G4Molecule Class Reference

#include <G4Molecule.hh>

Inheritance diagram for G4Molecule:

Collaboration 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
	operator int () const
virtual G4ITType	GetITSubType () const
	G4Molecule (G4MoleculeDefinition *molecule)
	G4Molecule (G4MoleculeDefinition *molDef, int charge)
	G4Molecule (G4MoleculeDefinition *molecule, G4int, G4int)
	G4Molecule (G4MoleculeDefinition *molecule, G4int, G4bool)
	G4Molecule (G4MolecularConfiguration *)
virtual	~G4Molecule ()
const G4String &	GetName () const
const G4String &	GetFormatedName () 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 G4MolecularDissociationChannel * > *	GetDecayChannel () const
G4int	GetFakeParticleID () const
G4int	GetMoleculeID () const
const G4MoleculeDefinition *	GetDefinition () const
void	SetDiffusionCoefficient (G4double)
G4double	GetDiffusionCoefficient () const
G4double	GetDiffusionCoefficient (const G4Material *, double temperature) 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
const G4String &	GetLabel () const
void	SetLabel (const G4String &label)
void	ChangeConfigurationToLabel (const G4String &label)
G4MolecularConfiguration *	GetMolecularConfiguration () const
Public Member Functions inherited from G4IT
	G4IT ()
	G4IT (G4Track *)
virtual	~G4IT ()
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 ()
const G4ThreeVector &	GetPosition () const
double	operator[] (int i) const
const G4ThreeVector &	GetPreStepPosition () const
G4double	GetPreStepLocalTime () const
G4double	GetPreStepGlobalTime () const
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_Base *)
G4KDNode_Base *	GetNode () const
void	SetParentID (int, int)
void	GetParentID (int &, int &)
G4TrackingInformation *	GetTrackingInfo ()
G4TrackListNode *	GetListNode ()
void	SetListNode (G4TrackListNode *node)
virtual const G4ITType	GetITType () const =0

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

Private Member Functions
	G4Molecule ()

Private Attributes
G4MolecularConfiguration *	fpMolecularConfiguration

Additional Inherited Members
Public Types inherited from G4IT
enum	ELimited {   kDoNot, kUnique, kSharedTransport, kSharedOther,   kUndefLimited }
Protected Member Functions inherited from G4IT
	G4IT (const G4IT &)
G4IT &	operator= (const G4IT &)
Protected Attributes inherited from G4IT
G4Track *	fpTrack

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 94 of file G4Molecule.hh.

Constructor & Destructor Documentation

G4Molecule() [1/7]

G4Molecule::G4Molecule

(

const G4Molecule &

right

)

Definition at line 97 of file G4Molecule.cc.

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

G4Molecule() [2/7]

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 172 of file G4Molecule.cc.

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

G4Molecule() [3/7]

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

Definition at line 182 of file G4Molecule.cc.

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

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G4Molecule() [4/7]

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 195 of file G4Molecule.cc.

                                            :
    G4VUserTrackInformation("G4Molecule"), G4IT()
{
  if (moleculeDefinition->GetGroundStateElectronOccupancy())
  {
    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::GetOrCreateMolecularConfiguration(
            moleculeDefinition, dynElectronOccupancy);
  }
  else
  {
    fpMolecularConfiguration = 0;
    G4Exception(
        "G4Molecule::G4Molecule(G4MoleculeDefinition * moleculeDefinition, "
        "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");
  }
}

G4Molecule() [5/7]

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 242 of file G4Molecule.cc.

                                          :
    G4VUserTrackInformation("G4Molecule"), G4IT()
{
  if (moleculeDefinition->GetGroundStateElectronOccupancy())
  {
    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::GetOrCreateMolecularConfiguration(
            moleculeDefinition, dynElectronOccupancy);
  }
  else
  {
    fpMolecularConfiguration = 0;
    G4Exception(
        "G4Molecule::G4Molecule(G4MoleculeDefinition * moleculeDefinition, "
        "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");

  }
}

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G4Molecule() [6/7]

G4Molecule::G4Molecule

(

G4MolecularConfiguration *

molConf

)

Definition at line 285 of file G4Molecule.cc.

{
  fpMolecularConfiguration = molConf;
}

~G4Molecule()

G4Molecule::~G4Molecule ( )

virtual

Definition at line 153 of file G4Molecule.cc.

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

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G4Molecule() [7/7]

G4Molecule::G4Molecule ( )

private

Default molecule builder

Definition at line 144 of file G4Molecule.cc.

                       :
    G4VUserTrackInformation("G4Molecule"), G4IT()

{
  fpMolecularConfiguration = 0;
}

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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 321 of file G4Molecule.cc.

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

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BuildTrack()

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

Definition at line 380 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();

  G4DynamicParticle* dynamicParticle = new G4DynamicParticle(
      fpMolecularConfiguration->GetDefinition(), MomentumDirection,
      KineticEnergy);

  if (G4MoleculeCounter::InUse())
  {
    G4MoleculeCounter::GetMoleculeCounter()->AddAMoleculeAtTime(fpMolecularConfiguration,
                                                                globalTime);
  }

  //Set the Track
  fpTrack = new G4Track(dynamicParticle, globalTime, position);
  fpTrack->SetUserInformation(this);

  return fpTrack;
}

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ChangeConfigurationToLabel()

void G4Molecule::ChangeConfigurationToLabel

(

const G4String &

label

)

Definition at line 600 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!=0);
}

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ExciteMolecule()

void G4Molecule::ExciteMolecule

(

G4int

ExcitedLevel

)

Method used in Geant4-DNA to excite water molecules

Definition at line 303 of file G4Molecule.cc.

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

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GetAtomsNumber()

G4int G4Molecule::GetAtomsNumber

(

)

const

Returns the nomber of atoms compouning the molecule

Definition at line 359 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetAtomsNumber();
}

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GetCharge()

G4int G4Molecule::GetCharge

(

)

const

Returns the charge of molecule.

Definition at line 507 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetCharge();
}

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GetDecayChannel()

const vector< const G4MolecularDissociationChannel * > * G4Molecule::GetDecayChannel

(

)

const

Definition at line 458 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetDecayChannel();
}

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GetDecayTime()

G4double G4Molecule::GetDecayTime

(

)

const

Returns the decay time of the molecule.

Definition at line 486 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetDecayTime();
}

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GetDefinition()

const G4MoleculeDefinition * G4Molecule::GetDefinition

(

)

const

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

Definition at line 535 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetDefinition();
}

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GetDiffusionCoefficient() [1/2]

G4double G4Molecule::GetDiffusionCoefficient

(

)

const

Returns the diffusion coefficient D.

Definition at line 549 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetDiffusionCoefficient();
}

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GetDiffusionCoefficient() [2/2]

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

Returns the diffusion coefficient D.

Definition at line 556 of file G4Molecule.cc.

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

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GetDiffusionVelocity()

G4double G4Molecule::GetDiffusionVelocity

(

)

const

Definition at line 433 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
}

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GetElectronOccupancy()

const G4ElectronOccupancy * G4Molecule::GetElectronOccupancy

(

)

const

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

Definition at line 528 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetElectronOccupancy();
}

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GetFakeParticleID()

G4int G4Molecule::GetFakeParticleID

(

)

const

Definition at line 465 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetFakeParticleID();
}

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GetFormatedName()

const G4String & G4Molecule::GetFormatedName

(

)

const

Returns the formated name of the molecule

Definition at line 352 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetFormatedName();
}

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GetITSubType()

virtual G4ITType G4Molecule::GetITSubType ( ) const

inlinevirtual

Reimplemented from G4IT.

Definition at line 124 of file G4Molecule.hh.

  {
    return GetMoleculeID();
  }

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GetKineticEnergy()

G4double G4Molecule::GetKineticEnergy

(

)

const

Definition at line 421 of file G4Molecule.cc.

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

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GetLabel()

const G4String & G4Molecule::GetLabel

(

)

const

Returns the label of the molecule configuration

Definition at line 586 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetLabel();
}

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GetMass()

G4double G4Molecule::GetMass

(

)

const

Returns the total mass of the molecule.

Definition at line 521 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetMass();
}

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GetMolecularConfiguration()

G4MolecularConfiguration * G4Molecule::GetMolecularConfiguration

(

)

const

Definition at line 565 of file G4Molecule.cc.

{
  return fpMolecularConfiguration;
}

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GetMolecule()

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

static

Definition at line 83 of file G4Molecule.cc.

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

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GetMoleculeID()

G4int G4Molecule::GetMoleculeID

(

)

const

Definition at line 472 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetMoleculeID();
}

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GetName()

const G4String & G4Molecule::GetName ( void  ) const

virtual

Returns the name of the molecule

Implements G4IT.

Definition at line 345 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetName();
}

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GetNbElectrons()

G4double G4Molecule::GetNbElectrons

(

)

const

Returns the number of electron.

Definition at line 366 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetNbElectrons();
}

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GetVanDerVaalsRadius()

G4double G4Molecule::GetVanDerVaalsRadius

(

)

const

Definition at line 500 of file G4Molecule.cc.

{
  return fpMolecularConfiguration->GetVanDerVaalsRadius();
}

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IonizeMolecule()

void G4Molecule::IonizeMolecule

(

G4int

IonizedLevel

)

Method used in Geant4-DNA to ionize water molecules

Definition at line 313 of file G4Molecule.cc.

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

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ITDef()

G4Molecule::ITDef

(

G4Molecule

)

const

MoveOneElectron()

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

Move one electron from an orbit to another.

Definition at line 337 of file G4Molecule.cc.

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

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operator delete()

void G4Molecule::operator delete ( void *  aMolecule )

inline

Definition at line 312 of file G4Molecule.hh.

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

operator int()

G4Molecule::operator int ( ) const

inline

Definition at line 119 of file G4Molecule.hh.

  {
    return GetMoleculeID();
  }

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operator new()

void * G4Molecule::operator new ( size_t  )

inline

Definition at line 304 of file G4Molecule.hh.

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

operator!=()

G4bool G4Molecule::operator!=

(

const G4Molecule &

right

)

const

Definition at line 125 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 136 of file G4Molecule.cc.

{
  return fpMolecularConfiguration < right.fpMolecularConfiguration;
}

operator=()

G4Molecule & G4Molecule::operator=

(

const G4Molecule &

right

)

Definition at line 105 of file G4Molecule.cc.

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

operator==()

G4bool G4Molecule::operator==

(

const G4Molecule &

right

)

const

Definition at line 114 of file G4Molecule.cc.

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

PrintState()

void G4Molecule::PrintState

(

)

const

Show the electronic state of the molecule.

Definition at line 373 of file G4Molecule.cc.

{
  fpMolecularConfiguration->PrintState();
}

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RemoveElectron()

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

Remove n electrons to a given orbit.

Definition at line 329 of file G4Molecule.cc.

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

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SetDecayTime()

void G4Molecule::SetDecayTime

(

G4double

dynDecayTime

)

Set the decay time of the molecule.

Definition at line 479 of file G4Molecule.cc.

{
  fpMolecularConfiguration->SetDecayTime(dynDecayTime);
}

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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 542 of file G4Molecule.cc.

{
  fpMolecularConfiguration->SetDiffusionCoefficient(dynDiffusionCoefficient);
}

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SetElectronOccupancy()

void G4Molecule::SetElectronOccupancy

(

const G4ElectronOccupancy *

occ

)

Will set up the correct molecularConfiguration given an electron configuration

Definition at line 292 of file G4Molecule.cc.

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

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SetLabel()

void G4Molecule::SetLabel

(

const G4String &

label

)

Definition at line 593 of file G4Molecule.cc.

{
  fpMolecularConfiguration->SetLabel(label);
}

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SetMass()

void G4Molecule::SetMass

(

G4double

aMass

)

Set the total mass of the molecule.

Definition at line 514 of file G4Molecule.cc.

{
  fpMolecularConfiguration->SetMass(aMass);
}

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SetVanDerVaalsRadius()

void G4Molecule::SetVanDerVaalsRadius

(

G4double

dynVanDerVaalsRadius

)

The Van Der Valls Radius of the molecule

Definition at line 493 of file G4Molecule.cc.

{
  fpMolecularConfiguration->SetVanDerVaalsRadius(dynVanDerVaalsRadius);
}

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Member Data Documentation

fpMolecularConfiguration

G4MolecularConfiguration* G4Molecule::fpMolecularConfiguration

private

Definition at line 290 of file G4Molecule.hh.

---

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

• G4Molecule.hh
• G4Molecule.cc