#include <G4Molecule.hh>

Inheritance diagram for G4Molecule:

Public Member Functions
	ITDef (G4Molecule) void Print() const

void *	operator new (size_t)

void	operator delete (void *aVUserTrackInformation)

	G4Molecule (const G4Molecule &)

G4Molecule &	operator= (const G4Molecule &right)

G4bool	operator== (const G4Molecule &right) const

G4bool	operator!= (const G4Molecule &right) const

G4bool	operator< (const G4Molecule &right) const

	G4Molecule (G4MoleculeDefinition *molecule)

	G4Molecule (G4MoleculeDefinition *molecule, G4int, G4int)

	G4Molecule (G4MoleculeDefinition *molecule, G4int, G4bool)

virtual	~G4Molecule ()

const G4String &	GetName () const

G4int	GetAtomsNumber () const

void	SetElectronOccupancy (const G4ElectronOccupancy *)

void	ExciteMolecule (G4int)

void	IonizeMolecule (G4int)

void	AddElectron (G4int orbit, G4int n=1)

void	RemoveElectron (G4int, G4int number=1)

void	MoveOneElectron (G4int, G4int)

G4double	GetNbElectrons () const

void	PrintState () const

G4Track *	BuildTrack (G4double globalTime, const G4ThreeVector &Position)

G4double	GetKineticEnergy () const

G4double	GetDiffusionVelocity () const

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

G4int	GetMoleculeID () const

const G4MoleculeDefinition *	GetDefinition () 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

G4MolecularConfiguration *	GetMolecularConfiguration ()

Public Member Functions inherited from G4IT
	G4IT ()

	G4IT (G4Track *)

virtual	~G4IT ()

void *	operator new (size_t)

void	operator delete (void *aIT)

virtual void	Print () const

virtual const G4String &	GetName () const =0

virtual G4bool	diff (const G4IT &right) const =0

virtual G4bool	equal (const G4IT &right) const =0

G4bool	operator< (const G4IT &right) const

G4bool	operator== (const G4IT &right) const

G4bool	operator!= (const G4IT &right) const

void	SetTrack (G4Track *)

G4Track *	GetTrack ()

const G4Track *	GetTrack () const

void	RecordCurrentPositionNTime ()

void	SetPrevious (G4IT *)

void	SetNext (G4IT *)

G4IT *	GetPrevious ()

G4IT *	GetNext ()

const G4IT *	GetPrevious () const

const G4IT *	GetNext () const

void	SetITBox (G4ITBox *)

const G4ITBox *	GetITBox () const

void	TakeOutBox ()

void	SetNode (G4KDNode *)

void	SetParentID (int, int)

void	GetParentID (int &, int &)

const G4ThreeVector &	GetPreStepPosition () const

G4double	GetPreStepLocalTime () const

G4double	GetPreStepGlobalTime () const

G4KDNode *	GetNode () const

G4TrackingInformation *	GetTrackingInfo ()

G4TrackListNode *	GetTrackListNode ()

void	SetTrackListNode (G4TrackListNode *node)

virtual const G4ITType	GetITType () const =0

Public Member Functions inherited from G4VUserTrackInformation
	G4VUserTrackInformation ()

	G4VUserTrackInformation (const G4String &infoType)

	G4VUserTrackInformation (const G4VUserTrackInformation &)

G4VUserTrackInformation &	operator= (const G4VUserTrackInformation &)

virtual	~G4VUserTrackInformation ()

virtual void	Print () const

const G4String &	GetType () const

Static Public Member Functions
static void	SetGlobalTemperature (double)

static double	GetGlobalTemperature ()

Additional Inherited Members
Protected Member Functions inherited from G4IT
	G4IT (const G4IT &)

G4IT &	operator= (const G4IT &)

Protected Attributes inherited from G4IT
G4Track *	fpTrack

Protected Attributes inherited from G4VUserTrackInformation
G4String *	pType

Detailed Description

Class Description The dynamic molecule holds all the data that change for a molecule It has a pointer to G4MoleculeDefinition object, which holds all the "ground level" information.

Definition at line 76 of file G4Molecule.hh.

Constructor & Destructor Documentation

◆ G4Molecule() [1/4]

G4Molecule::G4Molecule ( const G4Molecule & right )

Definition at line 82 of file G4Molecule.cc.

                                              :
    G4VUserTrackInformation("G4Molecule"), G4IT(right)
{
    Init();
    fMolecularConfiguration = right . fMolecularConfiguration;
}

Referenced by G4Molecule().

◆ G4Molecule() [2/4]

G4Molecule::G4Molecule ( G4MoleculeDefinition * moleculeDefinition )

To build a molecule at ground state according to a given G4MoleculeDefinition that can be obtained from G4GenericMoleculeManager

Build a molecule at ground state according to a given G4MoleculeDefinition that can be obtained from G4GenericMoleculeManager

Definition at line 160 of file G4Molecule.cc.

                                                                :
    G4VUserTrackInformation("G4Molecule"), G4IT()
  //////////////////////////
{
    Init();
    fMolecularConfiguration = G4MolecularConfiguration::GetMolecularConfiguration(moleculeDefinition);
}

◆ G4Molecule() [3/4]

G4Molecule::G4Molecule	(	G4MoleculeDefinition *	moleculeDefinition,
		G4int	OrbitalToFree,
		G4int	OrbitalToFill
	)

To build a molecule at a specific excitation/ionisation state according to a ground state that can be obtained from G4GenericMoleculeManager

Build a molecule at a specific excitation/ionisation state according to a ground state that can be obtained from G4GenericMoleculeManager. Put 0 in the second option if this is a ionisation.

Definition at line 173 of file G4Molecule.cc.

                                                                                                         :
    G4VUserTrackInformation("G4Molecule"), G4IT()
  //////////////////////////
{
    Init();
 
    G4ElectronOccupancy dynElectronOccupancy (*moleculeDefinition->GetGroundStateElectronOccupancy());
 
    if (OrbitalToFill != 0)
    {
        dynElectronOccupancy.RemoveElectron(OrbitalToFree-1,1);
        dynElectronOccupancy.AddElectron(OrbitalToFill-1,1);
        // dynElectronOccupancy.DumpInfo(); // DEBUG
    }
 
    if (OrbitalToFill == 0)
    {
        dynElectronOccupancy.RemoveElectron(OrbitalToFree-1,1);
        // dynElectronOccupancy.DumpInfo(); // DEBUG
    }
 
    fMolecularConfiguration = G4MolecularConfiguration::GetMolecularConfiguration(moleculeDefinition, dynElectronOccupancy);
}

◆ G4Molecule() [4/4]

G4Molecule::G4Molecule	(	G4MoleculeDefinition *	moleculeDefinition,
		G4int	Level,
		G4bool	Excitation
	)

Specific builder for water molecules to be used in Geant4-DNA, the last option Excitation is true if the molecule is excited, is false is the molecule is ionized.

Definition at line 202 of file G4Molecule.cc.

                                                                                               :
    G4VUserTrackInformation("G4Molecule"), G4IT()
{
    Init();
 
    G4ElectronOccupancy dynElectronOccupancy (*moleculeDefinition->GetGroundStateElectronOccupancy());
 
    if (Excitation == true)
    {
        dynElectronOccupancy.RemoveElectron(Level,1);
        dynElectronOccupancy.AddElectron(5,1);
        // dynElectronOccupancy.DumpInfo(); // DEBUG
    }
 
    if (Excitation == false)
    {
        dynElectronOccupancy.RemoveElectron(Level,1);
        // dynElectronOccupancy.DumpInfo(); // DEBUG
    }
 
    fMolecularConfiguration = G4MolecularConfiguration::GetMolecularConfiguration(moleculeDefinition, dynElectronOccupancy);
}

◆ ~G4Molecule()

G4Molecule::~G4Molecule ( )

virtual

Definition at line 138 of file G4Molecule.cc.

{
    if(fpTrack!=NULL)
    {
        if(G4MoleculeCounter::GetMoleculeCounter()->InUse())
        {
            G4MoleculeCounter::GetMoleculeCounter()->RemoveAMoleculeAtTime(*this,
                                                                           fpTrack->GetGlobalTime());
        }
        fpTrack = 0;
    }
    fMolecularConfiguration = 0;
    fDynamicParticle = 0;
    // DEBUG
    // G4cout<<"Molecule killed"<<G4endl;
}

Member Function Documentation

◆ AddElectron()

void G4Molecule::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 244 of file G4Molecule.cc.

{
    fMolecularConfiguration = fMolecularConfiguration->AddElectron(orbit,number);
}

Referenced by G4EmDNAPhysicsChemistry::ConstructDecayChannels(), and G4EmDNAPhysicsChemistry::ConstructReactionTable().

◆ BuildTrack()

G4Track * G4Molecule::BuildTrack	(	G4double	globalTime,
		const G4ThreeVector &	Position
	)

Definition at line 279 of file G4Molecule.cc.

{
    if(fpTrack != 0)
    {
        G4Exception("G4Molecule::BuildTrack","Molecule001",
                    FatalErrorInArgument,"A track was already assigned to this molecule");
    }
 
    // Kinetic Values
    // Set a random direction to the molecule
    G4double costheta = (2*G4UniformRand()-1);
    G4double theta = acos (costheta);
    G4double phi = 2*pi*G4UniformRand();
 
    G4double xMomentum = cos(phi)* sin(theta);
    G4double yMomentum = sin(theta)*sin(phi);
    G4double zMomentum = costheta;
 
    G4ThreeVector MomentumDirection(xMomentum, yMomentum, zMomentum);
    G4double KineticEnergy = GetKineticEnergy();
    // G4cout << " **** KineticEnergy : " << KineticEnergy << G4endl;
    fDynamicParticle = new G4DynamicParticle(fMolecularConfiguration->GetDefinition(),
                                             MomentumDirection,
                                             KineticEnergy);
 
    if(G4MoleculeCounter::GetMoleculeCounter()->InUse())
        G4MoleculeCounter::GetMoleculeCounter()->AddAMoleculeAtTime(*this,globalTime);
 
    //Set the Track
    fpTrack = new G4Track(fDynamicParticle, globalTime, Position);
    fpTrack -> SetUserInformation (this);
 
    return fpTrack;
}

Referenced by G4DNAChemistryManager::CreateSolvatedElectron(), G4DNAChemistryManager::CreateWaterMolecule(), G4DNAMolecularDecay::DecayIt(), G4DNAMolecularReaction::MakeReaction(), G4DNAChemistryManager::PushMolecule(), and G4DNAChemistryManager::PushMoleculeAtParentTimeAndPlace().

◆ ExciteMolecule()

void G4Molecule::ExciteMolecule ( G4int ExcitedLevel )

Method used in Geant4-DNA to excite water molecules

Definition at line 232 of file G4Molecule.cc.

{
    fMolecularConfiguration = fMolecularConfiguration->ExciteMolecule(ExcitedLevel);
}

◆ GetAtomsNumber()

G4int G4Molecule::GetAtomsNumber ( ) const

Returns the nomber of atoms compouning the molecule

Definition at line 264 of file G4Molecule.cc.

{
    return fMolecularConfiguration->GetAtomsNumber();
}

◆ GetCharge()

G4int G4Molecule::GetCharge ( ) const

Returns the charge of molecule.

Definition at line 375 of file G4Molecule.cc.

{
    return fMolecularConfiguration->GetCharge() ;
}

◆ GetDecayChannel()

const vector< const G4MolecularDecayChannel * > * G4Molecule::GetDecayChannel ( ) const

Definition at line 345 of file G4Molecule.cc.

{
    return fMolecularConfiguration->GetDecayChannel();
}

◆ GetDecayTime()

G4double G4Molecule::GetDecayTime ( ) const

Returns the decay time of the molecule.

Definition at line 360 of file G4Molecule.cc.

{
    return fMolecularConfiguration->GetDecayTime();
}

◆ GetDefinition()

const G4MoleculeDefinition * G4Molecule::GetDefinition ( ) const

Get molecule definition. This G4MoleculeDefinition has the ground electronic state of the molecule.

Definition at line 395 of file G4Molecule.cc.

{
    return fMolecularConfiguration->GetDefinition();
}

Referenced by G4MoleculeCounter::AddAMoleculeAtTime(), G4DNAMolecularDecay::DecayIt(), G4DNAMolecularDecayDisplacer::GetProductsDisplacement(), and G4MoleculeCounter::RemoveAMoleculeAtTime().

◆ GetDiffusionCoefficient()

G4double G4Molecule::GetDiffusionCoefficient ( ) const

Returns the diffusion coefficient D.

Definition at line 405 of file G4Molecule.cc.

{
    return fMolecularConfiguration->GetDiffusionCoefficient();
}

Referenced by G4DNABrownianTransportation::AlongStepGetPhysicalInteractionLength(), G4DNABrownianTransportation::ComputeStep(), G4DNASmoluchowskiReactionModel::FindReaction(), G4DNAMolecularReactionData::G4DNAMolecularReactionData(), and G4DNAMolecularReaction::MakeReaction().

◆ GetDiffusionVelocity()

G4double G4Molecule::GetDiffusionVelocity ( ) const

Definition at line 324 of file G4Molecule.cc.

{
    double moleculeMass = fMolecularConfiguration->GetMass()/(c_squared);
 
    ////
    // Different possibilities
    ////
    // Ideal Gaz case : Maxwell Boltzmann Distribution
    //    double sigma = k_Boltzmann * fgTemperature / mass;
    //    return G4RandGauss::shoot( 0, sigma );
    ////
    // Ideal Gaz case : mean velocity from equipartition theorem
    return sqrt(3*k_Boltzmann*fgTemperature/moleculeMass);
    ////
    // Using this approximation for liquid is wrong
    // However the brownian process avoid taking
    // care of energy consideration and plays only
    // with positions
}

Referenced by GetKineticEnergy().

◆ GetElectronOccupancy()

const G4ElectronOccupancy * G4Molecule::GetElectronOccupancy ( ) const

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

Definition at line 390 of file G4Molecule.cc.

{
    return fMolecularConfiguration->GetElectronOccupancy();
}

Referenced by G4DNAMolecularDecay::DecayIt().

◆ GetGlobalTemperature()

double G4Molecule::GetGlobalTemperature ( )

inlinestatic

Definition at line 283 of file G4Molecule.hh.

{
    return fgTemperature;
}

◆ GetKineticEnergy()

G4double G4Molecule::GetKineticEnergy ( ) const

Definition at line 314 of file G4Molecule.cc.

{
    ////
    // Ideal Gaz case
    double v = GetDiffusionVelocity();
    double E = (fMolecularConfiguration->GetMass()/(c_squared))*(v*v)/2.;
    ////
    return E;
}

Referenced by BuildTrack().

◆ GetMass()

G4double G4Molecule::GetMass ( ) const

Returns the total mass of the molecule.

Definition at line 385 of file G4Molecule.cc.

{
    return fMolecularConfiguration->GetMass();
}

◆ GetMolecularConfiguration()

G4MolecularConfiguration * G4Molecule::GetMolecularConfiguration ( )

inline

Definition at line 273 of file G4Molecule.hh.

{
    return fMolecularConfiguration ;
}

Referenced by G4DNASecondOrderReaction::PostStepGetPhysicalInteractionLength().

◆ GetMoleculeID()

G4int G4Molecule::GetMoleculeID ( ) const

Definition at line 350 of file G4Molecule.cc.

{
    return fMolecularConfiguration->GetMoleculeID();
}

◆ GetName()

const G4String & G4Molecule::GetName ( ) const

virtual

Returns the name of the molecule

Implements G4IT.

Definition at line 259 of file G4Molecule.cc.

{
    return fMolecularConfiguration->GetName();
}

Referenced by G4MoleculeCounter::AddAMoleculeAtTime(), G4DNAMoleculeEncounterStepper::CalculateStep(), G4DNAMolecularReactionTable::CanReactWith(), G4DNAMolecularDecay::DecayIt(), G4DNABrownianTransportation::Diffusion(), G4DNASmoluchowskiReactionModel::FindReaction(), G4DNAMolecularReactionTable::GetReactionData(), G4DNAMolecularReactionTable::GetReativesNData(), G4DNASecondOrderReaction::PostStepDoIt(), G4DNAIndirectHit::Print(), G4DNAMolecularReactionTable::PrintTable(), G4DNAChemistryManager::PushMolecule(), G4DNAChemistryManager::PushMoleculeAtParentTimeAndPlace(), G4MoleculeCounter::RemoveAMoleculeAtTime(), and G4DNAMolecularReaction::TestReactibility().

◆ GetNbElectrons()

G4double G4Molecule::GetNbElectrons ( ) const

Returns the number of electron.

Definition at line 269 of file G4Molecule.cc.

{
    return fMolecularConfiguration->GetNbElectrons();
}

◆ GetVanDerVaalsRadius()

G4double G4Molecule::GetVanDerVaalsRadius ( ) const

Definition at line 370 of file G4Molecule.cc.

{
    return fMolecularConfiguration->GetVanDerVaalsRadius();
}

◆ IonizeMolecule()

void G4Molecule::IonizeMolecule ( G4int IonizedLevel )

Method used in Geant4-DNA to ionize water molecules

Definition at line 239 of file G4Molecule.cc.

{
    fMolecularConfiguration = fMolecularConfiguration->IonizeMolecule(IonizedLevel);
}

◆ ITDef()

G4Molecule::ITDef ( G4Molecule ) const

◆ MoveOneElectron()

void G4Molecule::MoveOneElectron	(	G4int	orbitToFree,
		G4int	orbitToFill
	)

Move one electron from an orbit to another.

Definition at line 254 of file G4Molecule.cc.

{
    fMolecularConfiguration = fMolecularConfiguration->MoveOneElectron(orbitToFree,orbitToFill);
}

◆ operator delete()

void G4Molecule::operator delete ( void * aVUserTrackInformation )

inline

Definition at line 265 of file G4Molecule.hh.

{
    // DEBUG
    // G4cout<<"G4Molecule::operator delete(void * aMolecule) called"<<G4endl;
    aMoleculeAllocator.FreeSingle((G4Molecule *) aMolecule);
}

◆ operator new()

void * G4Molecule::operator new ( size_t )

inline

Definition at line 256 of file G4Molecule.hh.

{
    void * aMolecule;
    aMolecule = (void *) aMoleculeAllocator.MallocSingle();
    return aMolecule;
}

◆ operator!=()

G4bool G4Molecule::operator!= ( const G4Molecule & right ) const

Definition at line 106 of file G4Molecule.cc.

{
    return !(*this == right);
}

◆ operator<()

G4bool G4Molecule::operator< ( const G4Molecule & right ) const

The two methods below are the most called of the simulation : compare molecules in the MoleculeStackManager or in the InteractionTable

Definition at line 116 of file G4Molecule.cc.

{
    return fMolecularConfiguration < right.fMolecularConfiguration ;
}

◆ operator=()

G4Molecule & G4Molecule::operator= ( const G4Molecule & right )

Definition at line 89 of file G4Molecule.cc.

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

◆ operator==()

G4bool G4Molecule::operator== ( const G4Molecule & right ) const

Definition at line 97 of file G4Molecule.cc.

{
    if(fMolecularConfiguration==right.fMolecularConfiguration)
    {
        return true;
    }
    return false;
}

◆ PrintState()

void G4Molecule::PrintState ( ) const

Show the electronic state of the molecule.

Definition at line 274 of file G4Molecule.cc.

{
    fMolecularConfiguration->PrintState();
}

Referenced by G4MoleculeCounter::RemoveAMoleculeAtTime().

◆ RemoveElectron()

void G4Molecule::RemoveElectron	(	G4int	orbit,
		G4int	number = `1`
	)

Remove n electrons to a given orbit.

Definition at line 249 of file G4Molecule.cc.

{
    fMolecularConfiguration = fMolecularConfiguration->RemoveElectron(orbit,number);
}

Referenced by G4EmDNAPhysicsChemistry::ConstructReactionTable().

◆ SetDecayTime()

void G4Molecule::SetDecayTime ( G4double dynDecayTime )

Set the decay time of the molecule.

Definition at line 355 of file G4Molecule.cc.

{
    fMolecularConfiguration->SetDecayTime(dynDecayTime);
}

◆ SetDiffusionCoefficient()

void G4Molecule::SetDiffusionCoefficient ( G4double dynDiffusionCoefficient )

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 400 of file G4Molecule.cc.

{
    fMolecularConfiguration->SetDiffusionCoefficient(dynDiffusionCoefficient);
}

Referenced by G4EmDNAPhysicsChemistry::ConstructDecayChannels(), and G4EmDNAPhysicsChemistry::ConstructReactionTable().

◆ SetElectronOccupancy()

void G4Molecule::SetElectronOccupancy ( const G4ElectronOccupancy * occ )

Will set up the correct molecularConfiguration given an electron configuration

Definition at line 225 of file G4Molecule.cc.

{
    fMolecularConfiguration = G4MolecularConfiguration::GetMolecularConfiguration(fMolecularConfiguration->GetDefinition(), *occ);
}

◆ SetGlobalTemperature()

void G4Molecule::SetGlobalTemperature ( double temperature )

inlinestatic

Definition at line 278 of file G4Molecule.hh.

{
    fgTemperature = temperature;
}

◆ SetMass()

void G4Molecule::SetMass ( G4double aMass )

Set the total mass of the molecule.

Definition at line 380 of file G4Molecule.cc.

{
    fMolecularConfiguration->SetMass(aMass);
}

Referenced by G4EmDNAPhysicsChemistry::ConstructDecayChannels(), and G4EmDNAPhysicsChemistry::ConstructReactionTable().

◆ SetVanDerVaalsRadius()

void G4Molecule::SetVanDerVaalsRadius ( G4double dynVanDerVaalsRadius )

The Van Der Valls Radius of the molecule

Definition at line 365 of file G4Molecule.cc.

{
    fMolecularConfiguration->SetVanDerVaalsRadius(dynVanDerVaalsRadius);
}

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

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ G4Molecule() [1/4]

◆ G4Molecule() [2/4]

◆ G4Molecule() [3/4]

◆ G4Molecule() [4/4]

◆ ~G4Molecule()

Member Function Documentation

◆ AddElectron()

◆ BuildTrack()

◆ ExciteMolecule()

◆ GetAtomsNumber()

◆ GetCharge()

◆ GetDecayChannel()

◆ GetDecayTime()

◆ GetDefinition()

◆ GetDiffusionCoefficient()

◆ GetDiffusionVelocity()

◆ GetElectronOccupancy()

◆ GetGlobalTemperature()

◆ GetKineticEnergy()

◆ GetMass()

◆ GetMolecularConfiguration()

◆ GetMoleculeID()

◆ GetName()

◆ GetNbElectrons()

◆ GetVanDerVaalsRadius()

◆ IonizeMolecule()

◆ ITDef()

◆ MoveOneElectron()

◆ operator delete()

◆ operator new()

◆ operator!=()

◆ operator<()

◆ operator=()

◆ operator==()

◆ PrintState()

◆ RemoveElectron()

◆ SetDecayTime()

◆ SetDiffusionCoefficient()

◆ SetElectronOccupancy()

◆ SetGlobalTemperature()

◆ SetMass()

◆ SetVanDerVaalsRadius()