#include <G4Molecule.hh>

Inheritance diagram for G4Molecule:

Public Member Functions
void	AddElectron (G4int orbit, G4int n=1)

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

void	ChangeConfigurationToLabel (const G4String &label)

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

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

void	ExciteMolecule (G4int)

	G4Molecule (const G4MolecularConfiguration *)

	G4Molecule (const G4Molecule &)

	G4Molecule (G4MoleculeDefinition *pMoleculeDefinition)

	G4Molecule (G4MoleculeDefinition *pMoleculeDefinition, G4int, G4bool)

	G4Molecule (G4MoleculeDefinition *pMoleculeDefinition, G4int, G4int)

	G4Molecule (G4MoleculeDefinition *pMoleculeDefinition, int charge)

G4int	GetAtomsNumber () const

G4int	GetCharge () const

G4double	GetDecayTime () const

const G4MoleculeDefinition *	GetDefinition () const

G4double	GetDiffusionCoefficient () const

G4double	GetDiffusionCoefficient (const G4Material *, double temperature) const

G4double	GetDiffusionVelocity () const

const std::vector< const G4MolecularDissociationChannel * > *	GetDissociationChannels () const

const G4ElectronOccupancy *	GetElectronOccupancy () const

G4int	GetFakeParticleID () const

const G4String &	GetFormatedName () const

const G4ITBox *	GetITBox () const

virtual G4ITType	GetITSubType () const

virtual const G4ITType	GetITType () const =0

G4double	GetKineticEnergy () const

const G4String &	GetLabel () const

G4TrackListNode *	GetListNode ()

G4double	GetMass () const

const G4MolecularConfiguration *	GetMolecularConfiguration () const

G4int	GetMoleculeID () const

const G4String &	GetName () const

G4double	GetNbElectrons () const

G4IT *	GetNext ()

const G4IT *	GetNext () const

G4KDNode_Base *	GetNode () const

void	GetParentID (int &, int &)

const G4ThreeVector &	GetPosition () const

G4double	GetPreStepGlobalTime () const

G4double	GetPreStepLocalTime () const

const G4ThreeVector &	GetPreStepPosition () const

G4IT *	GetPrevious ()

const G4IT *	GetPrevious () const

G4Track *	GetTrack ()

const G4Track *	GetTrack () const

G4TrackingInformation *	GetTrackingInfo ()

const G4String &	GetType () const

G4double	GetVanDerVaalsRadius () const

void	IonizeMolecule (G4int)

	ITDef (G4Molecule) void Print() const

void	MoveOneElectron (G4int, G4int)

void	operator delete (void *)

	operator int () const

void *	operator new (size_t)

G4bool	operator!= (const G4IT &right) const

G4bool	operator!= (const G4Molecule &right) const

G4bool	operator< (const G4IT &right) const

G4bool	operator< (const G4Molecule &right) const

G4Molecule &	operator= (const G4Molecule &right)

G4bool	operator== (const G4IT &right) const

G4bool	operator== (const G4Molecule &right) const

double	operator[] (int i) const

virtual void	Print () const

void	PrintState () const

void	RecordCurrentPositionNTime ()

void	RemoveElectron (G4int, G4int number=1)

void	SetDecayTime (G4double)

void	SetDiffusionCoefficient (G4double)

void	SetElectronOccupancy (const G4ElectronOccupancy *)

void	SetITBox (G4ITBox *)

void	SetLabel (const G4String &label)

void	SetListNode (G4TrackListNode *node)

void	SetMass (G4double)

void	SetNext (G4IT *)

void	SetNode (G4KDNode_Base *)

void	SetParentID (int, int)

void	SetPrevious (G4IT *)

void	SetTrack (G4Track *)

void	SetVanDerVaalsRadius (G4double)

void	TakeOutBox ()

virtual	~G4Molecule ()

Static Public Member Functions
static G4Molecule *	GetMolecule (const G4Track *)

Protected Attributes
G4Track *	fpTrack

G4String *	pType = nullptr

Private Member Functions
	G4Molecule ()

Private Attributes
int	fParentID_A

int	fParentID_B

G4ITBox *	fpITBox

G4KDNode_Base *	fpKDNode

const G4MolecularConfiguration *	fpMolecularConfiguration

G4IT *	fpNextIT

G4IT *	fpPreviousIT

G4TrackingInformation *	fpTrackingInformation

G4TrackListNode *	fpTrackNode

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 98 of file G4Molecule.hh.

Constructor & Destructor Documentation

◆ G4Molecule() [1/7]

G4Molecule::G4Molecule ( const G4Molecule & right )

Definition at line 104 of file G4Molecule.cc.

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

References fpMolecularConfiguration.

◆ G4Molecule() [2/7]

G4Molecule::G4Molecule ( G4MoleculeDefinition * pMoleculeDefinition )

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 180 of file G4Molecule.cc.

    : G4VUserTrackInformation("G4Molecule")
    , G4IT()
{
    fpMolecularConfiguration = G4MolecularConfiguration::GetOrCreateMolecularConfiguration(pMoleculeDefinition);
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetOrCreateMolecularConfiguration().

◆ G4Molecule() [3/7]

G4Molecule::G4Molecule	(	G4MoleculeDefinition *	pMoleculeDefinition,
		int	charge
	)

Definition at line 189 of file G4Molecule.cc.

{
    fpMolecularConfiguration = G4MolecularConfiguration::GetOrCreateMolecularConfiguration(pMoleculeDefinition,
                                                                                           charge);
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetOrCreateMolecularConfiguration().

◆ G4Molecule() [4/7]

G4Molecule::G4Molecule	(	G4MoleculeDefinition *	pMoleculeDefinition,
		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 200 of file G4Molecule.cc.

   : G4VUserTrackInformation("G4Molecule")
   , G4IT()
{
    if (pMoleculeDefinition->GetGroundStateElectronOccupancy())
    {
        G4ElectronOccupancy dynElectronOccupancy(*pMoleculeDefinition->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::GetOrCreateMolecularConfiguration(
                pMoleculeDefinition, dynElectronOccupancy);
    }
    else
    {
        fpMolecularConfiguration = nullptr;
        G4Exception(
            "G4Molecule::G4Molecule(G4MoleculeDefinition* pMoleculeDefinition, "
            "G4int OrbitalToFree, G4int OrbitalToFill)",
            "G4Molecule_wrong_usage_of_constructor",
            FatalErrorInArgument,
            "If you want to use this constructor, the molecule definition has to be "
            "first defined with electron occupancies");
    }
}

References G4ElectronOccupancy::AddElectron(), FatalErrorInArgument, fpMolecularConfiguration, G4Exception(), G4MoleculeDefinition::GetGroundStateElectronOccupancy(), G4MolecularConfiguration::GetOrCreateMolecularConfiguration(), and G4ElectronOccupancy::RemoveElectron().

◆ G4Molecule() [5/7]

G4Molecule::G4Molecule	(	G4MoleculeDefinition *	pMoleculeDefinition,
		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 245 of file G4Molecule.cc.

    : G4VUserTrackInformation("G4Molecule")
    , G4IT()
{
    if (pMoleculeDefinition->GetGroundStateElectronOccupancy())
    {
        G4ElectronOccupancy dynElectronOccupancy(*pMoleculeDefinition->GetGroundStateElectronOccupancy());
 
        if (excitation)
        {
            dynElectronOccupancy.RemoveElectron(level, 1);
            dynElectronOccupancy.AddElectron(5, 1);
            // dynElectronOccupancy.DumpInfo(); // DEBUG
        }
        else
        {
            dynElectronOccupancy.RemoveElectron(level, 1);
            // dynElectronOccupancy.DumpInfo(); // DEBUG
        }
 
        fpMolecularConfiguration = G4MolecularConfiguration::GetOrCreateMolecularConfiguration(pMoleculeDefinition,
                dynElectronOccupancy);
    }
    else
    {
        fpMolecularConfiguration = nullptr;
        G4Exception(
            "G4Molecule::G4Molecule(G4MoleculeDefinition* pMoleculeDefinition, "
            "G4int OrbitalToFree, G4int OrbitalToFill)",
            "G4Molecule_wrong_usage_of_constructor",
            FatalErrorInArgument,
            "If you want to use this constructor, the molecule definition has to be "
            "first defined with electron occupancies");
    }
}

References G4ElectronOccupancy::AddElectron(), FatalErrorInArgument, fpMolecularConfiguration, G4Exception(), G4MoleculeDefinition::GetGroundStateElectronOccupancy(), G4MolecularConfiguration::GetOrCreateMolecularConfiguration(), and G4ElectronOccupancy::RemoveElectron().

◆ G4Molecule() [6/7]

G4Molecule::G4Molecule ( const G4MolecularConfiguration * pMolecularConfiguration )

Definition at line 285 of file G4Molecule.cc.

{
    fpMolecularConfiguration = pMolecularConfiguration;
}

References fpMolecularConfiguration.

◆ ~G4Molecule()

G4Molecule::~G4Molecule ( )

virtual

Definition at line 160 of file G4Molecule.cc.

{
    if (fpTrack != nullptr)
    {
        if (G4VMoleculeCounter::Instance()->InUse())
        {
            G4VMoleculeCounter::Instance()->
                RemoveAMoleculeAtTime(fpMolecularConfiguration,
                                      fpTrack->GetGlobalTime(),
                                      &(fpTrack->GetPosition()));
        }
        fpTrack = nullptr;
    }
    fpMolecularConfiguration = nullptr;
}

References fpMolecularConfiguration, G4IT::fpTrack, G4Track::GetGlobalTime(), G4Track::GetPosition(), and G4VMoleculeCounter::Instance().

◆ G4Molecule() [7/7]

G4Molecule::G4Molecule ( )

private

Default molecule builder

Definition at line 151 of file G4Molecule.cc.

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

References fpMolecularConfiguration.

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 315 of file G4Molecule.cc.

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

References G4MolecularConfiguration::AddElectron(), and fpMolecularConfiguration.

Referenced by G4DNAChemistryManager::CreateWaterMolecule().

◆ BuildTrack()

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

Definition at line 373 of file G4Molecule.cc.

{
    if (fpTrack != nullptr)
    {
        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 (G4VMoleculeCounter::InUse())
    {
        G4VMoleculeCounter::Instance()->
            AddAMoleculeAtTime(fpMolecularConfiguration,
                               globalTime,
                               &(fpTrack->GetPosition()));
    }
 
    //Set the Track
    fpTrack = new G4Track(dynamicParticle, globalTime, position);
    fpTrack->SetUserInformation(this);
 
    return fpTrack;
}

References FatalErrorInArgument, fpMolecularConfiguration, G4IT::fpTrack, G4Exception(), G4UniformRand, G4MolecularConfiguration::GetDefinition(), GetKineticEnergy(), G4Track::GetPosition(), G4VMoleculeCounter::Instance(), G4VMoleculeCounter::InUse(), pi, and G4Track::SetUserInformation().

Referenced by G4MoleculeGun::BuildAndPushTrack(), G4DNAChemistryManager::CreateWaterMolecule(), G4DNAIRT::Sampling(), and G4DNAIRT_geometries::Sampling().

◆ ChangeConfigurationToLabel()

void G4Molecule::ChangeConfigurationToLabel ( const G4String & label )

Definition at line 546 of file G4Molecule.cc.

{
    // TODO check fpMolecularConfiguration already exists
    // and new one as well
    // TODO notify for stack change
    fpMolecularConfiguration = G4MolecularConfiguration::GetMolecularConfiguration(
        fpMolecularConfiguration->GetDefinition(), label);
 
    assert(fpMolecularConfiguration != nullptr);
}

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

Referenced by G4DNAElectronHoleRecombination::MakeReaction().

◆ diff()

virtual G4bool G4IT::diff ( const G4IT & right ) const

pure virtualinherited

Referenced by G4IT::operator<().

◆ equal()

virtual G4bool G4IT::equal ( const G4IT & right ) const

pure virtualinherited

Referenced by G4IT::operator==().

◆ ExciteMolecule()

void G4Molecule::ExciteMolecule ( G4int excitationLevel )

Method used in Geant4-DNA to excite water molecules

Definition at line 301 of file G4Molecule.cc.

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

References G4MolecularConfiguration::ExciteMolecule(), and fpMolecularConfiguration.

Referenced by G4DNAChemistryManager::CreateWaterMolecule().

◆ GetAtomsNumber()

G4int G4Molecule::GetAtomsNumber ( ) const

Returns the nomber of atoms compouning the molecule

Definition at line 352 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetAtomsNumber();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetAtomsNumber().

◆ GetCharge()

G4int G4Molecule::GetCharge ( ) const

Returns the charge of molecule.

Definition at line 488 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetCharge();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetCharge().

◆ GetDecayTime()

G4double G4Molecule::GetDecayTime ( ) const

Returns the decay time of the molecule.

Definition at line 474 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetDecayTime();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetDecayTime().

Referenced by G4DNAMolecularDissociation::GetMeanLifeTime().

◆ GetDefinition()

const G4MoleculeDefinition * G4Molecule::GetDefinition ( ) const

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

Definition at line 509 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetDefinition();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetDefinition().

◆ GetDiffusionCoefficient() [1/2]

G4double G4Molecule::GetDiffusionCoefficient ( ) const

Returns the diffusion coefficient D.

Definition at line 516 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetDiffusionCoefficient();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetDiffusionCoefficient().

Referenced by G4DNABrownianTransportation::AlongStepGetPhysicalInteractionLength(), G4DNABrownianTransportation::ComputeStep(), G4DNAIRT::Sampling(), G4DNAIRT_geometries::Sampling(), G4DNAIRT_geometries::SpaceBinning(), G4DNAIRTMoleculeEncounterStepper::Utils::Utils(), and G4DNAMoleculeEncounterStepper::Utils::Utils().

◆ GetDiffusionCoefficient() [2/2]

G4double G4Molecule::GetDiffusionCoefficient	(	const G4Material *	pMaterial,
		double	temperature
	)		const

Returns the diffusion coefficient D.

Definition at line 523 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetDiffusionCoefficient(pMaterial,
                                                             temperature);
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetDiffusionCoefficient().

◆ GetDiffusionVelocity()

G4double G4Molecule::GetDiffusionVelocity ( ) const

Definition at line 428 of file G4Molecule.cc.

{
    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 *
                G4MolecularConfiguration::GetGlobalTemperature() / moleculeMass);
    // Using this approximation for liquid is wrong
    // However the brownian process avoid taking
    // care of energy consideration and plays only
    // with positions
}

References source.hepunit::c_squared, fpMolecularConfiguration, G4MolecularConfiguration::GetGlobalTemperature(), G4MolecularConfiguration::GetMass(), and source.hepunit::k_Boltzmann.

Referenced by GetKineticEnergy().

◆ GetDissociationChannels()

const vector< const G4MolecularDissociationChannel * > * G4Molecule::GetDissociationChannels ( ) const

Definition at line 453 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetDissociationChannels();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetDissociationChannels().

◆ GetElectronOccupancy()

const G4ElectronOccupancy * G4Molecule::GetElectronOccupancy ( ) const

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

Definition at line 502 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetElectronOccupancy();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetElectronOccupancy().

◆ GetFakeParticleID()

G4int G4Molecule::GetFakeParticleID ( ) const

Definition at line 460 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetFakeParticleID();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetFakeParticleID().

◆ GetFormatedName()

const G4String & G4Molecule::GetFormatedName ( ) const

Returns the formated name of the molecule

Definition at line 345 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetFormatedName();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetFormatedName().

◆ GetITBox()

const G4ITBox * G4IT::GetITBox ( ) const

inlineinherited

Definition at line 183 of file G4IT.hh.

{
  return fpITBox;
}

References G4IT::fpITBox.

◆ GetITSubType()

virtual G4ITType G4Molecule::GetITSubType ( ) const

inlinevirtual

Reimplemented from G4IT.

Definition at line 130 of file G4Molecule.hh.

    {
        return GetMoleculeID();
    }

References GetMoleculeID().

◆ GetITType()

virtual const G4ITType G4IT::GetITType ( ) const

pure virtualinherited

Referenced by G4IT::operator<(), G4IT::operator==(), and G4AllITFinder::Push().

◆ GetKineticEnergy()

G4double G4Molecule::GetKineticEnergy ( ) const

Definition at line 416 of file G4Molecule.cc.

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

References source.hepunit::c_squared, fpMolecularConfiguration, GetDiffusionVelocity(), and G4MolecularConfiguration::GetMass().

Referenced by BuildTrack().

◆ GetLabel()

const G4String & G4Molecule::GetLabel ( ) const

Returns the label of the molecule configuration

Definition at line 539 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetLabel();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetLabel().

◆ GetListNode()

G4TrackListNode * G4IT::GetListNode ( )

inlineinherited

Definition at line 148 of file G4IT.hh.

  {
    return fpTrackNode;
  }

References G4IT::fpTrackNode.

◆ GetMass()

G4double G4Molecule::GetMass ( ) const

Returns the total mass of the molecule.

Definition at line 495 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetMass();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetMass().

◆ GetMolecularConfiguration()

const G4MolecularConfiguration * G4Molecule::GetMolecularConfiguration ( ) const

Definition at line 532 of file G4Molecule.cc.

{
    return fpMolecularConfiguration;
}

References fpMolecularConfiguration.

Referenced by G4DNAIndependentReactionTimeStepper::GetReactionType(), G4DNAPartiallyDiffusionControlled::GetTimeToEncounter(), G4DNATotallyDiffusionControlled::GetTimeToEncounter(), G4DNAIRT::MakeReaction(), G4DNAIRT_geometries::MakeReaction(), G4DNAMakeReaction::MakeReaction(), G4DNAMolecularReaction::MakeReaction(), G4DNAScavengerProcess::PostStepDoIt(), G4DNASecondOrderReaction::PostStepGetPhysicalInteractionLength(), G4DNAScavengerProcess::PostStepGetPhysicalInteractionLength(), G4DNAIRT::Sampling(), G4DNAIRT_geometries::Sampling(), G4DNAMolecularReaction::TestReactibility(), G4DNAMakeReaction::UpdatePositionForReaction(), and G4DNAEventScheduler::Voxelizing().

◆ GetMolecule()

G4Molecule * G4Molecule::GetMolecule ( const G4Track * track )

static

Definition at line 90 of file G4Molecule.cc.

{
    return (G4Molecule*)(GetIT(track));
}

References GetIT().

Referenced by G4DNAIRT::Sampling(), and G4DNAIRT_geometries::Sampling().

◆ GetMoleculeID()

G4int G4Molecule::GetMoleculeID ( ) const

Definition at line 467 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetMoleculeID();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetMoleculeID().

Referenced by G4DNAElectronHoleRecombination::FindReactant(), GetITSubType(), and operator int().

◆ GetName()

const G4String & G4Molecule::GetName ( ) const

virtual

Returns the name of the molecule

Implements G4IT.

Definition at line 338 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetName();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetName().

Referenced by G4DNAIRTMoleculeEncounterStepper::CalculateStep(), G4DNAMoleculeEncounterStepper::CalculateStep(), G4DNAIndependentReactionTimeStepper::CalculateStep(), G4DNAIRTMoleculeEncounterStepper::CheckAndRecordResults(), G4DNAMoleculeEncounterStepper::CheckAndRecordResults(), G4DNAIndependentReactionTimeStepper::CheckAndRecordResults(), G4DNABrownianTransportation::ComputeStep(), G4DNABrownianTransportation::Diffusion(), G4DNAIndependentReactionTimeStepper::GetTimeToEncounter(), G4DNASecondOrderReaction::PostStepDoIt(), G4DNAScavengerProcess::PostStepDoIt(), G4DNABrownianTransportation::PostStepDoIt(), G4DNAIndirectHit::Print(), and G4DNAMakeReaction::UpdatePositionForReaction().

◆ GetNbElectrons()

G4double G4Molecule::GetNbElectrons ( ) const

Returns the number of electron.

Definition at line 359 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetNbElectrons();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetNbElectrons().

◆ GetNext() [1/2]

G4IT * G4IT::GetNext ( )

inlineinherited

Definition at line 208 of file G4IT.hh.

{
  return fpNextIT;
}

References G4IT::fpNextIT.

Referenced by G4ITBox::Extract(), G4ITBox::TransferTo(), and G4ITBox::~G4ITBox().

◆ GetNext() [2/2]

const G4IT * G4IT::GetNext ( ) const

inlineinherited

Definition at line 245 of file G4IT.hh.

{
  return fpNextIT;
}

References G4IT::fpNextIT.

◆ GetNode()

G4KDNode_Base * G4IT::GetNode ( ) const

inlineinherited

Definition at line 255 of file G4IT.hh.

{
  return fpKDNode;
}

References G4IT::fpKDNode.

◆ GetParentID()

void G4IT::GetParentID	(	int &	p_a,
		int &	p_b
	)

inlineinherited

Definition at line 234 of file G4IT.hh.

{
  p_a = fParentID_A;
  p_b = fParentID_B;
}

References G4IT::fParentID_A, and G4IT::fParentID_B.

◆ GetPosition()

const G4ThreeVector & G4IT::GetPosition ( ) const

inherited

Definition at line 214 of file G4IT.cc.

{
  if (fpTrack) return GetTrack()->GetPosition();
  return *(new G4ThreeVector());
}

References G4IT::fpTrack, G4Track::GetPosition(), and G4IT::GetTrack().

◆ GetPreStepGlobalTime()

G4double G4IT::GetPreStepGlobalTime ( ) const

inherited

Definition at line 228 of file G4IT.cc.

{
  return fpTrackingInformation->GetPreStepGlobalTime();
}

References G4IT::fpTrackingInformation, and G4TrackingInformation::GetPreStepGlobalTime().

◆ GetPreStepLocalTime()

G4double G4IT::GetPreStepLocalTime ( ) const

inherited

Definition at line 233 of file G4IT.cc.

{
  return fpTrackingInformation->GetPreStepLocalTime();
}

References G4IT::fpTrackingInformation, and G4TrackingInformation::GetPreStepLocalTime().

◆ GetPreStepPosition()

const G4ThreeVector & G4IT::GetPreStepPosition ( ) const

inherited

Definition at line 238 of file G4IT.cc.

{
  return fpTrackingInformation->GetPreStepPosition();
}

References G4IT::fpTrackingInformation, and G4TrackingInformation::GetPreStepPosition().

◆ GetPrevious() [1/2]

G4IT * G4IT::GetPrevious ( )

inlineinherited

Definition at line 203 of file G4IT.hh.

{
  return fpPreviousIT;
}

References G4IT::fpPreviousIT.

Referenced by G4ITBox::Extract(), and G4ITBox::FindIT().

◆ GetPrevious() [2/2]

const G4IT * G4IT::GetPrevious ( ) const

inlineinherited

Definition at line 240 of file G4IT.hh.

{
  return fpPreviousIT;
}

References G4IT::fpPreviousIT.

◆ GetTrack() [1/2]

G4Track * G4IT::GetTrack ( )

inlineinherited

Definition at line 218 of file G4IT.hh.

{
  return fpTrack;
}

References G4IT::fpTrack.

Referenced by G4DNAIRTMoleculeEncounterStepper::CheckAndRecordResults(), G4DNAMoleculeEncounterStepper::CheckAndRecordResults(), G4ITStepProcessor::FindTransportationStep(), and G4IT::GetPosition().

◆ GetTrack() [2/2]

const G4Track * G4IT::GetTrack ( ) const

inlineinherited

Definition at line 223 of file G4IT.hh.

{
  return fpTrack;
}

References G4IT::fpTrack.

◆ GetTrackingInfo()

G4TrackingInformation * G4IT::GetTrackingInfo ( )

inlineinherited

Definition at line 143 of file G4IT.hh.

  {
    return fpTrackingInformation;
  }

References G4IT::fpTrackingInformation.

Referenced by G4ITTransportation::AlongStepGetPhysicalInteractionLength(), G4DNABrownianTransportation::ComputeGeomLimit(), G4ITStepProcessor::DoDefinePhysicalStepLength(), G4ITStepProcessor::DoStepping(), G4ITStepProcessor::InitDefineStep(), G4ITLeadingTracks::PrepareLeadingTracks(), G4ITLeadingTracks::Reset(), G4ITStepProcessor::SetInitialStep(), G4ITStepProcessor::SetTrack(), G4ITStepProcessor::SetupMembers(), and G4VITProcess::StartTracking().

◆ GetType()

const G4String & G4VUserTrackInformation::GetType ( ) const

inherited

Definition at line 75 of file G4VUserTrackInformation.cc.

{
  static const G4String NOTYPE = "NONE";
  if(pType != nullptr)
    return *pType;
  else
    return NOTYPE;
}

References G4VUserTrackInformation::pType.

Referenced by G4ScintillationTrackInformation::IsScintillationTrackInformation().

◆ GetVanDerVaalsRadius()

G4double G4Molecule::GetVanDerVaalsRadius ( ) const

Definition at line 481 of file G4Molecule.cc.

{
    return fpMolecularConfiguration->GetVanDerVaalsRadius();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::GetVanDerVaalsRadius().

◆ IonizeMolecule()

void G4Molecule::IonizeMolecule ( G4int ionizationLevel )

Method used in Geant4-DNA to ionize water molecules

Definition at line 308 of file G4Molecule.cc.

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

References fpMolecularConfiguration, and G4MolecularConfiguration::IonizeMolecule().

Referenced by G4DNAChemistryManager::CreateWaterMolecule().

◆ ITDef()

G4Molecule::ITDef ( G4Molecule ) const

◆ MoveOneElectron()

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

Move one electron from an orbit to another.

Definition at line 330 of file G4Molecule.cc.

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

References fpMolecularConfiguration, and G4MolecularConfiguration::MoveOneElectron().

◆ operator delete()

void G4Molecule::operator delete ( void * aMolecule )

inline

Definition at line 313 of file G4Molecule.hh.

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

References aMoleculeAllocator().

◆ operator int()

G4Molecule::operator int ( ) const

inline

Definition at line 125 of file G4Molecule.hh.

    {
        return GetMoleculeID();
    }

References GetMoleculeID().

◆ operator new()

void * G4Molecule::operator new ( size_t )

inline

Definition at line 302 of file G4Molecule.hh.

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

References aMoleculeAllocator().

◆ operator!=() [1/2]

G4bool G4IT::operator!= ( const G4IT & right ) const

inherited

Definition at line 202 of file G4IT.cc.

{
  return !(this->operator==(right));
}

References G4IT::operator==().

◆ operator!=() [2/2]

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

Definition at line 133 of file G4Molecule.cc.

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

◆ operator<() [1/2]

G4bool G4IT::operator< ( const G4IT & right ) const

inherited

Definition at line 180 of file G4IT.cc.

{
  if (GetITType() == right.GetITType())
  {
    return (this->diff(right));
  }
  else
  {
    return (GetITType() < right.GetITType());
  }
  return false;
}

References G4IT::diff(), and G4IT::GetITType().

◆ operator<() [2/2]

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 144 of file G4Molecule.cc.

{
    return fpMolecularConfiguration < right.fpMolecularConfiguration;
}

References fpMolecularConfiguration.

◆ operator=()

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

Definition at line 113 of file G4Molecule.cc.

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

References fpMolecularConfiguration.

◆ operator==() [1/2]

G4bool G4IT::operator== ( const G4IT & right ) const

inherited

Definition at line 193 of file G4IT.cc.

{
  if (GetITType() == right.GetITType())
  {
    return this->equal(right);
  }
  return false;
}

References G4IT::equal(), and G4IT::GetITType().

Referenced by G4IT::operator!=().

◆ operator==() [2/2]

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

Definition at line 122 of file G4Molecule.cc.

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

References fpMolecularConfiguration.

◆ operator[]()

double G4IT::operator[] ( int i ) const

inherited

Definition at line 207 of file G4IT.cc.

{
  return fpTrack->GetPosition()[i];
}

References G4IT::fpTrack, and G4Track::GetPosition().

◆ Print()

virtual void G4IT::Print ( ) const

inlinevirtualinherited

Reimplemented from G4VUserTrackInformation.

Definition at line 97 of file G4IT.hh.

  {
    ;
  }

◆ PrintState()

void G4Molecule::PrintState ( ) const

Show the electronic state of the molecule.

Definition at line 366 of file G4Molecule.cc.

{
    fpMolecularConfiguration->PrintState();
}

References fpMolecularConfiguration, and G4MolecularConfiguration::PrintState().

◆ RecordCurrentPositionNTime()

void G4IT::RecordCurrentPositionNTime ( )

inherited

Definition at line 220 of file G4IT.cc.

{
  if (fpTrack)
  {
    fpTrackingInformation->RecordCurrentPositionNTime(fpTrack);
  }
}

References G4IT::fpTrack, G4IT::fpTrackingInformation, and G4TrackingInformation::RecordCurrentPositionNTime().

Referenced by G4IT::G4IT().

◆ RemoveElectron()

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

Remove n electrons to a given orbit.

Definition at line 322 of file G4Molecule.cc.

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

References fpMolecularConfiguration, and G4MolecularConfiguration::RemoveElectron().

◆ SetDecayTime()

void G4Molecule::SetDecayTime ( G4double )

Set the decay time of the molecule.

◆ SetDiffusionCoefficient()

void G4Molecule::SetDiffusionCoefficient ( G4double )

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.

◆ SetElectronOccupancy()

void G4Molecule::SetElectronOccupancy ( const G4ElectronOccupancy * pElectronOcc )

Will set up the correct molecularConfiguration given an electron configuration

Definition at line 292 of file G4Molecule.cc.

{
    fpMolecularConfiguration = 
        G4MolecularConfiguration::GetOrCreateMolecularConfiguration(fpMolecularConfiguration->GetDefinition(),
                                                                    *pElectronOcc);
}

References fpMolecularConfiguration, G4MolecularConfiguration::GetDefinition(), and G4MolecularConfiguration::GetOrCreateMolecularConfiguration().

◆ SetITBox()

void G4IT::SetITBox ( G4ITBox * aITBox )

inlineinherited

Definition at line 188 of file G4IT.hh.

{
  fpITBox = aITBox;
}

References G4IT::fpITBox.

Referenced by G4ITBox::Extract(), and G4ITBox::Push().

◆ SetLabel()

void G4Molecule::SetLabel ( const G4String & label )

◆ SetListNode()

void G4IT::SetListNode ( G4TrackListNode * node )

inlineinherited

Definition at line 152 of file G4IT.hh.

  {
    fpTrackNode = node;
  }

References G4IT::fpTrackNode.

◆ SetMass()

void G4Molecule::SetMass ( G4double )

Set the total mass of the molecule.

◆ SetNext()

void G4IT::SetNext ( G4IT * aIT )

inlineinherited

Definition at line 198 of file G4IT.hh.

{
  fpNextIT = aIT;
}

References G4IT::fpNextIT.

Referenced by G4ITBox::Extract(), and G4ITBox::Push().

◆ SetNode()

void G4IT::SetNode ( G4KDNode_Base * aNode )

inlineinherited

Definition at line 250 of file G4IT.hh.

{
  fpKDNode = aNode;
}

References G4IT::fpKDNode.

◆ SetParentID()

void G4IT::SetParentID	(	int	p_a,
		int	p_b
	)

inlineinherited

Definition at line 228 of file G4IT.hh.

{
  fParentID_A = p_a;
  fParentID_B = p_b;
}

References G4IT::fParentID_A, and G4IT::fParentID_B.

Referenced by G4ITModelProcessor::ComputeTrackReaction().

◆ SetPrevious()

void G4IT::SetPrevious ( G4IT * aIT )

inlineinherited

Definition at line 193 of file G4IT.hh.

{
  fpPreviousIT = aIT;
}

References G4IT::fpPreviousIT.

Referenced by G4ITBox::Extract(), and G4ITBox::Push().

◆ SetTrack()

void G4IT::SetTrack ( G4Track * track )

inlineinherited

Definition at line 213 of file G4IT.hh.

{
  fpTrack = track;
}

References G4IT::fpTrack.

◆ SetVanDerVaalsRadius()

void G4Molecule::SetVanDerVaalsRadius ( G4double )

The Van Der Valls Radius of the molecule

◆ TakeOutBox()

void G4IT::TakeOutBox ( )

inherited

Definition at line 139 of file G4IT.cc.

{
  if(fpITBox)
  {
    fpITBox->Extract(this);
    fpITBox = nullptr;
  }
 
  if(fpTrackNode)
  {
    delete fpTrackNode;
    fpTrackNode = nullptr;
  }
 
  if(fpKDNode)
  {
    InactiveNode(fpKDNode);
    fpKDNode = nullptr;
  }
}

References G4ITBox::Extract(), G4IT::fpITBox, G4IT::fpKDNode, G4IT::fpTrackNode, and InactiveNode().

Referenced by G4IT::~G4IT().

Field Documentation

◆ fParentID_A

int G4IT::fParentID_A

privateinherited

Definition at line 175 of file G4IT.hh.

Referenced by G4IT::G4IT(), G4IT::GetParentID(), G4IT::operator=(), and G4IT::SetParentID().

◆ fParentID_B

int G4IT::fParentID_B

privateinherited

Definition at line 176 of file G4IT.hh.

Referenced by G4IT::G4IT(), G4IT::GetParentID(), G4IT::operator=(), and G4IT::SetParentID().

◆ fpITBox

G4ITBox* G4IT::fpITBox

privateinherited

Definition at line 170 of file G4IT.hh.

Referenced by G4IT::G4IT(), G4IT::GetITBox(), G4IT::operator=(), G4IT::SetITBox(), and G4IT::TakeOutBox().

◆ fpKDNode

G4KDNode_Base* G4IT::fpKDNode

privateinherited

Definition at line 173 of file G4IT.hh.

Referenced by G4IT::G4IT(), G4IT::GetNode(), G4IT::operator=(), G4IT::SetNode(), and G4IT::TakeOutBox().

◆ fpMolecularConfiguration

const G4MolecularConfiguration* G4Molecule::fpMolecularConfiguration

private

◆ fpNextIT

G4IT* G4IT::fpNextIT

privateinherited

Definition at line 172 of file G4IT.hh.

Referenced by G4IT::GetNext(), G4IT::operator=(), and G4IT::SetNext().

◆ fpPreviousIT

G4IT* G4IT::fpPreviousIT

privateinherited

Definition at line 171 of file G4IT.hh.

Referenced by G4IT::GetPrevious(), G4IT::operator=(), and G4IT::SetPrevious().

◆ fpTrack

G4Track* G4IT::fpTrack

protectedinherited

Definition at line 167 of file G4IT.hh.

Referenced by BuildTrack(), G4IT::G4IT(), G4IT::GetPosition(), G4IT::GetTrack(), G4IT::operator=(), G4IT::operator[](), G4IT::RecordCurrentPositionNTime(), G4IT::SetTrack(), and ~G4Molecule().

◆ fpTrackingInformation

G4TrackingInformation* G4IT::fpTrackingInformation

privateinherited

Definition at line 178 of file G4IT.hh.

Referenced by G4IT::GetPreStepGlobalTime(), G4IT::GetPreStepLocalTime(), G4IT::GetPreStepPosition(), G4IT::GetTrackingInfo(), G4IT::operator=(), G4IT::RecordCurrentPositionNTime(), and G4IT::~G4IT().

◆ fpTrackNode

G4TrackListNode* G4IT::fpTrackNode

privateinherited

Definition at line 179 of file G4IT.hh.

Referenced by G4IT::G4IT(), G4IT::GetListNode(), G4IT::operator=(), G4IT::SetListNode(), and G4IT::TakeOutBox().

◆ pType

G4String* G4VUserTrackInformation::pType = nullptr

protectedinherited

Definition at line 75 of file G4VUserTrackInformation.hh.

Referenced by G4VUserTrackInformation::G4VUserTrackInformation(), G4VUserTrackInformation::GetType(), G4VUserTrackInformation::operator=(), and G4VUserTrackInformation::~G4VUserTrackInformation().

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

source/processes/electromagnetic/dna/molecules/management/include/G4Molecule.hh
source/processes/electromagnetic/dna/molecules/management/src/G4Molecule.cc

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ G4Molecule() [1/7]

◆ G4Molecule() [2/7]

◆ G4Molecule() [3/7]

◆ G4Molecule() [4/7]

◆ G4Molecule() [5/7]

◆ G4Molecule() [6/7]

◆ ~G4Molecule()

◆ G4Molecule() [7/7]

Member Function Documentation

◆ AddElectron()

◆ BuildTrack()

◆ ChangeConfigurationToLabel()

◆ diff()

◆ equal()

◆ ExciteMolecule()

◆ GetAtomsNumber()

◆ GetCharge()

◆ GetDecayTime()

◆ GetDefinition()

◆ GetDiffusionCoefficient() [1/2]

◆ GetDiffusionCoefficient() [2/2]

◆ GetDiffusionVelocity()

◆ GetDissociationChannels()

◆ GetElectronOccupancy()

◆ GetFakeParticleID()

◆ GetFormatedName()

◆ GetITBox()

◆ GetITSubType()

◆ GetITType()

◆ GetKineticEnergy()

◆ GetLabel()

◆ GetListNode()

◆ GetMass()

◆ GetMolecularConfiguration()

◆ GetMolecule()

◆ GetMoleculeID()

◆ GetName()

◆ GetNbElectrons()

◆ GetNext() [1/2]

◆ GetNext() [2/2]

◆ GetNode()

◆ GetParentID()

◆ GetPosition()

◆ GetPreStepGlobalTime()

◆ GetPreStepLocalTime()

◆ GetPreStepPosition()

◆ GetPrevious() [1/2]

◆ GetPrevious() [2/2]

◆ GetTrack() [1/2]

◆ GetTrack() [2/2]

◆ GetTrackingInfo()

◆ GetType()

◆ GetVanDerVaalsRadius()

◆ IonizeMolecule()

◆ ITDef()

◆ MoveOneElectron()

◆ operator delete()

◆ operator int()

◆ operator new()

◆ operator!=() [1/2]

◆ operator!=() [2/2]

◆ operator<() [1/2]

◆ operator<() [2/2]

◆ operator=()

◆ operator==() [1/2]

◆ operator==() [2/2]

◆ operator[]()

◆ Print()

◆ PrintState()

◆ RecordCurrentPositionNTime()

◆ RemoveElectron()

◆ SetDecayTime()

◆ SetDiffusionCoefficient()