ScoreSpecies Class Reference

#include <ScoreSpecies.hh>

Inheritance diagram for ScoreSpecies:

Collaboration diagram for ScoreSpecies:

Classes
struct	SpeciesInfo

Public Member Functions
	ScoreSpecies (G4String name, G4int depth=0)
virtual	~ScoreSpecies ()
void	AddTimeToRecord (double time)
void	ClearTimeToRecord ()
int	GetNumberOfRecordedEvents () const
void	ASCII ()
void	WriteWithAnalysisManager (G4VAnalysisManager *)
virtual void	Initialize (G4HCofThisEvent *)
virtual void	EndOfEvent (G4HCofThisEvent *)
virtual void	clear ()
virtual void	DrawAll ()
virtual void	PrintAll ()
virtual void	AbsorbResultsFromWorkerScorer (G4VPrimitiveScorer *)
virtual void	OutputAndClear ()
SpeciesMap	GetSpeciesInfo ()
Public Member Functions inherited from G4VPrimitiveScorer
	G4VPrimitiveScorer (G4String name, G4int depth=0)
virtual	~G4VPrimitiveScorer ()
G4int	GetCollectionID (G4int)
void	SetUnit (const G4String &unit)
const G4String &	GetUnit () const
G4double	GetUnitValue () const
void	SetMultiFunctionalDetector (G4MultiFunctionalDetector *d)
G4MultiFunctionalDetector *	GetMultiFunctionalDetector () const
G4String	GetName () const
void	SetFilter (G4VSDFilter *f)
G4VSDFilter *	GetFilter () const
void	SetVerboseLevel (G4int vl)
G4int	GetVerboseLevel () const
void	SetNijk (G4int i, G4int j, G4int k)

Protected Member Functions
virtual G4bool	ProcessHits (G4Step *, G4TouchableHistory *)
Protected Member Functions inherited from G4VPrimitiveScorer
virtual G4int	GetIndex (G4Step *)
void	CheckAndSetUnit (const G4String &unit, const G4String &category)

Additional Inherited Members
Protected Attributes inherited from G4VPrimitiveScorer
G4String	primitiveName
G4MultiFunctionalDetector *	detector
G4VSDFilter *	filter
G4int	verboseLevel
G4int	indexDepth
G4String	unitName
G4double	unitValue
G4int	fNi
G4int	fNj
G4int	fNk

Detailed Description

This is a primitive scorer class for molecular species. The number of species is recorded for all times (predetermined or user chosen). It also scores the energy deposition in order to compute the radiochemical yields.

Definition at line 56 of file ScoreSpecies.hh.

Constructor & Destructor Documentation

ScoreSpecies::ScoreSpecies	(	G4String	name,
		G4int	depth = 0
	)

Definition at line 62 of file ScoreSpecies.cc.

: G4VPrimitiveScorer(name,depth),
  fEdep(0),
  fOutputToRoot(true),
  fOutputToXml(false),
  fOutputToCsv(false),
  fHCID(-1),
  fEvtMap(0)
{
  fNEvent = 0;
  AddTimeToRecord(1 * CLHEP::picosecond);
  AddTimeToRecord(10 * CLHEP::picosecond);
  AddTimeToRecord(100 * CLHEP::picosecond);
  AddTimeToRecord(1000 * CLHEP::picosecond);
  AddTimeToRecord(10000 * CLHEP::picosecond);
  AddTimeToRecord(100000 * CLHEP::picosecond);
  AddTimeToRecord(999999 * CLHEP::picosecond);
  fEdep = 0;
}

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ScoreSpecies::~ScoreSpecies ( )

virtual

Definition at line 84 of file ScoreSpecies.cc.

{;}

Member Function Documentation

void ScoreSpecies::AbsorbResultsFromWorkerScorer ( G4VPrimitiveScorer *  workerScorer )

virtual

Method used in multithreading mode in order to merge the results

Definition at line 198 of file ScoreSpecies.cc.

{
  ScoreSpecies* right =
  dynamic_cast<ScoreSpecies*>(dynamic_cast<G4VPrimitiveScorer*>(workerScorer));

  if(right == 0)
  {
    return;
  }
  if(right == this)
  {
    return;
  }

  // G4cout<<"ScoreSpecies::AbsorbResultsFromWorkerScorer"<<G4endl;
  {
  SpeciesMap::iterator it_map1 = right->fSpeciesInfoPerTime.begin();
  SpeciesMap::iterator end_map1 = right->fSpeciesInfoPerTime.end();

  for(; it_map1 != end_map1; ++it_map1)
  {
    InnerSpeciesMap& map2 = it_map1->second;
    InnerSpeciesMap::iterator it_map2 = map2.begin();
    InnerSpeciesMap::iterator end_map2 = map2.end();

    for(; it_map2 != end_map2; ++it_map2)
    {
      SpeciesInfo& molInfo =
      fSpeciesInfoPerTime[it_map1->first][it_map2->first] ;
      molInfo.fNumber  += it_map2->second.fNumber;
      molInfo.fG += it_map2->second.fG;
      molInfo.fG2 += it_map2->second.fG2;

      //      G4cout << "In AbsorbeResultsFromWorkerScorer: fNumber "
      //             << molInfo.fNumber
      //             << " fG "
      //             << molInfo.fG
      //             << G4endl;
    }
  }
  }
  //---------------------------------------------------------
#ifdef _ScoreSpecies_FOR_ALL_EVENTS
  {
  SpeciesMapPerEvent::iterator it_map1 = right->fSpeciesInfoPerEvent.begin();
  SpeciesMapPerEvent::iterator end_map1 = right->fSpeciesInfoPerEvent.end();
  
  for(; it_map1 != end_map1; ++it_map1)
  {
    auto& map2 = it_map1->second;
    InnerSpeciesMapPerEvent::iterator it_map2 = map2.begin();
    InnerSpeciesMapPerEvent::iterator end_map2 = map2.end();
    
    for(; it_map2 != end_map2; ++it_map2)
    {
      SpeciesInfoSOA& molInfo =
      fSpeciesInfoPerEvent[it_map1->first][it_map2->first] ;
      molInfo.fNumber.insert(molInfo.fNumber.end(),
                             it_map2->second.fNumber.begin(),
                             it_map2->second.fNumber.end());
      molInfo.fG.insert(molInfo.fG.end(),
                        it_map2->second.fG.begin(),
                        it_map2->second.fG.end());
      molInfo.fG2.insert(molInfo.fG2.end(),
                         it_map2->second.fG2.begin(),
                         it_map2->second.fG2.end());
      molInfo.fEventID.insert(molInfo.fEventID.end(),
                         it_map2->second.fEventID.begin(),
                         it_map2->second.fEventID.end());
      // G4cout << "In AbsorbeResultsFromWorkerScorer: fNumber "
      //        << molInfo.fNumber
      //        << " fG "
      //        << molInfo.fG
      //        << G4endl;
    }
  }
  right->fSpeciesInfoPerEvent.clear();
  }
#endif
  
  fNEvent += right->fNEvent;
  right->fNEvent = 0;
  right->fEdep = 0.;
}

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void ScoreSpecies::AddTimeToRecord ( double  time )

inline

Add a time at which the number of species should be recorded. Default times are set up to 1 microsecond.

Definition at line 65 of file ScoreSpecies.hh.

  {
    fTimeToRecord.insert(time);
  }

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void ScoreSpecies::ASCII

(

)

Write results to an text file

Definition at line 319 of file ScoreSpecies.cc.

{
  std::ofstream out("Species.Txt");
  if(!out) return;

  out << "Time is in ns" << G4endl;

  for(auto it_map1: fSpeciesInfoPerTime)
  {
    InnerSpeciesMap& map2 = it_map1.second;

    out << it_map1.first << G4endl;

    for(auto it_map2: map2)
    {
      out << it_map2.first->GetName()<< " "
          << it_map2.second.fNumber << G4endl;
    }
  }

  out.close();
}

void ScoreSpecies::clear ( void  )

virtual

Reimplemented from G4VPrimitiveScorer.

Definition at line 285 of file ScoreSpecies.cc.

{
  fEvtMap->clear();
  fNEvent = 0;
  fEdep = 0;
  fSpeciesInfoPerTime.clear();
}

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void ScoreSpecies::ClearTimeToRecord ( )

inline

Remove all times to record, must be reset by user.

Definition at line 71 of file ScoreSpecies.hh.

  {
    fTimeToRecord.clear();
  }

void ScoreSpecies::DrawAll ( void  )

virtual

Reimplemented from G4VPrimitiveScorer.

Definition at line 295 of file ScoreSpecies.cc.

{;}

void ScoreSpecies::EndOfEvent ( G4HCofThisEvent *  )

virtual

Reimplemented from G4VPrimitiveScorer.

Definition at line 120 of file ScoreSpecies.cc.

{
  if(G4EventManager::GetEventManager()->GetConstCurrentEvent()->IsAborted())
  {
    fEdep = 0.;
    G4MoleculeCounter::Instance()->ResetCounter();
    return;
  }
  
  auto species = G4MoleculeCounter::Instance()->GetRecordedMolecules();

  if(species.get() == 0 || species->size() == 0)
  {
    G4cout << "No molecule recorded, energy deposited= "
           << G4BestUnit(fEdep, "Energy") << G4endl;
    ++fNEvent;
    fEdep = 0.;
    G4MoleculeCounter::Instance()->ResetCounter();
    return;
  }
  
  //  G4cout << "ScoreSpecies::EndOfEvent"<<G4endl;
//  G4cout << "End of event, deposited energy: "
//  << G4BestUnit(fEdep, "Energy") << G4endl;
  
#ifdef _ScoreSpecies_FOR_ALL_EVENTS
  int eventID=
  G4EventManager::GetEventManager()->GetConstCurrentEvent()->GetEventID();
#endif
  
  for(auto molecule: *species)
  {
    for(auto time_mol: fTimeToRecord)
    {
      double n_mol =
          G4MoleculeCounter::Instance()->GetNMoleculesAtTime(molecule,
                                                             time_mol);

      if(n_mol < 0)
      {
        G4cerr << "N molecules not valid < 0 " << G4endl;
        G4Exception("","N<0",FatalException,"");
      }

      SpeciesInfo& molInfo =
        fSpeciesInfoPerTime[time_mol][molecule];
      molInfo.fNumber += n_mol;
      double gValue = (n_mol/(fEdep/eV)) * 100.;
      molInfo.fG += gValue;
      molInfo.fG2 += gValue*gValue;
      
#ifdef _ScoreSpecies_FOR_ALL_EVENTS
      SpeciesInfoSOA& molInfoPerEvent =
        fSpeciesInfoPerEvent[time_mol][molecule];
      molInfoPerEvent.fNumber.push_back(n_mol);
      molInfoPerEvent.fG.push_back(gValue);
      molInfoPerEvent.fG2.push_back(gValue*gValue);
      molInfoPerEvent.fEventID.push_back(eventID);
#endif
      //      G4cout << "In Save molucule: fNumber " << molInfo.fNumber
      //            << " fG " << molInfo.fG
      //            << " fEdep " << fEdep/eV
      //            << G4endl;
    }
  }

  ++fNEvent;
  
//  G4cout << "End of event " << fNEvent
//         << ", energy deposited=" << G4BestUnit(fEdep, "Energy") << G4endl;
  
  fEdep = 0.;
  G4MoleculeCounter::Instance()->ResetCounter();
}

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int ScoreSpecies::GetNumberOfRecordedEvents ( ) const

inline

Get number of recorded events

Definition at line 77 of file ScoreSpecies.hh.

  {
    return fNEvent;
  }

SpeciesMap ScoreSpecies::GetSpeciesInfo ( )

inline

Definition at line 181 of file ScoreSpecies.hh.

{return fSpeciesInfoPerTime;}

void ScoreSpecies::Initialize ( G4HCofThisEvent *  HCE )

virtual

Reimplemented from G4VPrimitiveScorer.

Definition at line 105 of file ScoreSpecies.cc.

{
  fEvtMap = new G4THitsMap<G4double>(GetMultiFunctionalDetector()->GetName(),
                                    GetName());

  if(fHCID < 0)
  {
    fHCID = GetCollectionID(0);
  }

  HCE->AddHitsCollection(fHCID, (G4VHitsCollection*)fEvtMap);
}

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void ScoreSpecies::OutputAndClear ( )

virtual

Definition at line 344 of file ScoreSpecies.cc.

{
  if(G4Threading::IsWorkerThread()) return;

  //----------------------------------------------------------------------------
  // Save results

  G4VAnalysisManager* analysisManager(0);

  if(fOutputToCsv)
  {
    analysisManager = G4CsvAnalysisManager::Instance(); // TODO?
    // this->ASCII(); // useful ?
  }
  else  if (fOutputToRoot)
  {
    analysisManager = G4Root::G4AnalysisManager::Instance();
  }
  else if(fOutputToXml)
  {
    analysisManager = G4Xml::G4AnalysisManager::Instance();

  }
  if(analysisManager)
  {
    this->WriteWithAnalysisManager(analysisManager);
  }

  fNEvent = 0;
  fSpeciesInfoPerTime.clear();
}

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void ScoreSpecies::PrintAll ( void  )

virtual

Reimplemented from G4VPrimitiveScorer.

Definition at line 300 of file ScoreSpecies.cc.

{
   G4cout << " MultiFunctionalDet  " << detector->GetName() << G4endl;
   G4cout << " PrimitiveScorer " << GetName() << G4endl;
   G4cout << " Number of events " << fNEvent << G4endl;
   G4cout << " Number of energy deposition recorded "
          << fEvtMap->entries() << G4endl;
  
  for(auto itr : *fEvtMap->GetMap()) {
     G4cout << "  copy no.: " << itr.first
     << "  energy deposit: "
     << *(itr.second)/GetUnitValue()
     << " [" << GetUnit()<<"]"
     << G4endl;
   }
}

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G4bool ScoreSpecies::ProcessHits ( G4Step *  aStep, G4TouchableHistory *    )

protectedvirtual

Implements G4VPrimitiveScorer.

Definition at line 89 of file ScoreSpecies.cc.

{
  G4double edep = aStep->GetTotalEnergyDeposit();

  if ( edep == 0. ) return FALSE;

  edep *= aStep->GetPreStepPoint()->GetWeight(); // (Particle Weight)
  G4int  index = GetIndex(aStep);
  fEvtMap->add(index,edep);
  fEdep+=edep;

  return TRUE;
}

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void ScoreSpecies::WriteWithAnalysisManager

(

G4VAnalysisManager *

analysisManager

)

Write results to whatever chosen file format

Definition at line 379 of file ScoreSpecies.cc.

{
  //  G4cout << "ScoreSpecies::WriteWithAnalysisManager" << G4endl;
  analysisManager->OpenFile("Species.root");
  int fNtupleID = analysisManager->CreateNtuple("species", "species");
  analysisManager->CreateNtupleIColumn(fNtupleID, "speciesID");
  analysisManager->CreateNtupleIColumn(fNtupleID, "number");
  analysisManager->CreateNtupleIColumn(fNtupleID, "nEvent");
  analysisManager->CreateNtupleSColumn(fNtupleID, "speciesName");
  analysisManager->CreateNtupleDColumn(fNtupleID, "time");
  analysisManager->CreateNtupleDColumn(fNtupleID, "sumG");
  analysisManager->CreateNtupleDColumn(fNtupleID, "sumG2");
  analysisManager->FinishNtuple(fNtupleID);

  for(auto it_map1: fSpeciesInfoPerTime)
  {
    InnerSpeciesMap& map2 = it_map1.second;

    for(auto it_map2 : map2)
    {
      double time = it_map1.first;
      const Species& species = it_map2.first;
      const G4String& name = species->GetName();
      int molID = it_map2.first->GetMoleculeID();
      int number = it_map2.second.fNumber;
      double G = it_map2.second.fG;
      double G2 = it_map2.second.fG2;

      analysisManager->FillNtupleIColumn(fNtupleID, 0, molID);  // MolID
      analysisManager->FillNtupleIColumn(fNtupleID, 1, number); // Number
      analysisManager->FillNtupleIColumn(fNtupleID,
                                         2, fNEvent); // Total nb events
      analysisManager->FillNtupleSColumn(fNtupleID, 3, name);   // molName
      analysisManager->FillNtupleDColumn(fNtupleID, 4, time);   // time
      analysisManager->FillNtupleDColumn(fNtupleID, 5, G);      // G
      analysisManager->FillNtupleDColumn(fNtupleID, 6, G2);     // G2
      analysisManager->AddNtupleRow(fNtupleID);
    }
  }
  
  //----------------------------------------------------------------------------
  
#ifdef _ScoreSpecies_FOR_ALL_EVENTS
  fNtupleID = analysisManager->CreateNtuple("species_all", "species_all");
  analysisManager->CreateNtupleIColumn(fNtupleID, "speciesID");
  analysisManager->CreateNtupleIColumn(fNtupleID, "number");
  analysisManager->CreateNtupleIColumn(fNtupleID, "nEvent");
  analysisManager->CreateNtupleSColumn(fNtupleID, "speciesName");
  analysisManager->CreateNtupleDColumn(fNtupleID, "time");
  analysisManager->CreateNtupleDColumn(fNtupleID, "G");
  analysisManager->CreateNtupleDColumn(fNtupleID, "G2");
  analysisManager->CreateNtupleIColumn(fNtupleID, "eventID");
  analysisManager->FinishNtuple(fNtupleID);
  
  for(auto it_map1: fSpeciesInfoPerEvent)
  {
    InnerSpeciesMapPerEvent& map2 = it_map1.second;
    
    for(auto it_map2 : map2)
    {
      double time = it_map1.first;
      const Species& species = it_map2.first;
      const G4String& name = species->GetName();
      int molID = it_map2.first->GetMoleculeID();
      
      size_t nG = it_map2.second.fG.size();
      
      for(size_t i=0; i<nG;++i){
        int number = it_map2.second.fNumber[i];
        double G = it_map2.second.fG[i];
        double G2 = it_map2.second.fG2[i];
        int eventID = it_map2.second.fEventID[i];
        
        analysisManager->FillNtupleIColumn(fNtupleID, 0, molID);   // MolID
        analysisManager->FillNtupleIColumn(fNtupleID, 1, number);  // Number
        analysisManager->FillNtupleIColumn(fNtupleID,
                                           2, fNEvent);       // Total nb events
        analysisManager->FillNtupleSColumn(fNtupleID, 3, name);    // molName
        analysisManager->FillNtupleDColumn(fNtupleID, 4, time);    // time
        analysisManager->FillNtupleDColumn(fNtupleID, 5, G);       // G
        analysisManager->FillNtupleDColumn(fNtupleID, 6, G2);      // G2
        analysisManager->FillNtupleIColumn(fNtupleID, 7, eventID); // EventID
        analysisManager->AddNtupleRow(fNtupleID);
      }
    }
  }
#endif
  
  analysisManager->Write();
  analysisManager->CloseFile();
}

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---

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

• source/geant4.10.03.p03/examples/extended/medical/dna/chem4/include/ScoreSpecies.hh
• source/geant4.10.03.p03/examples/extended/medical/dna/chem4/src/ScoreSpecies.cc