#include <G4Molecule.hh>

Inheritance diagram for G4Molecule:

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

void *	operator new (size_t)

void	operator delete (void *)

	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 () const

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 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 ()

const G4String &	GetType () const

Static Public Member Functions
static void	SetGlobalTemperature (G4double)

static G4double	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::G4Molecule ( const G4Molecule & right )

Definition at line 82 of file G4Molecule.cc.

References G4Molecule().

Referenced by G4Molecule().

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

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 149 of file G4Molecule.cc.

References G4Molecule(), and G4MolecularConfiguration::GetMolecularConfiguration().

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

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 161 of file G4Molecule.cc.

References G4Molecule(), G4MoleculeDefinition::GetGroundStateElectronOccupancy(), G4MolecularConfiguration::GetMolecularConfiguration(), and G4ElectronOccupancy::RemoveElectron().

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

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 188 of file G4Molecule.cc.

References G4Molecule(), G4MoleculeDefinition::GetGroundStateElectronOccupancy(), G4MolecularConfiguration::GetMolecularConfiguration(), and G4ElectronOccupancy::RemoveElectron().

                                                                                                :
     G4VUserTrackInformation("G4Molecule"), G4IT()
 {
     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
     }
 
     fpMolecularConfiguration = G4MolecularConfiguration::GetMolecularConfiguration(moleculeDefinition, dynElectronOccupancy);
 }

G4Molecule::~G4Molecule ( )

virtual

Definition at line 130 of file G4Molecule.cc.

References G4IT::fpTrack, G4Track::GetGlobalTime(), G4MoleculeCounter::GetMoleculeCounter(), and G4MoleculeCounter::RemoveAMoleculeAtTime().

 {
     if(fpTrack!=NULL)
     {
         if(G4MoleculeCounter::GetMoleculeCounter()->InUse())
         {
             G4MoleculeCounter::GetMoleculeCounter()->RemoveAMoleculeAtTime(*this,
                                                                            fpTrack->GetGlobalTime());
         }
         fpTrack = 0;
     }
     fpMolecularConfiguration = 0;
 }

Member Function Documentation

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 228 of file G4Molecule.cc.

References G4MolecularConfiguration::AddElectron().

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

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

Definition at line 263 of file G4Molecule.cc.

References G4MoleculeCounter::AddAMoleculeAtTime(), FatalErrorInArgument, G4IT::fpTrack, G4Exception(), G4UniformRand, G4MolecularConfiguration::GetDefinition(), GetKineticEnergy(), G4MoleculeCounter::GetMoleculeCounter(), G4MoleculeCounter::InUse(), and python.hepunit::pi.

Referenced by G4DNAChemistryManager::CreateSolvatedElectron(), G4DNAChemistryManager::CreateWaterMolecule(), G4DNAMolecularDissociation::DecayIt(), G4DNAMolecularReaction::MakeReaction(), G4DNAChemistryManager::PushMolecule(), and G4DNAChemistryManager::PushMoleculeAtParentTimeAndPlace().

 {
     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();
 
     G4DynamicParticle* dynamicParticle = new G4DynamicParticle(fpMolecularConfiguration->GetDefinition(),
                                              MomentumDirection,
                                              KineticEnergy);
 
     if(G4MoleculeCounter::GetMoleculeCounter()->InUse())
         G4MoleculeCounter::GetMoleculeCounter()->AddAMoleculeAtTime(*this,globalTime);
 
     //Set the Track
     fpTrack = new G4Track(dynamicParticle, globalTime, Position);
     fpTrack -> SetUserInformation (this);
 
     return fpTrack;
 }

void G4Molecule::ExciteMolecule ( G4int ExcitedLevel )

Method used in Geant4-DNA to excite water molecules

Definition at line 216 of file G4Molecule.cc.

References G4MolecularConfiguration::ExciteMolecule().

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

G4int G4Molecule::GetAtomsNumber ( ) const

Returns the nomber of atoms compouning the molecule

Definition at line 248 of file G4Molecule.cc.

References G4MolecularConfiguration::GetAtomsNumber().

 {
     return fpMolecularConfiguration->GetAtomsNumber();
 }

G4int G4Molecule::GetCharge ( ) const

Returns the charge of molecule.

Definition at line 359 of file G4Molecule.cc.

References G4MolecularConfiguration::GetCharge().

 {
     return fpMolecularConfiguration->GetCharge() ;
 }

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

Definition at line 329 of file G4Molecule.cc.

References G4MolecularConfiguration::GetDecayChannel().

 {
     return fpMolecularConfiguration->GetDecayChannel();
 }

G4double G4Molecule::GetDecayTime ( ) const

Returns the decay time of the molecule.

Definition at line 344 of file G4Molecule.cc.

References G4MolecularConfiguration::GetDecayTime().

 {
     return fpMolecularConfiguration->GetDecayTime();
 }

const G4MoleculeDefinition * G4Molecule::GetDefinition ( ) const

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

Definition at line 379 of file G4Molecule.cc.

References G4MolecularConfiguration::GetDefinition().

Referenced by G4MoleculeCounter::AddAMoleculeAtTime(), G4DNAMolecularDissociation::DecayIt(), G4DNAWaterDissociationDisplacer::GetProductsDisplacement(), and G4MoleculeCounter::RemoveAMoleculeAtTime().

 {
     return fpMolecularConfiguration->GetDefinition();
 }

G4double G4Molecule::GetDiffusionCoefficient ( ) const

Returns the diffusion coefficient D.

Definition at line 389 of file G4Molecule.cc.

References G4MolecularConfiguration::GetDiffusionCoefficient().

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

 {
     return fpMolecularConfiguration->GetDiffusionCoefficient();
 }

G4double G4Molecule::GetDiffusionVelocity ( ) const

Definition at line 308 of file G4Molecule.cc.

References python.hepunit::c_squared, G4MolecularConfiguration::GetMass(), and python.hepunit::k_Boltzmann.

Referenced by GetKineticEnergy().

 {
     double moleculeMass = fpMolecularConfiguration->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
 }

const G4ElectronOccupancy * G4Molecule::GetElectronOccupancy ( ) const

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

Definition at line 374 of file G4Molecule.cc.

References G4MolecularConfiguration::GetElectronOccupancy().

Referenced by G4DNAMolecularDissociation::DecayIt().

 {
     return fpMolecularConfiguration->GetElectronOccupancy();
 }

G4double G4Molecule::GetGlobalTemperature ( )

static

Definition at line 404 of file G4Molecule.cc.

 {
     return fgTemperature;
 }

G4double G4Molecule::GetKineticEnergy ( ) const

Definition at line 298 of file G4Molecule.cc.

References python.hepunit::c_squared, GetDiffusionVelocity(), G4MolecularConfiguration::GetMass(), and test::v.

Referenced by BuildTrack().

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

G4double G4Molecule::GetMass ( ) const

Returns the total mass of the molecule.

Definition at line 369 of file G4Molecule.cc.

References G4MolecularConfiguration::GetMass().

 {
     return fpMolecularConfiguration->GetMass();
 }

G4MolecularConfiguration * G4Molecule::GetMolecularConfiguration ( ) const

Definition at line 394 of file G4Molecule.cc.

Referenced by G4DNASecondOrderReaction::PostStepGetPhysicalInteractionLength().

 {
     return fpMolecularConfiguration ;
 }

G4int G4Molecule::GetMoleculeID ( ) const

Definition at line 334 of file G4Molecule.cc.

References G4MolecularConfiguration::GetMoleculeID().

 {
     return fpMolecularConfiguration->GetMoleculeID();
 }

const G4String & G4Molecule::GetName ( void ) const

virtual

Returns the name of the molecule

Implements G4IT.

Definition at line 243 of file G4Molecule.cc.

References G4MolecularConfiguration::GetName().

Referenced by G4MoleculeCounter::AddAMoleculeAtTime(), G4DNAMoleculeEncounterStepper::CalculateStep(), G4DNAMolecularReactionTable::CanReactWith(), G4DNAMolecularDissociation::DecayIt(), G4DNABrownianTransportation::Diffusion(), G4DNASmoluchowskiReactionModel::FindReaction(), G4DNAMolecularReactionTable::GetReactionData(), G4DNAMolecularReactionTable::GetReativesNData(), G4DNASecondOrderReaction::PostStepDoIt(), G4DNAIndirectHit::Print(), G4DNAMolecularReactionTable::PrintTable(), G4DNAChemistryManager::PushMolecule(), G4DNAChemistryManager::PushMoleculeAtParentTimeAndPlace(), G4MoleculeCounter::RemoveAMoleculeAtTime(), and G4DNAMolecularReaction::TestReactibility().

 {
     return fpMolecularConfiguration->GetName();
 }

G4double G4Molecule::GetNbElectrons ( ) const

Returns the number of electron.

Definition at line 253 of file G4Molecule.cc.

References G4MolecularConfiguration::GetNbElectrons().

 {
     return fpMolecularConfiguration->GetNbElectrons();
 }

G4double G4Molecule::GetVanDerVaalsRadius ( ) const

Definition at line 354 of file G4Molecule.cc.

References G4MolecularConfiguration::GetVanDerVaalsRadius().

 {
     return fpMolecularConfiguration->GetVanDerVaalsRadius();
 }

void G4Molecule::IonizeMolecule ( G4int IonizedLevel )

Method used in Geant4-DNA to ionize water molecules

Definition at line 223 of file G4Molecule.cc.

References G4MolecularConfiguration::IonizeMolecule().

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

G4Molecule::ITDef ( G4Molecule ) const

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

Move one electron from an orbit to another.

Definition at line 238 of file G4Molecule.cc.

References G4MolecularConfiguration::MoveOneElectron().

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

void G4Molecule::operator delete ( void * aMolecule )

inline

Definition at line 261 of file G4Molecule.hh.

References aMoleculeAllocator.

 {
     aMoleculeAllocator->FreeSingle((G4Molecule *) aMolecule);
 }

void * G4Molecule::operator new ( size_t )

inline

Definition at line 253 of file G4Molecule.hh.

References aMoleculeAllocator.

 {
     if (!aMoleculeAllocator)  aMoleculeAllocator = new G4Allocator<G4Molecule>;
     return (void *) aMoleculeAllocator->MallocSingle();
 }

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

Definition at line 104 of file G4Molecule.cc.

References right.

 {
     return !(*this == right);
 }

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 114 of file G4Molecule.cc.

 {
     return fpMolecularConfiguration < right.fpMolecularConfiguration ;
 }

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

Definition at line 88 of file G4Molecule.cc.

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

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

Definition at line 95 of file G4Molecule.cc.

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

void G4Molecule::PrintState ( ) const

Show the electronic state of the molecule.

Definition at line 258 of file G4Molecule.cc.

References G4MolecularConfiguration::PrintState().

Referenced by G4MoleculeCounter::RemoveAMoleculeAtTime().

 {
     fpMolecularConfiguration->PrintState();
 }

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

Remove n electrons to a given orbit.

Definition at line 233 of file G4Molecule.cc.

References G4MolecularConfiguration::RemoveElectron().

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

void G4Molecule::SetDecayTime ( G4double dynDecayTime )

Set the decay time of the molecule.

Definition at line 339 of file G4Molecule.cc.

References G4MolecularConfiguration::SetDecayTime().

 {
     fpMolecularConfiguration->SetDecayTime(dynDecayTime);
 }

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 384 of file G4Molecule.cc.

References G4MolecularConfiguration::SetDiffusionCoefficient().

 {
     fpMolecularConfiguration->SetDiffusionCoefficient(dynDiffusionCoefficient);
 }

void G4Molecule::SetElectronOccupancy ( const G4ElectronOccupancy * occ )

Will set up the correct molecularConfiguration given an electron configuration

Definition at line 209 of file G4Molecule.cc.

References G4MolecularConfiguration::GetDefinition(), and G4MolecularConfiguration::GetMolecularConfiguration().

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

void G4Molecule::SetGlobalTemperature ( G4double temperature )

static

Definition at line 399 of file G4Molecule.cc.

 {
     fgTemperature = temperature;
 }

void G4Molecule::SetMass ( G4double aMass )

Set the total mass of the molecule.

Definition at line 364 of file G4Molecule.cc.

References G4MolecularConfiguration::SetMass().

 {
     fpMolecularConfiguration->SetMass(aMass);
 }

void G4Molecule::SetVanDerVaalsRadius ( G4double dynVanDerVaalsRadius )

The Van Der Valls Radius of the molecule

Definition at line 349 of file G4Molecule.cc.

References G4MolecularConfiguration::SetVanDerVaalsRadius().

 {
     fpMolecularConfiguration->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

Member Function Documentation