Geant4 11.2.2
Toolkit for the simulation of the passage of particles through matter
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#include <G4MolecularConfiguration.hh>
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class | G4MolecularConfigurationManager |
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using | G4DiffCoeffParam = std::function<double (const G4Material *, double, const G4MolecularConfiguration *)> |
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G4MolecularConfiguration (const G4MoleculeDefinition *, const G4ElectronOccupancy &, const G4String &label="") | |
G4MolecularConfiguration (const G4MoleculeDefinition *, int charge) | |
G4MolecularConfiguration (const G4MoleculeDefinition *, const G4String &label, int charge) | |
G4MolecularConfiguration (std::istream &) | |
G4MolecularConfiguration (const G4MolecularConfiguration &) | |
G4MolecularConfiguration & | operator= (G4MolecularConfiguration &right) |
~G4MolecularConfiguration () | |
G4MolecularConfiguration * | ChangeConfiguration (const G4ElectronOccupancy &newElectronOccupancy) const |
G4MolecularConfiguration * | ChangeConfiguration (int charge) const |
void | CheckElectronOccupancy (const char *line) const |
void | MakeExceptionIfFinalized () |
void | CreateDefaultDiffCoeffParam () |
Static Protected Member Functions | |
static void | ScaleAllDiffusionCoefficientsOnWater (double temperature_K) |
static G4MolecularConfigurationManager * | GetManager () |
static double | ReturnDefaultDiffCoeff (const G4Material *, double, const G4MolecularConfiguration *molConf) |
Static Protected Attributes | |
static G4MolecularConfigurationManager * | fgManager = nullptr |
static double | fgTemperature = 298 |
The pointer G4MolecularConfiguration will be shared by all the molecules having the same molecule definition and the same electron occupancy BE CAREFUlL !!! : If you change the mass for instance of a OH^-, this will affect all the OH^- molecule diffusing around
Definition at line 97 of file G4MolecularConfiguration.hh.
using G4MolecularConfiguration::G4DiffCoeffParam = std::function<double (const G4Material *, double, const G4MolecularConfiguration *)> |
Definition at line 101 of file G4MolecularConfiguration.hh.
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Definition at line 417 of file G4MolecularConfiguration.cc.
Referenced by ChangeConfiguration(), ChangeConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), G4MolecularConfiguration::G4MolecularConfigurationManager::GetOrCreateMolecularConfiguration(), G4MolecularConfiguration::G4MolecularConfigurationManager::GetOrCreateMolecularConfiguration(), GetOrCreateMolecularConfiguration(), GetOrCreateMolecularConfiguration(), and Load().
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Definition at line 470 of file G4MolecularConfiguration.cc.
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Definition at line 78 of file G4MolecularConfiguration.cc.
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Definition at line 1393 of file G4MolecularConfiguration.cc.
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Definition at line 507 of file G4MolecularConfiguration.cc.
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Definition at line 572 of file G4MolecularConfiguration.hh.
G4MolecularConfiguration * G4MolecularConfiguration::AddElectron | ( | G4int | orbit, |
G4int | n = 1 ) const |
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 616 of file G4MolecularConfiguration.cc.
Referenced by G4Molecule::AddElectron().
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Definition at line 524 of file G4MolecularConfiguration.cc.
Referenced by AddElectron(), ExciteMolecule(), IonizeMolecule(), MoveOneElectron(), and RemoveElectron().
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Definition at line 542 of file G4MolecularConfiguration.cc.
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Definition at line 788 of file G4MolecularConfiguration.cc.
Referenced by AddElectron(), ExciteMolecule(), GetNbElectrons(), IonizeMolecule(), MoveOneElectron(), and RemoveElectron().
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Definition at line 1465 of file G4MolecularConfiguration.cc.
Referenced by Finalize().
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Definition at line 1059 of file G4MolecularConfiguration.cc.
Referenced by G4MoleculeTable::CreateConfiguration(), G4MoleculeTable::CreateConfiguration(), G4MoleculeTable::CreateConfiguration(), G4MoleculeTable::CreateConfiguration(), CreateMolecularConfiguration(), G4MoleculeDefinition::NewConfiguration(), G4MoleculeDefinition::NewConfigurationWithElectronOccupancy(), and G4MoleculeTableMessenger::SetNewValue().
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Definition at line 1136 of file G4MolecularConfiguration.cc.
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Definition at line 1202 of file G4MolecularConfiguration.cc.
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Definition at line 969 of file G4MolecularConfiguration.cc.
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Definition at line 407 of file G4MolecularConfiguration.cc.
Referenced by G4DNAChemistryManager::Clear().
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Definition at line 1432 of file G4MolecularConfiguration.cc.
Referenced by ScaleAllDiffusionCoefficientsOnWater(), and G4DNAMolecularReactionData::ScaledParameterization().
G4MolecularConfiguration * G4MolecularConfiguration::ExciteMolecule | ( | G4int | ExcitedLevel | ) | const |
Method used in Geant4-DNA to excite water molecules
Definition at line 568 of file G4MolecularConfiguration.cc.
Referenced by G4Molecule::ExciteMolecule().
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Definition at line 561 of file G4MolecularConfiguration.hh.
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Definition at line 1511 of file G4MolecularConfiguration.cc.
Referenced by G4MoleculeTable::Finalize().
G4int G4MolecularConfiguration::GetAtomsNumber | ( | ) | const |
Returns the nomber of atoms compouning the molecule
Definition at line 701 of file G4MolecularConfiguration.cc.
Referenced by G4Molecule::GetAtomsNumber().
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Returns the charge of molecule.
Definition at line 518 of file G4MolecularConfiguration.hh.
Referenced by G4DNAMolecularReactionData::ComputeEffectiveRadius(), and G4Molecule::GetCharge().
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Returns the decay time of the molecule.
Definition at line 502 of file G4MolecularConfiguration.hh.
Referenced by G4Molecule::GetDecayTime().
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Definition at line 475 of file G4MolecularConfiguration.hh.
Referenced by G4MoleculeCounter::AddAMoleculeAtTime(), G4Molecule::BuildTrack(), G4Molecule::ChangeConfigurationToLabel(), CreateMolecularConfiguration(), G4Molecule::GetDefinition(), G4MoleculeCounter::RemoveAMoleculeAtTime(), G4MolecularConfiguration::G4MolecularConfigurationManager::RemoveMolecularConfigurationFromTable(), and G4Molecule::SetElectronOccupancy().
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Returns the diffusion coefficient D.
Definition at line 491 of file G4MolecularConfiguration.hh.
Referenced by G4DNAMolecularReactionData::ComputeEffectiveRadius(), G4Molecule::GetDiffusionCoefficient(), G4Molecule::GetDiffusionCoefficient(), G4DNAIRT::GetIndependentReactionTime(), G4DiffusionControlledReactionModel::GetTimeToEncounter(), G4DNAGillespieDirectMethod::PropensityFunction(), G4DNAIRT::Sampling(), ScaleAllDiffusionCoefficientsOnWater(), G4DNAMolecularReactionData::SetReactionType(), and G4DNAMakeReaction::UpdatePositionForReaction().
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Definition at line 579 of file G4MolecularConfiguration.hh.
const vector< const G4MolecularDissociationChannel * > * G4MolecularConfiguration::GetDissociationChannels | ( | ) | const |
Definition at line 754 of file G4MolecularConfiguration.cc.
Referenced by G4Molecule::GetDissociationChannels().
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Returns the object ElectronOccupancy describing the electronic configuration of the molecule.
Definition at line 480 of file G4MolecularConfiguration.hh.
Referenced by CreateMolecularConfiguration(), G4Molecule::GetElectronOccupancy(), and G4MolecularConfiguration::G4MolecularConfigurationManager::RemoveMolecularConfigurationFromTable().
G4int G4MolecularConfiguration::GetFakeParticleID | ( | ) | const |
Definition at line 762 of file G4MolecularConfiguration.cc.
Referenced by G4Molecule::GetFakeParticleID().
const G4String & G4MolecularConfiguration::GetFormatedName | ( | ) | const |
Returns the formated name of the molecule
Definition at line 694 of file G4MolecularConfiguration.cc.
Referenced by G4Molecule::GetFormatedName().
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Definition at line 1483 of file G4MolecularConfiguration.cc.
Referenced by G4DNAChemistryManager::GetCurrentValue(), and G4Molecule::GetDiffusionVelocity().
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Definition at line 553 of file G4MolecularConfiguration.hh.
Referenced by CreateMolecularConfiguration(), CreateMolecularConfiguration(), G4Molecule::GetLabel(), and PrintState().
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Definition at line 129 of file G4MolecularConfiguration.cc.
Referenced by ChangeConfiguration(), ChangeConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), FinalizeAll(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetMolecularConfiguration(), GetMolecularConfiguration(), GetMolecularConfiguration(), GetNumberOfSpecies(), GetOrCreateMolecularConfiguration(), GetOrCreateMolecularConfiguration(), GetOrCreateMolecularConfiguration(), GetUserIDTable(), PrintAll(), and SetUserID().
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Returns the total mass of the molecule.
Definition at line 529 of file G4MolecularConfiguration.hh.
Referenced by G4Molecule::GetDiffusionVelocity(), G4Molecule::GetKineticEnergy(), and G4Molecule::GetMass().
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Definition at line 952 of file G4MolecularConfiguration.cc.
Referenced by G4MoleculeDefinition::AddDecayChannel(), G4Molecule::ChangeConfigurationToLabel(), G4MoleculeTable::GetConfiguration(), G4MoleculeTable::GetConfiguration(), G4MoleculeDefinition::GetConfigurationWithLabel(), and G4MoleculeTableMessenger::SetNewValue().
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Definition at line 1504 of file G4MolecularConfiguration.cc.
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Definition at line 961 of file G4MolecularConfiguration.cc.
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Definition at line 534 of file G4MolecularConfiguration.hh.
Referenced by G4DNAIRTMoleculeEncounterStepper::CalculateStep(), G4DNAMoleculeEncounterStepper::CalculateStep(), and G4Molecule::GetMoleculeID().
const G4String & G4MolecularConfiguration::GetName | ( | ) | const |
Returns the name of the molecule
Definition at line 687 of file G4MolecularConfiguration.cc.
Referenced by G4DNAScavengerMaterial::AddAMoleculeAtTime(), G4MoleculeCounter::AddAMoleculeAtTime(), G4DNAMolecularReactionTable::CanReactWith(), G4Molecule::GetName(), G4DNAScavengerMaterial::GetNMoleculesAtTime(), G4DNAScavengerMaterial::GetNumberMoleculePerVolumeUnitForMaterialConf(), G4DNAMolecularReactionTable::GetReactionData(), G4DNAMolecularReactionTable::GetReactionData(), G4DiffusionControlledReactionModel::GetReactionRadius(), G4DNAMolecularReactionTable::GetReativesNData(), G4ChemEquilibrium::Initialize(), IonizeMolecule(), MakeExceptionIfFinalized(), MoveOneElectron(), G4DNAScavengerProcess::PostStepDoIt(), G4DNAScavengerProcess::PostStepGetPhysicalInteractionLength(), G4ChemEquilibrium::PrintInfo(), PrintState(), G4DNAMolecularReactionTable::PrintTable(), G4DNAScavengerMaterial::RemoveAMoleculeAtTime(), G4MoleculeCounter::RemoveAMoleculeAtTime(), RemoveElectron(), G4DNAIRT::Sampling(), G4ChemEquilibrium::SetEquilibrium(), G4DNAScavengerProcess::SetReaction(), and G4DNAUpdateSystemModel::UpdateSystem().
G4double G4MolecularConfiguration::GetNbElectrons | ( | ) | const |
Returns the number of electron.
Definition at line 708 of file G4MolecularConfiguration.cc.
Referenced by G4Molecule::GetNbElectrons().
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Definition at line 65 of file G4MolecularConfiguration.cc.
Referenced by G4MoleculeTable::GetNumberOfDefinedSpecies().
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Definition at line 326 of file G4MolecularConfiguration.cc.
Referenced by G4Molecule::G4Molecule(), G4Molecule::G4Molecule(), G4Molecule::G4Molecule(), G4Molecule::G4Molecule(), G4MoleculeTable::PrepareMolecularConfiguration(), G4Molecule::SetElectronOccupancy(), and G4MoleculeTableMessenger::SetNewValue().
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Definition at line 364 of file G4MolecularConfiguration.cc.
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Definition at line 388 of file G4MolecularConfiguration.cc.
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Definition at line 567 of file G4MolecularConfiguration.hh.
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Definition at line 166 of file G4MolecularConfiguration.hh.
Referenced by G4MoleculeTable::GetConfigurationIterator().
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Definition at line 513 of file G4MolecularConfiguration.hh.
Referenced by G4Molecule::GetVanDerVaalsRadius(), and G4DNAMolecularReactionData::SetReactionType().
G4MolecularConfiguration * G4MolecularConfiguration::IonizeMolecule | ( | G4int | IonizedLevel | ) | const |
Method used in Geant4-DNA to ionize water molecules
Definition at line 585 of file G4MolecularConfiguration.cc.
Referenced by G4Molecule::IonizeMolecule().
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Definition at line 1386 of file G4MolecularConfiguration.cc.
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Definition at line 113 of file G4MolecularConfiguration.cc.
Referenced by SetDecayTime(), SetDiffusionCoefficient(), SetMass(), and SetVanDerVaalsRadius().
G4MolecularConfiguration * G4MolecularConfiguration::MoveOneElectron | ( | G4int | orbitToFree, |
G4int | orbitToFill ) const |
Move one electron from an orbit to another.
Definition at line 658 of file G4MolecularConfiguration.cc.
Referenced by G4Molecule::MoveOneElectron().
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Definition at line 557 of file G4MolecularConfiguration.cc.
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Definition at line 1523 of file G4MolecularConfiguration.cc.
Referenced by G4MoleculeTableMessenger::SetNewValue().
void G4MolecularConfiguration::PrintState | ( | ) | const |
Display the electronic state of the molecule.
Definition at line 716 of file G4MolecularConfiguration.cc.
Referenced by CreateMolecularConfiguration(), CreateMolecularConfiguration(), IonizeMolecule(), MoveOneElectron(), G4Molecule::PrintState(), G4MoleculeCounter::RemoveAMoleculeAtTime(), and RemoveElectron().
G4MolecularConfiguration * G4MolecularConfiguration::RemoveElectron | ( | G4int | orbit, |
G4int | number = 1 ) const |
Remove n electrons to a given orbit.
Definition at line 629 of file G4MolecularConfiguration.cc.
Referenced by G4Molecule::RemoveElectron().
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Definition at line 70 of file G4MolecularConfiguration.cc.
Referenced by CreateDefaultDiffCoeffParam(), G4MolecularConfiguration(), G4MolecularConfiguration(), and G4MolecularConfiguration().
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Definition at line 1443 of file G4MolecularConfiguration.cc.
Referenced by SetGlobalTemperature().
void G4MolecularConfiguration::Serialize | ( | std::ostream & | out | ) |
Definition at line 1336 of file G4MolecularConfiguration.cc.
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Set the decay time of the molecule.
Definition at line 496 of file G4MolecularConfiguration.hh.
Referenced by G4MoleculeDefinition::NewConfigurationWithElectronOccupancy().
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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.
Note : Diffusion Coefficient in one medium only For the time being, we will consider only one diffusion coefficient for the all simulation => diffusion in one medium only If the user needs to use the diffusion in different materials, she/he should contact the developers/maintainers of this package
Definition at line 485 of file G4MolecularConfiguration.hh.
Referenced by G4EmDNAChemistry_option1::ConstructMolecule(), G4MoleculeTable::CreateConfiguration(), and ScaleAllDiffusionCoefficientsOnWater().
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Definition at line 1475 of file G4MolecularConfiguration.cc.
Referenced by G4DNAChemistryManager::SetGlobalTemperature().
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Definition at line 539 of file G4MolecularConfiguration.hh.
Referenced by CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), and G4MolecularConfiguration().
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Set the total mass of the molecule.
Definition at line 523 of file G4MolecularConfiguration.hh.
Referenced by G4ChemDissociationChannels::ConstructMolecule(), and G4ChemDissociationChannels_option1::ConstructMolecule().
void G4MolecularConfiguration::SetUserID | ( | const G4String & | userID | ) |
Definition at line 1423 of file G4MolecularConfiguration.cc.
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The Van Der Valls Radius of the molecule
Definition at line 507 of file G4MolecularConfiguration.hh.
Referenced by G4ChemDissociationChannels_option1::ConstructMolecule().
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Definition at line 585 of file G4MolecularConfiguration.hh.
void G4MolecularConfiguration::Unserialize | ( | std::istream & | in | ) |
Definition at line 1358 of file G4MolecularConfiguration.cc.
Referenced by G4MolecularConfiguration().
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Definition at line 466 of file G4MolecularConfiguration.hh.
Referenced by AddDiffCoeffParameterization(), CreateDefaultDiffCoeffParam(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), and GetDiffusionCoefficient().
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Definition at line 459 of file G4MolecularConfiguration.hh.
Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetCharge(), PrintState(), Serialize(), and Unserialize().
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Definition at line 457 of file G4MolecularConfiguration.hh.
Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetDecayTime(), Serialize(), SetDecayTime(), and Unserialize().
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Definition at line 455 of file G4MolecularConfiguration.hh.
Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetDiffusionCoefficient(), ReturnDefaultDiffCoeff(), Serialize(), SetDiffusionCoefficient(), and Unserialize().
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Definition at line 458 of file G4MolecularConfiguration.hh.
Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetMass(), Serialize(), SetMass(), and Unserialize().
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Definition at line 456 of file G4MolecularConfiguration.hh.
Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetVanDerVaalsRadius(), Serialize(), SetVanDerVaalsRadius(), and Unserialize().
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Definition at line 451 of file G4MolecularConfiguration.hh.
Referenced by AddElectron(), CheckElectronOccupancy(), ExciteMolecule(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetElectronOccupancy(), GetNbElectrons(), IonizeMolecule(), MoveOneElectron(), PrintState(), RemoveElectron(), and G4MolecularConfiguration::G4MolecularConfigurationManager::RemoveMolecularConfigurationFromTable().
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Definition at line 461 of file G4MolecularConfiguration.hh.
Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetFormatedName(), Serialize(), and Unserialize().
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Definition at line 447 of file G4MolecularConfiguration.hh.
Referenced by DeleteManager(), GetManager(), SetLabel(), and ~G4MolecularConfiguration().
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Definition at line 467 of file G4MolecularConfiguration.hh.
Referenced by GetGlobalTemperature(), ScaleAllDiffusionCoefficientsOnWater(), and SetGlobalTemperature().
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Definition at line 464 of file G4MolecularConfiguration.hh.
Referenced by Finalize(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), MakeExceptionIfFinalized(), Serialize(), UnFinalize(), and Unserialize().
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Definition at line 453 of file G4MolecularConfiguration.hh.
Referenced by CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetLabel(), PrintState(), G4MolecularConfiguration::G4MolecularConfigurationManager::RecordNewlyLabeledConfiguration(), and SetLabel().
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Definition at line 450 of file G4MolecularConfiguration.hh.
Referenced by ChangeConfiguration(), ChangeConfiguration(), CheckElectronOccupancy(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetAtomsNumber(), GetDefinition(), GetDissociationChannels(), GetFakeParticleID(), PrintState(), G4MolecularConfiguration::G4MolecularConfigurationManager::RecordNewlyLabeledConfiguration(), Serialize(), and Unserialize().
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Definition at line 460 of file G4MolecularConfiguration.hh.
Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetMoleculeID(), Serialize(), and Unserialize().
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Definition at line 462 of file G4MolecularConfiguration.hh.
Referenced by G4MolecularConfiguration(), G4MolecularConfiguration(), G4MolecularConfiguration(), GetName(), Serialize(), and Unserialize().
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Definition at line 463 of file G4MolecularConfiguration.hh.
Referenced by CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), CreateMolecularConfiguration(), GetUserID(), and SetUserID().