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. More...
#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 |
| The two methods below are the most called of the simulation : compare molecules in the MoleculeStackManager or in the InteractionTable. More... | |
| G4Molecule (G4MoleculeDefinition *molecule) | |
| To build a molecule at ground state according to a given G4MoleculeDefinition that can be obtained from G4GenericMoleculeManager. More... | |
| G4Molecule (G4MoleculeDefinition *molecule, G4int, G4int) | |
| To build a molecule at a specific excitation/ionisation state according to a ground state that can be obtained from G4GenericMoleculeManager. More... | |
| G4Molecule (G4MoleculeDefinition *molecule, G4int, G4bool) | |
| 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. More... | |
| virtual | ~G4Molecule () |
| const G4String & | GetName () const |
| Returns the name of the molecule. More... | |
| G4int | GetAtomsNumber () const |
| Returns the nomber of atoms compouning the molecule. More... | |
| void | SetElectronOccupancy (const G4ElectronOccupancy *) |
| Will set up the correct molecularConfiguration given an electron configuration. More... | |
| void | ExciteMolecule (G4int) |
| Method used in Geant4-DNA to excite water molecules. More... | |
| void | IonizeMolecule (G4int) |
| Method used in Geant4-DNA to ionize water molecules. More... | |
| void | AddElectron (G4int orbit, G4int n=1) |
| Add n electrons to a given orbit. More... | |
| void | RemoveElectron (G4int, G4int number=1) |
| Remove n electrons to a given orbit. More... | |
| void | MoveOneElectron (G4int, G4int) |
| Move one electron from an orbit to another. More... | |
| G4double | GetNbElectrons () const |
| Returns the number of electron. More... | |
| void | PrintState () const |
| Show the electronic state of the molecule. More... | |
| 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 |
| Get molecule definition. More... | |
| void | 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. More... | |
| G4double | GetDiffusionCoefficient () const |
| Returns the diffusion coefficient D. More... | |
| void | SetDecayTime (G4double) |
| Set the decay time of the molecule. More... | |
| G4double | GetDecayTime () const |
| Returns the decay time of the molecule. More... | |
| void | SetVanDerVaalsRadius (G4double) |
| The Van Der Valls Radius of the molecule. More... | |
| G4double | GetVanDerVaalsRadius () const |
| const G4ElectronOccupancy * | GetElectronOccupancy () const |
| Returns the object ElectronOccupancy describing the electronic configuration of the molecule. More... | |
| G4int | GetCharge () const |
| Returns the charge of molecule. More... | |
| void | SetMass (G4double) |
| Set the total mass of the molecule. More... | |
| G4double | GetMass () const |
| Returns the total mass of the molecule. More... | |
| 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 () |
Private Member Functions | |
| bool | CompareElectronOccupancy (const G4ElectronOccupancy *, const G4int &, const G4int &) const |
| G4Molecule () | |
| Default molecule builder. More... | |
Private Attributes | |
| G4MolecularConfiguration * | fpMolecularConfiguration |
Static Private Attributes | |
| static double | fgTemperature = 310 |
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 fpMolecularConfiguration.
| G4Molecule::G4Molecule | ( | G4MoleculeDefinition * | molecule | ) |
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.
| 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.
| G4Molecule::G4Molecule | ( | G4MoleculeDefinition * | molecule, |
| 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 fpMolecularConfiguration, G4MoleculeDefinition::GetGroundStateElectronOccupancy(), G4MolecularConfiguration::GetMolecularConfiguration(), and G4ElectronOccupancy::RemoveElectron().
Here is the call graph for this function:
|
virtual |
Definition at line 130 of file G4Molecule.cc.
References fpMolecularConfiguration, G4IT::fpTrack, G4Track::GetGlobalTime(), G4MoleculeCounter::GetMoleculeCounter(), and G4MoleculeCounter::RemoveAMoleculeAtTime().
Here is the call graph for this function:
|
private |
Default molecule builder.
Definition at line 123 of file G4Molecule.cc.
Member Function Documentation
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(), and fpMolecularConfiguration.
Here is the call graph for this function:| G4Track * G4Molecule::BuildTrack | ( | G4double | globalTime, |
| const G4ThreeVector & | Position | ||
| ) |
Definition at line 263 of file G4Molecule.cc.
References G4MoleculeCounter::AddAMoleculeAtTime(), FatalErrorInArgument, fpMolecularConfiguration, G4IT::fpTrack, G4Exception(), G4UniformRand, G4MolecularConfiguration::GetDefinition(), GetKineticEnergy(), G4MoleculeCounter::GetMoleculeCounter(), G4MoleculeCounter::InUse(), and G4INCL::Math::pi.
Referenced by G4DNAChemistryManager::CreateSolvatedElectron(), G4DNAChemistryManager::CreateWaterMolecule(), G4DNAMolecularDissociation::DecayIt(), G4DNAMolecularReaction::MakeReaction(), G4DNAChemistryManager::PushMolecule(), and G4DNAChemistryManager::PushMoleculeAtParentTimeAndPlace().
Here is the call graph for this function: Here is the caller graph for this function:
|
private |
| 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(), and fpMolecularConfiguration.
Here is the call graph for this function:| G4int G4Molecule::GetAtomsNumber | ( | ) | const |
Returns the nomber of atoms compouning the molecule.
Definition at line 248 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::GetAtomsNumber().
Here is the call graph for this function:| G4int G4Molecule::GetCharge | ( | ) | const |
Returns the charge of molecule.
Definition at line 359 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::GetCharge().
Here is the call graph for this function:| const vector< const G4MolecularDecayChannel * > * G4Molecule::GetDecayChannel | ( | ) | const |
Definition at line 329 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::GetDecayChannel().
Here is the call graph for this function:| G4double G4Molecule::GetDecayTime | ( | ) | const |
Returns the decay time of the molecule.
Definition at line 344 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::GetDecayTime().
Here is the call graph for this function:| 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 fpMolecularConfiguration, and G4MolecularConfiguration::GetDefinition().
Referenced by G4MoleculeCounter::AddAMoleculeAtTime(), G4DNAMolecularDissociation::DecayIt(), G4DNAWaterDissociationDisplacer::GetProductsDisplacement(), and G4MoleculeCounter::RemoveAMoleculeAtTime().
Here is the call graph for this function: Here is the caller graph for this function:| G4double G4Molecule::GetDiffusionCoefficient | ( | ) | const |
Returns the diffusion coefficient D.
Definition at line 389 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::GetDiffusionCoefficient().
Referenced by G4DNABrownianTransportation::AlongStepGetPhysicalInteractionLength(), G4DNABrownianTransportation::ComputeStep(), G4DNASmoluchowskiReactionModel::FindReaction(), G4DNAMolecularReactionData::G4DNAMolecularReactionData(), G4DNAMolecularReaction::MakeReaction(), and G4DNAMoleculeEncounterStepper::RetrieveResults().
Here is the call graph for this function: Here is the caller graph for this function:| G4double G4Molecule::GetDiffusionVelocity | ( | ) | const |
Definition at line 308 of file G4Molecule.cc.
References fgTemperature, fpMolecularConfiguration, and G4MolecularConfiguration::GetMass().
Referenced by GetKineticEnergy().
Here is the call graph for this function: Here is the caller graph for this function:| 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 fpMolecularConfiguration, and G4MolecularConfiguration::GetElectronOccupancy().
Referenced by G4DNAMolecularDissociation::DecayIt().
Here is the call graph for this function: Here is the caller graph for this function:
|
static |
Definition at line 404 of file G4Molecule.cc.
References fgTemperature.
| G4double G4Molecule::GetKineticEnergy | ( | ) | const |
Definition at line 298 of file G4Molecule.cc.
References fpMolecularConfiguration, GetDiffusionVelocity(), and G4MolecularConfiguration::GetMass().
Referenced by BuildTrack().
Here is the call graph for this function: Here is the caller graph for this function:| G4double G4Molecule::GetMass | ( | ) | const |
Returns the total mass of the molecule.
Definition at line 369 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::GetMass().
Here is the call graph for this function:| G4MolecularConfiguration * G4Molecule::GetMolecularConfiguration | ( | ) | const |
Definition at line 394 of file G4Molecule.cc.
References fpMolecularConfiguration.
Referenced by G4DNASecondOrderReaction::PostStepGetPhysicalInteractionLength().
Here is the caller graph for this function:| G4int G4Molecule::GetMoleculeID | ( | ) | const |
Definition at line 334 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::GetMoleculeID().
Here is the call graph for this function:
|
virtual |
Returns the name of the molecule.
Implements G4IT.
Definition at line 243 of file G4Molecule.cc.
References fpMolecularConfiguration, and 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(), G4DNAMoleculeEncounterStepper::RetrieveResults(), and G4DNAMolecularReaction::TestReactibility().
Here is the call graph for this function: Here is the caller graph for this function:| G4double G4Molecule::GetNbElectrons | ( | ) | const |
Returns the number of electron.
Definition at line 253 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::GetNbElectrons().
Here is the call graph for this function:| G4double G4Molecule::GetVanDerVaalsRadius | ( | ) | const |
Definition at line 354 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::GetVanDerVaalsRadius().
Here is the call graph for this function:| void G4Molecule::IonizeMolecule | ( | G4int | IonizedLevel | ) |
Method used in Geant4-DNA to ionize water molecules.
Definition at line 223 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::IonizeMolecule().
Here is the call graph for this function:| G4Molecule::ITDef | ( | G4Molecule | ) | const |
Move one electron from an orbit to another.
Definition at line 238 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::MoveOneElectron().
Here is the call graph for this function:
|
inline |
Definition at line 261 of file G4Molecule.hh.
References aMoleculeAllocator.
|
inline |
Definition at line 253 of file G4Molecule.hh.
References aMoleculeAllocator.
| G4bool G4Molecule::operator!= | ( | const G4Molecule & | right | ) | const |
Definition at line 104 of file G4Molecule.cc.
References 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.
References fpMolecularConfiguration.
| G4Molecule & G4Molecule::operator= | ( | const G4Molecule & | right | ) |
Definition at line 88 of file G4Molecule.cc.
References fpMolecularConfiguration.
| G4bool G4Molecule::operator== | ( | const G4Molecule & | right | ) | const |
Definition at line 95 of file G4Molecule.cc.
References fpMolecularConfiguration.
| void G4Molecule::PrintState | ( | ) | const |
Show the electronic state of the molecule.
Definition at line 258 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::PrintState().
Referenced by G4MoleculeCounter::RemoveAMoleculeAtTime().
Here is the call graph for this function: Here is the caller graph for this function:Remove n electrons to a given orbit.
Definition at line 233 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::RemoveElectron().
Here is the call graph for this function:| void G4Molecule::SetDecayTime | ( | G4double | dynDecayTime | ) |
Set the decay time of the molecule.
Definition at line 339 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::SetDecayTime().
Here is the call graph for this function:| 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 fpMolecularConfiguration, and G4MolecularConfiguration::SetDiffusionCoefficient().
Here is the call graph for this function:| 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 fpMolecularConfiguration, G4MolecularConfiguration::GetDefinition(), and G4MolecularConfiguration::GetMolecularConfiguration().
Here is the call graph for this function:
|
static |
Definition at line 399 of file G4Molecule.cc.
References fgTemperature.
| void G4Molecule::SetMass | ( | G4double | aMass | ) |
Set the total mass of the molecule.
Definition at line 364 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::SetMass().
Here is the call graph for this function:| void G4Molecule::SetVanDerVaalsRadius | ( | G4double | dynVanDerVaalsRadius | ) |
The Van Der Valls Radius of the molecule.
Definition at line 349 of file G4Molecule.cc.
References fpMolecularConfiguration, and G4MolecularConfiguration::SetVanDerVaalsRadius().
Here is the call graph for this function:Member Data Documentation
|
staticprivate |
Definition at line 241 of file G4Molecule.hh.
Referenced by GetDiffusionVelocity(), GetGlobalTemperature(), and SetGlobalTemperature().
|
private |
Definition at line 239 of file G4Molecule.hh.
Referenced by AddElectron(), BuildTrack(), ExciteMolecule(), G4Molecule(), GetAtomsNumber(), GetCharge(), GetDecayChannel(), GetDecayTime(), GetDefinition(), GetDiffusionCoefficient(), GetDiffusionVelocity(), GetElectronOccupancy(), GetKineticEnergy(), GetMass(), GetMolecularConfiguration(), GetMoleculeID(), GetName(), GetNbElectrons(), GetVanDerVaalsRadius(), IonizeMolecule(), MoveOneElectron(), operator<(), operator=(), operator==(), PrintState(), RemoveElectron(), SetDecayTime(), SetDiffusionCoefficient(), SetElectronOccupancy(), SetMass(), SetVanDerVaalsRadius(), and ~G4Molecule().
The documentation for this class was generated from the following files:
- source/source/processes/electromagnetic/dna/molecules/management/include/G4Molecule.hh
- source/source/processes/electromagnetic/dna/molecules/management/src/G4Molecule.cc
