration.hh.

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

Data Structures

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Field Documentation