G4DNAMolecularReaction Class Reference

#include <G4DNAMolecularReaction.hh>

Inheritance diagram for G4DNAMolecularReaction:

Collaboration diagram for G4DNAMolecularReaction:

Public Member Functions
	G4DNAMolecularReaction ()
virtual	~G4DNAMolecularReaction ()
	G4DNAMolecularReaction (const G4DNAMolecularReaction &other)
G4DNAMolecularReaction &	operator= (const G4DNAMolecularReaction &other)
virtual G4bool	TestReactibility (const G4Track &, const G4Track &, const double currentStepTime, const double previousStepTime, bool userStepTimeLimit)
virtual G4ITReactionChange *	MakeReaction (const G4Track &, const G4Track &)
void	SetReactionModel (G4VDNAReactionModel *)
void	SetReactionTable (const G4DNAMolecularReactionTable *)
void	SetVerbose (int)
Public Member Functions inherited from G4VITReactionProcess
	G4VITReactionProcess ()
virtual	~G4VITReactionProcess ()
	G4VITReactionProcess (const G4VITReactionProcess &other)
G4VITReactionProcess &	operator= (const G4VITReactionProcess &other)
virtual void	Initialize ()
virtual G4bool	IsApplicable (G4ITType, G4ITType) const
void	SetReactionTable (const G4ITReactionTable *)
void	ResetChanges ()

Protected Attributes
const G4DNAMolecularReactionTable *&	fMolReactionTable
G4VDNAReactionModel *	fReactionModel
G4int	fVerbose
G4double	fReactionRadius
G4double	fDistance
Protected Attributes inherited from G4VITReactionProcess
const G4ITReactionTable *	fpReactionTable
G4ITReactionChange *	fpChanges
G4String	fName

Detailed Description

G4DNAMolecularReaction is the reaction process used in G4DNAMolecularStepByStepModel between two molecules. After the global track steps, it test whether the molecules can react. If so, the reaction is made.

Definition at line 64 of file G4DNAMolecularReaction.hh.

Constructor & Destructor Documentation

G4DNAMolecularReaction::G4DNAMolecularReaction

(

)

Default constructor

Definition at line 48 of file G4DNAMolecularReaction.cc.

                                               :
    G4VITReactionProcess(),
    fMolReactionTable(
        reference_cast<const G4DNAMolecularReactionTable*>(fpReactionTable))
{
  //ctor
  fVerbose = 0;
  fReactionModel = 0;
  fReactionRadius = -1;
  fDistance = -1;
}

G4DNAMolecularReaction::~G4DNAMolecularReaction ( )

virtual

Default destructor

Definition at line 60 of file G4DNAMolecularReaction.cc.

{
  //dtor
  if (fpChanges) delete fpChanges;
}

G4DNAMolecularReaction::G4DNAMolecularReaction

(

const G4DNAMolecularReaction &

other

)

Copy constructor

Parameters

other

Object to copy from

Definition at line 66 of file G4DNAMolecularReaction.cc.

                                                                                  :
    G4VITReactionProcess(other),
    fMolReactionTable(
        reference_cast<const G4DNAMolecularReactionTable*>(fpReactionTable))
{
  //copy ctor
  fVerbose = other.fVerbose;
  fMolReactionTable = other.fMolReactionTable;
  fReactionModel = 0;
  fReactionRadius = -1;
  fDistance = -1;
}

Member Function Documentation

G4ITReactionChange * G4DNAMolecularReaction::MakeReaction ( const G4Track &  trackA, const G4Track &  trackB  )

virtual

Will generate the products of the two given tracks

Implements G4VITReactionProcess.

Definition at line 160 of file G4DNAMolecularReaction.cc.

{
  fpChanges = new G4ITReactionChange();
  fpChanges->Initialize(trackA, trackB);

  G4MolecularConfiguration* moleculeA =
      GetMolecule(trackA)->GetMolecularConfiguration();
  G4MolecularConfiguration* moleculeB =
      GetMolecule(trackB)->GetMolecularConfiguration();

#ifdef G4VERBOSE
  // DEBUG
  if (fVerbose)
  {
    G4cout << "G4DNAMolecularReaction::MakeReaction" << G4endl;
    G4cout<<"TrackA n°" << trackA.GetTrackID()
    <<"\t | Track B n°" << trackB.GetTrackID() << G4endl;

    G4cout<<"Track A : Position : " << G4BestUnit(trackA.GetPosition(),"Length")
    <<"\t Global Time : " << G4BestUnit(trackA.GetGlobalTime(), "Time")<< G4endl;

    G4cout<<"Track B : Position : " << G4BestUnit(trackB.GetPosition() ,"Length")
    <<"\t Global Time : " << G4BestUnit(trackB.GetGlobalTime(), "Time")<< G4endl;

    G4cout<<"Reaction range : " << G4BestUnit(fReactionRadius,"Length")
    << " \t Separation distance : " << G4BestUnit(fDistance,"Length")<< G4endl;
    G4cout << "--------------------------------------------" << G4endl;
  }
#endif

  const G4DNAMolecularReactionData* reactionData = fMolReactionTable
      ->GetReactionData(moleculeA, moleculeB);

  G4int nbProducts = reactionData->GetNbProducts();

  if (nbProducts)
  {
    G4double D1 = moleculeA->GetDiffusionCoefficient();
    G4double D2 = moleculeB->GetDiffusionCoefficient();
    G4double sqrD1 = sqrt(D1);
    G4double sqrD2 = sqrt(D2);
    G4double numerator = sqrD1 + sqrD2;
    G4ThreeVector reactionSite = sqrD1 / numerator * trackA.GetPosition()
        + sqrD2 / numerator * trackB.GetPosition();

    for (G4int j = 0; j < nbProducts; j++)
    {
      G4Molecule* product = new G4Molecule(reactionData->GetProduct(j));
      G4Track* productTrack = product->BuildTrack(trackA.GetGlobalTime(),
                                                  reactionSite);

//            G4cout << ">> G4DNAMolecularReaction::MakeReaction " << G4endl
//                  << "\t track A ("<< trackA.GetTrackID() <<"): " << trackA.GetGlobalTime() << G4endl
//                  << "\t track B ("<< trackB.GetTrackID() <<"): " << trackB.GetGlobalTime() << G4endl;

      productTrack->SetTrackStatus(fAlive);

      fpChanges->AddSecondary(productTrack);
      G4MoleculeFinder::Instance()->Push(productTrack);
    }
  }

  fpChanges->KillParents(true);

  return fpChanges;
}

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G4DNAMolecularReaction & G4DNAMolecularReaction::operator=

(

const G4DNAMolecularReaction &

other

)

Assignment operator

Parameters

other

Object to assign from

Returns

A reference to this

Definition at line 79 of file G4DNAMolecularReaction.cc.

{
  if (this == &rhs) return *this; // handle self assignment

  fVerbose = rhs.fVerbose;
  fMolReactionTable = rhs.fMolReactionTable;
  fReactionRadius = -1;
  fDistance = -1;

  //assignment operator
  return *this;
}

void G4DNAMolecularReaction::SetReactionModel ( G4VDNAReactionModel *  model )

inline

Definition at line 111 of file G4DNAMolecularReaction.hh.

{
    fReactionModel = model;
}

void G4DNAMolecularReaction::SetReactionTable ( const G4DNAMolecularReactionTable *  )

inline

void G4DNAMolecularReaction::SetVerbose ( int  verb )

inline

Definition at line 116 of file G4DNAMolecularReaction.hh.

{
    fVerbose = verb;
}

G4bool G4DNAMolecularReaction::TestReactibility ( const G4Track &  trackA, const G4Track &  trackB, const double  currentStepTime, const double  previousStepTime, bool  userStepTimeLimit  )

virtual

Given two tracks, it tells you whether they can react

Implements G4VITReactionProcess.

Definition at line 92 of file G4DNAMolecularReaction.cc.

{
  G4MolecularConfiguration* moleculeA =
      GetMolecule(trackA)->GetMolecularConfiguration();
  G4MolecularConfiguration* moleculeB =
      GetMolecule(trackB)->GetMolecularConfiguration();

  if (!fReactionModel)
  {
    G4ExceptionDescription exceptionDescription(
        "You have to give a reaction model to the molecular reaction process");
    G4Exception("G4DNAMolecularReaction::TestReactibility",
                "MolecularReaction001", FatalErrorInArgument,
                exceptionDescription);
    return false; // makes coverity happy
  }
  if (fMolReactionTable == 0)
  {
    G4ExceptionDescription exceptionDescription(
        "You have to give a reaction table to the molecular reaction process");
    G4Exception("G4DNAMolecularReaction::TestReactibility",
                "MolecularReaction002", FatalErrorInArgument,
                exceptionDescription);
    return false; // makes coverity happy
  }

  // Retrieve reaction range
  fReactionRadius = -1; // reaction Range
  fReactionRadius = fReactionModel->GetReactionRadius(moleculeA, moleculeB);

  fDistance = -1; // separation distance

  if (currentStepTime == 0.)
  {
    userStepTimeLimit = false;
  }

  G4bool output = fReactionModel->FindReaction(trackA, trackB, fReactionRadius,
                                               fDistance, userStepTimeLimit);

#ifdef G4VERBOSE
  //    DEBUG
  if (fVerbose > 1)
  {
    G4cout << "\033[1;39;36m" << "G4MolecularReaction " << G4endl;
    G4cout << "FindReaction returned : " << G4BestUnit(output,"Length") << G4endl;
    G4cout << " reaction radius : " << G4BestUnit(fReactionRadius,"Length")
    << " real distance : " << G4BestUnit((trackA.GetPosition() - trackB.GetPosition()).mag(), "Length")
    << " calculated distance by model (= -1 if real distance > reaction radius and the user limitation step is not reached) : "
    << G4BestUnit(fDistance,"Length")
    << G4endl;

    G4cout << "TrackID A : " << trackA.GetTrackID()
    << ", TrackID B : " << trackB.GetTrackID()
    << " | MolA " << moleculeA->GetName()
    << ", MolB " << moleculeB->GetName()
    <<"\033[0m\n"
    << G4endl;
    G4cout << "--------------------------------------------" << G4endl;
  }
#endif
  return output;
}

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Member Data Documentation

G4double G4DNAMolecularReaction::fDistance

protected

Definition at line 107 of file G4DNAMolecularReaction.hh.

const G4DNAMolecularReactionTable*& G4DNAMolecularReaction::fMolReactionTable

protected

Definition at line 103 of file G4DNAMolecularReaction.hh.

G4VDNAReactionModel* G4DNAMolecularReaction::fReactionModel

protected

Definition at line 104 of file G4DNAMolecularReaction.hh.

G4double G4DNAMolecularReaction::fReactionRadius

protected

Definition at line 106 of file G4DNAMolecularReaction.hh.

G4int G4DNAMolecularReaction::fVerbose

protected

Definition at line 105 of file G4DNAMolecularReaction.hh.

---

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

• geant4.10.03.p01/source/processes/electromagnetic/dna/models/include/G4DNAMolecularReaction.hh
• geant4.10.03.p01/source/processes/electromagnetic/dna/models/src/G4DNAMolecularReaction.cc