G4MolecularConfiguration Class Reference

#include <G4MolecularConfiguration.hh>


Public Member Functions

const G4MoleculeDefinition * GetDefinition () const
const G4String & GetName () const
G4int GetAtomsNumber () const
G4MolecularConfiguration * ExciteMolecule (G4int)
G4MolecularConfiguration * IonizeMolecule (G4int)
G4MolecularConfiguration * AddElectron (G4int orbit, G4int n=1)
G4MolecularConfiguration * RemoveElectron (G4int, G4int number=1)
G4MolecularConfiguration * MoveOneElectron (G4int, G4int)
G4double GetNbElectrons () const
void PrintState () const
const std::vector< const G4MolecularDecayChannel * > * GetDecayChannel () const
G4int GetMoleculeID () const
void SetDiffusionCoefficient (G4double)
G4double GetDiffusionCoefficient () const
void SetDecayTime (G4double)
G4double GetDecayTime () const
void SetVanDerVaalsRadius (G4double)
G4double GetVanDerVaalsRadius () const
const G4ElectronOccupancy * GetElectronOccupancy () const
G4int GetCharge () const
void SetMass (G4double)
G4double GetMass () const

Static Public Member Functions

static G4MolecularConfiguration * GetMolecularConfiguration (const G4MoleculeDefinition *, const G4ElectronOccupancy &electronOccupancy)
static G4MolecularConfiguration * GetMolecularConfiguration (const G4MoleculeDefinition *)
static void DeleteManager ()

Protected Member Functions

 G4MolecularConfiguration (const G4MoleculeDefinition *, const G4ElectronOccupancy &)
 G4MolecularConfiguration (const G4MolecularConfiguration &)
G4MolecularConfiguration & operator= (G4MolecularConfiguration &right)
 ~G4MolecularConfiguration ()
G4MolecularConfiguration * ChangeConfiguration (const G4ElectronOccupancy &newElectronOccupancy)

Static Protected Member Functions

static G4MolecularConfigurationManager * GetManager ()

Protected Attributes

const G4MoleculeDefinition * fMoleculeDefinition
const G4ElectronOccupancy * fElectronOccupancy
G4double fDynDiffusionCoefficient
G4double fDynVanDerVaalsRadius
G4double fDynDecayTime
G4double fDynMass
G4int fDynCharge
G4String fName

Static Protected Attributes

static G4MolecularConfigurationManager * fgManager = 0

Data Structures

struct  G4MolecularConfigurationManager

Detailed Description

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 59 of file G4MolecularConfiguration.hh.

Constructor & Destructor Documentation

G4MolecularConfiguration::G4MolecularConfiguration ( const G4MoleculeDefinition *  ,
const G4ElectronOccupancy &   
) [protected]

Definition at line 111 of file G4MolecularConfiguration.cc.

References fDynCharge, fDynDecayTime, fDynDiffusionCoefficient, fDynMass, fDynVanDerVaalsRadius, fElectronOccupancy, fgManager, fMoleculeDefinition, G4MolecularConfiguration::G4MolecularConfigurationManager::fTable, G4MoleculeDefinition::GetDecayTime(), G4MoleculeDefinition::GetDiffusionCoefficient(), G4MoleculeDefinition::GetMass(), G4MoleculeDefinition::GetNbElectrons(), G4ElectronOccupancy::GetTotalOccupancy(), and G4MoleculeDefinition::GetVanDerVaalsRadius().

Referenced by ChangeConfiguration(), and GetMolecularConfiguration().

00113 {
00114     fMoleculeDefinition = moleculeDef ;
00115     fgManager->fTable[fMoleculeDefinition][elecOcc] = this;
00116     std::map<G4ElectronOccupancy, G4MolecularConfiguration*, comparator>::iterator it ;
00117     it = fgManager->fTable[moleculeDef].find(elecOcc);
00118     fElectronOccupancy = &(it->first);
00119 
00120     fDynCharge = fMoleculeDefinition->GetNbElectrons()-fElectronOccupancy->GetTotalOccupancy();
00121     fDynMass = fMoleculeDefinition->GetMass() ;
00122 
00123     fDynDiffusionCoefficient = fMoleculeDefinition->GetDiffusionCoefficient() ;
00124     fDynVanDerVaalsRadius = fMoleculeDefinition->GetVanDerVaalsRadius() ;
00125     fDynDecayTime = fMoleculeDefinition->GetDecayTime() ;
00126 }

G4MolecularConfiguration::G4MolecularConfiguration ( const G4MolecularConfiguration &   )  [protected]

G4MolecularConfiguration::~G4MolecularConfiguration (  )  [protected]

Definition at line 128 of file G4MolecularConfiguration.cc.

References fElectronOccupancy.

00129 {
00130     if(fElectronOccupancy)
00131     {
00132         delete fElectronOccupancy;
00133         fElectronOccupancy = 0;
00134     }
00135 }

Member Function Documentation

G4MolecularConfiguration * G4MolecularConfiguration::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 189 of file G4MolecularConfiguration.cc.

References G4ElectronOccupancy::AddElectron(), ChangeConfiguration(), and fElectronOccupancy.

Referenced by G4Molecule::AddElectron(), and MoveOneElectron().

00190 {
00191     G4ElectronOccupancy newElectronOccupancy(*fElectronOccupancy);
00192     newElectronOccupancy.AddElectron(orbit, number);
00193     return ChangeConfiguration(newElectronOccupancy);
00194 }

G4MolecularConfiguration * G4MolecularConfiguration::ChangeConfiguration ( const G4ElectronOccupancy &  newElectronOccupancy  )  [protected]

Definition at line 137 of file G4MolecularConfiguration.cc.

References fgManager, fMoleculeDefinition, G4MolecularConfiguration::G4MolecularConfigurationManager::fTable, and G4MolecularConfiguration().

Referenced by AddElectron(), ExciteMolecule(), IonizeMolecule(), MoveOneElectron(), and RemoveElectron().

00138 {
00139     G4MolecularConfiguration* output = fgManager->fTable[fMoleculeDefinition][newElectronOccupancy] ;
00140     if(! output)
00141     {
00142         output = new G4MolecularConfiguration(fMoleculeDefinition, newElectronOccupancy);
00143     }
00144     return output ;
00145 }

void G4MolecularConfiguration::DeleteManager (  )  [static]

Definition at line 103 of file G4MolecularConfiguration.cc.

References fgManager.

00104 {
00105     if(fgManager) delete fgManager;
00106     fgManager = 0;
00107 }

G4MolecularConfiguration * G4MolecularConfiguration::ExciteMolecule ( G4int   ) 

Method used in Geant4-DNA to excite water molecules

Definition at line 156 of file G4MolecularConfiguration.cc.

References G4ElectronOccupancy::AddElectron(), ChangeConfiguration(), fElectronOccupancy, and G4ElectronOccupancy::RemoveElectron().

Referenced by G4Molecule::ExciteMolecule().

00157 {
00158     G4ElectronOccupancy newElectronOccupancy (*fElectronOccupancy);
00159 
00160     newElectronOccupancy.RemoveElectron(ExcitedLevel,1);
00161     newElectronOccupancy.AddElectron(5,1);
00162 
00163     return ChangeConfiguration(newElectronOccupancy);
00164 }

G4int G4MolecularConfiguration::GetAtomsNumber (  )  const

Returns the nomber of atoms compouning the molecule

Definition at line 248 of file G4MolecularConfiguration.cc.

References fMoleculeDefinition, and G4MoleculeDefinition::GetAtomsNumber().

Referenced by G4Molecule::GetAtomsNumber().

00249 {
00250     return fMoleculeDefinition->GetAtomsNumber();
00251 }

G4int G4MolecularConfiguration::GetCharge (  )  const [inline]

Returns the charge of molecule.

Definition at line 275 of file G4MolecularConfiguration.hh.

References fDynCharge.

Referenced by G4Molecule::GetCharge().

00276 {
00277     return fDynCharge ;
00278 }

const vector< const G4MolecularDecayChannel * > * G4MolecularConfiguration::GetDecayChannel (  )  const

Definition at line 274 of file G4MolecularConfiguration.cc.

References fElectronOccupancy, and fMoleculeDefinition.

Referenced by G4Molecule::GetDecayChannel().

00275 {
00276     return fMoleculeDefinition-> GetDecayChannels(fElectronOccupancy);
00277 }

G4double G4MolecularConfiguration::GetDecayTime (  )  const [inline]

Returns the decay time of the molecule.

Definition at line 260 of file G4MolecularConfiguration.hh.

References fDynDecayTime.

Referenced by G4Molecule::GetDecayTime().

00261 {
00262     return fDynDecayTime;
00263 }

const G4MoleculeDefinition * G4MolecularConfiguration::GetDefinition (  )  const [inline]

Definition at line 235 of file G4MolecularConfiguration.hh.

References fMoleculeDefinition.

Referenced by G4Molecule::BuildTrack(), G4Molecule::GetDefinition(), and G4Molecule::SetElectronOccupancy().

00236 {
00237     return fMoleculeDefinition;
00238 }

G4double G4MolecularConfiguration::GetDiffusionCoefficient (  )  const [inline]

Returns the diffusion coefficient D.

Definition at line 250 of file G4MolecularConfiguration.hh.

References fDynDiffusionCoefficient.

Referenced by G4Molecule::GetDiffusionCoefficient().

00251 {
00252     return fDynDiffusionCoefficient;
00253 }

const G4ElectronOccupancy * G4MolecularConfiguration::GetElectronOccupancy (  )  const [inline]

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

Definition at line 240 of file G4MolecularConfiguration.hh.

References fElectronOccupancy.

Referenced by G4Molecule::GetElectronOccupancy().

00241 {
00242     return fElectronOccupancy ;
00243 }

G4MolecularConfiguration::G4MolecularConfigurationManager * G4MolecularConfiguration::GetManager (  )  [static, protected]

Definition at line 46 of file G4MolecularConfiguration.cc.

References fgManager.

Referenced by GetMolecularConfiguration().

00047 {
00048     if(!fgManager)
00049     {
00050         fgManager = new G4MolecularConfiguration::G4MolecularConfigurationManager;
00051     }
00052 
00053     return fgManager;
00054 }

G4double G4MolecularConfiguration::GetMass (  )  const [inline]

Returns the total mass of the molecule.

Definition at line 285 of file G4MolecularConfiguration.hh.

References fDynMass.

Referenced by G4Molecule::GetDiffusionVelocity(), G4Molecule::GetKineticEnergy(), and G4Molecule::GetMass().

00286 {
00287     return fDynMass;
00288 }

G4MolecularConfiguration * G4MolecularConfiguration::GetMolecularConfiguration ( const G4MoleculeDefinition *   )  [static]

Definition at line 75 of file G4MolecularConfiguration.cc.

References G4MolecularConfiguration::G4MolecularConfigurationManager::fTable, G4MolecularConfiguration(), G4MoleculeDefinition::GetGroundStateElectronOccupancy(), and GetManager().

00076 {
00077     const G4ElectronOccupancy& elecOcc = *molDef->GetGroundStateElectronOccupancy();
00078     if(GetManager()->fTable[molDef][elecOcc])
00079     {
00080         return GetManager()->fTable[molDef][elecOcc];
00081     }
00082     else
00083     {
00084         G4MolecularConfiguration* newConf = new G4MolecularConfiguration(molDef, elecOcc);
00085         return newConf ;
00086     }
00087 }

G4MolecularConfiguration * G4MolecularConfiguration::GetMolecularConfiguration ( const G4MoleculeDefinition *  ,
const G4ElectronOccupancy &  electronOccupancy 
) [static]

Definition at line 89 of file G4MolecularConfiguration.cc.

References G4MolecularConfiguration::G4MolecularConfigurationManager::fTable, G4MolecularConfiguration(), and GetManager().

Referenced by G4MoleculeDefinition::AddeConfToExcitedState(), G4Molecule::G4Molecule(), and G4Molecule::SetElectronOccupancy().

00091 {
00092     if(GetManager()->fTable[molDef][elecOcc])
00093     {
00094         return GetManager()->fTable[molDef][elecOcc];
00095     }
00096     else
00097     {
00098         G4MolecularConfiguration* newConf = new G4MolecularConfiguration(molDef, elecOcc);
00099         return newConf ;
00100     }
00101 }

G4int G4MolecularConfiguration::GetMoleculeID (  )  const

Definition at line 279 of file G4MolecularConfiguration.cc.

References FatalErrorInArgument, fMoleculeDefinition, G4Exception(), G4ParticleDefinition::GetPDGEncoding(), and INT_MAX.

Referenced by G4Molecule::GetMoleculeID().

00280 {
00281     if(fMoleculeDefinition)
00282         return fMoleculeDefinition->GetPDGEncoding();
00283     else
00284         G4Exception("G4Molecule::GetMoleculeID","",FatalErrorInArgument, "You should first enter a molecule defintion");
00285 
00286     return INT_MAX;
00287 }

const G4String & G4MolecularConfiguration::GetName (  )  const

Returns the name of the molecule

Definition at line 235 of file G4MolecularConfiguration.cc.

References G4UIcommand::ConvertToString(), fDynCharge, fMoleculeDefinition, fName, G4MoleculeDefinition::GetName(), and G4String::isNull().

Referenced by G4Molecule::GetName(), IonizeMolecule(), MoveOneElectron(), PrintState(), and RemoveElectron().

00236 {
00237     if(fName.isNull())
00238     {
00239         fName = fMoleculeDefinition->GetName();
00240         fName+= "^";
00241         fName+= "{";
00242         fName+= G4UIcommand::ConvertToString(fDynCharge);
00243         fName+= "}";
00244     }
00245     return fName;
00246 }

G4double G4MolecularConfiguration::GetNbElectrons (  )  const

Returns the number of electron.

Definition at line 253 of file G4MolecularConfiguration.cc.

References fElectronOccupancy, and G4ElectronOccupancy::GetTotalOccupancy().

Referenced by G4Molecule::GetNbElectrons().

00254 {
00255     return fElectronOccupancy->GetTotalOccupancy();
00256 }

G4double G4MolecularConfiguration::GetVanDerVaalsRadius (  )  const [inline]

Definition at line 270 of file G4MolecularConfiguration.hh.

References fDynVanDerVaalsRadius.

Referenced by G4Molecule::GetVanDerVaalsRadius().

00271 {
00272     return fDynVanDerVaalsRadius;
00273 }

G4MolecularConfiguration * G4MolecularConfiguration::IonizeMolecule ( G4int   ) 

Method used in Geant4-DNA to ionize water molecules

Definition at line 168 of file G4MolecularConfiguration.cc.

References ChangeConfiguration(), G4UIcommand::ConvertToString(), FatalErrorInArgument, fElectronOccupancy, G4Exception(), GetName(), G4ElectronOccupancy::GetOccupancy(), PrintState(), and G4ElectronOccupancy::RemoveElectron().

Referenced by G4Molecule::IonizeMolecule().

00169 {
00170     G4ElectronOccupancy newElectronOccupancy(*fElectronOccupancy);
00171 
00172     if(newElectronOccupancy.GetOccupancy(IonizedLevel) != 0)
00173     {
00174         newElectronOccupancy.RemoveElectron(IonizedLevel,1);
00175     }
00176     else
00177     {
00178         G4String errMsg = "There is no electron on the orbit " + G4UIcommand::ConvertToString(IonizedLevel) +
00179                           " you want to free. The molecule's name you want to ionized is "+ GetName();
00180         G4Exception("G4Molecule::IonizeMolecule","",FatalErrorInArgument, errMsg);
00181         PrintState();
00182     }
00183 
00184     // PrintState();
00185 
00186     return ChangeConfiguration(newElectronOccupancy);
00187 }

G4MolecularConfiguration * G4MolecularConfiguration::MoveOneElectron ( G4int  ,
G4int   
)

Move one electron from an orbit to another.

Definition at line 215 of file G4MolecularConfiguration.cc.

References AddElectron(), ChangeConfiguration(), G4UIcommand::ConvertToString(), FatalErrorInArgument, fElectronOccupancy, G4Exception(), GetName(), PrintState(), and RemoveElectron().

Referenced by G4Molecule::MoveOneElectron().

00216 {
00217     G4ElectronOccupancy newElectronOccupancy (*fElectronOccupancy);
00218 
00219     if(newElectronOccupancy . GetOccupancy(orbitToFree)>=1)
00220     {
00221         newElectronOccupancy . RemoveElectron(orbitToFree,1);
00222         newElectronOccupancy . AddElectron(orbitToFill,1);
00223     }
00224     else
00225     {
00226         G4String errMsg = "There is no electron on the orbit " + G4UIcommand::ConvertToString(orbitToFree) +
00227                           " you want to free. The molecule's name is "+ GetName();
00228         G4Exception("G4Molecule::MoveOneElectron","",FatalErrorInArgument, errMsg);
00229         PrintState();
00230     }
00231 
00232     return ChangeConfiguration(newElectronOccupancy);
00233 }

G4MolecularConfiguration & G4MolecularConfiguration::operator= ( G4MolecularConfiguration &  right  )  [protected]

Definition at line 147 of file G4MolecularConfiguration.cc.

00148 {
00149     if (&right==this) return *this;
00150     return *this;
00151 }

void G4MolecularConfiguration::PrintState (  )  const

Show the electronic state of the molecule.

Definition at line 258 of file G4MolecularConfiguration.cc.

References G4ElectronOccupancy::DumpInfo(), fElectronOccupancy, fMoleculeDefinition, G4cout, G4endl, G4MoleculeDefinition::GetDecayTable(), G4MoleculeDefinition::GetGroundStateElectronOccupancy(), and GetName().

Referenced by IonizeMolecule(), MoveOneElectron(), G4Molecule::PrintState(), and RemoveElectron().

00259 {
00260     G4cout<<"--------------Print electronic state of "<<GetName()<<"---------------"<<G4endl;
00261     fElectronOccupancy->DumpInfo();
00262     if(fElectronOccupancy==fMoleculeDefinition->GetGroundStateElectronOccupancy())
00263     {
00264         G4cout<<"At ground state"<<G4endl;
00265     }
00266     else
00267     {
00268         if(fMoleculeDefinition->GetDecayTable())
00269             G4cout<<"Transition :"<<(fMoleculeDefinition->GetDecayTable())->GetExcitedState(fElectronOccupancy)<<G4endl;
00270     }
00271 }

G4MolecularConfiguration * G4MolecularConfiguration::RemoveElectron ( G4int  ,
G4int  number = 1 
)

Remove n electrons to a given orbit.

Definition at line 196 of file G4MolecularConfiguration.cc.

References ChangeConfiguration(), G4UIcommand::ConvertToString(), fElectronOccupancy, G4Exception(), GetName(), G4ElectronOccupancy::GetOccupancy(), JustWarning, PrintState(), and G4ElectronOccupancy::RemoveElectron().

Referenced by MoveOneElectron(), and G4Molecule::RemoveElectron().

00197 {
00198     G4ElectronOccupancy newElectronOccupancy (*fElectronOccupancy);
00199 
00200     if(newElectronOccupancy.GetOccupancy(orbit) != 0)
00201     {
00202         newElectronOccupancy.RemoveElectron(orbit, number );
00203     }
00204     else
00205     {
00206         G4String errMsg = "There is already no electron into the orbit " + G4UIcommand::ConvertToString(orbit) +
00207                           " you want to free. The molecule's name is "+ GetName();
00208         G4Exception("G4Molecule::RemoveElectron","",JustWarning, errMsg);
00209         PrintState();
00210     }
00211 
00212     return ChangeConfiguration(newElectronOccupancy);
00213 }

void G4MolecularConfiguration::SetDecayTime ( G4double   )  [inline]

Set the decay time of the molecule.

Definition at line 255 of file G4MolecularConfiguration.hh.

References fDynDecayTime.

Referenced by G4MoleculeDefinition::AddeConfToExcitedState(), and G4Molecule::SetDecayTime().

00256 {
00257     fDynDecayTime = dynDecayTime;
00258 }

void G4MolecularConfiguration::SetDiffusionCoefficient ( G4double   )  [inline]

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 245 of file G4MolecularConfiguration.hh.

References fDynDiffusionCoefficient.

Referenced by G4Molecule::SetDiffusionCoefficient().

00246 {
00247     fDynDiffusionCoefficient = dynDiffusionCoefficient ;
00248 }

void G4MolecularConfiguration::SetMass ( G4double   )  [inline]

Set the total mass of the molecule.

Definition at line 280 of file G4MolecularConfiguration.hh.

References fDynMass.

Referenced by G4Molecule::SetMass().

00281 {
00282     fDynMass = aMass ;
00283 }

void G4MolecularConfiguration::SetVanDerVaalsRadius ( G4double   )  [inline]

The Van Der Valls Radius of the molecule

Definition at line 265 of file G4MolecularConfiguration.hh.

References fDynVanDerVaalsRadius.

Referenced by G4Molecule::SetVanDerVaalsRadius().

00266 {
00267     fDynVanDerVaalsRadius = dynVanDerVaalsRadius ;
00268 }

Field Documentation

G4int G4MolecularConfiguration::fDynCharge [protected]

Definition at line 190 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), GetCharge(), and GetName().

G4double G4MolecularConfiguration::fDynDecayTime [protected]

Definition at line 188 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), GetDecayTime(), and SetDecayTime().

G4double G4MolecularConfiguration::fDynDiffusionCoefficient [protected]

Definition at line 186 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), GetDiffusionCoefficient(), and SetDiffusionCoefficient().

G4double G4MolecularConfiguration::fDynMass [protected]

Definition at line 189 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), GetMass(), and SetMass().

G4double G4MolecularConfiguration::fDynVanDerVaalsRadius [protected]

Definition at line 187 of file G4MolecularConfiguration.hh.

Referenced by G4MolecularConfiguration(), GetVanDerVaalsRadius(), and SetVanDerVaalsRadius().

const G4ElectronOccupancy* G4MolecularConfiguration::fElectronOccupancy [protected]

Definition at line 171 of file G4MolecularConfiguration.hh.

Referenced by AddElectron(), ExciteMolecule(), G4MolecularConfiguration(), GetDecayChannel(), GetElectronOccupancy(), GetNbElectrons(), IonizeMolecule(), MoveOneElectron(), PrintState(), RemoveElectron(), and ~G4MolecularConfiguration().

G4MolecularConfiguration::G4MolecularConfigurationManager * G4MolecularConfiguration::fgManager = 0 [static, protected]

Definition at line 182 of file G4MolecularConfiguration.hh.

Referenced by ChangeConfiguration(), DeleteManager(), G4MolecularConfiguration(), and GetManager().

const G4MoleculeDefinition* G4MolecularConfiguration::fMoleculeDefinition [protected]

Definition at line 170 of file G4MolecularConfiguration.hh.

Referenced by ChangeConfiguration(), G4MolecularConfiguration(), GetAtomsNumber(), GetDecayChannel(), GetDefinition(), GetMoleculeID(), GetName(), and PrintState().

G4String G4MolecularConfiguration::fName [mutable, protected]

Definition at line 191 of file G4MolecularConfiguration.hh.

Referenced by GetName().

The documentation for this class was generated from the following files:
Generated on Mon May 27 17:52:30 2013 for Geant4 by  doxygen 1.4.7