G4DNAMolecularReaction.cc

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// $Id: G4DNAMolecularReaction.cc 64057 2012-10-30 15:04:49Z gcosmo $
//
// Author: Mathieu Karamitros ([email protected])
//
// WARNING : This class is released as a prototype.
// It might strongly evolve or even disapear in the next releases.
//
// History:
// -----------
// 10 Oct 2011 M.Karamitros created
//
// -------------------------------------------------------------------
 
#include "G4DNAMolecularReaction.hh"
#include "G4DNAMolecularReactionTable.hh"
#include "G4VDNAReactionModel.hh"
#include "G4ITManager.hh"
#include "G4UnitsTable.hh"
 
using namespace std;
 
G4DNAMolecularReaction::G4DNAMolecularReaction():G4VITReactionProcess(),
    fMolReactionTable(reference_cast<const G4DNAMolecularReactionTable*>(fpReactionTable))
{
    //ctor
    fVerbose        = 0;
    fReactionModel  = 0;
    fReactionRadius = -1;
    fDistance       = -1;
}
 
G4DNAMolecularReaction::~G4DNAMolecularReaction()
{
    //dtor
    if(fpChanges) delete fpChanges;
}
 
G4DNAMolecularReaction::G4DNAMolecularReaction(const G4DNAMolecularReaction& other):G4VITReactionProcess(other),
    fMolReactionTable(reference_cast<const G4DNAMolecularReactionTable*>(fpReactionTable))
{
    //copy ctor
    fVerbose            = other.fVerbose ;
    fMolReactionTable   = other.fMolReactionTable;
    fReactionModel      = 0;
    fReactionRadius     = -1;
    fDistance           = -1;
}
 
G4DNAMolecularReaction& G4DNAMolecularReaction::operator=(const G4DNAMolecularReaction& rhs)
{
    if (this == &rhs) return *this; // handle self assignment
 
    fVerbose            = rhs.fVerbose ;
    fMolReactionTable   = rhs.fMolReactionTable;
    fReactionRadius     = -1;
    fDistance           = -1;
 
    //assignment operator
    return *this;
}
 
G4bool G4DNAMolecularReaction::TestReactibility(const G4Track& trackA,
                                                const G4Track& trackB,
                                                const double currentStepTime,
                                                const double /*previousStepTime*/,
                                                bool userStepTimeLimit) /*const*/
{
    G4Molecule* moleculeA = GetMolecule(trackA);
    G4Molecule* moleculeB = GetMolecule(trackB);
 
    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 ;
}
 
 
G4ITReactionChange* G4DNAMolecularReaction::MakeReaction(const G4Track& trackA, const G4Track& trackB)
{
    fpChanges = new G4ITReactionChange();
    fpChanges->Initialize(trackA, trackB);
 
    G4Molecule* moleculeA = GetMolecule(trackA);
    G4Molecule* moleculeB = GetMolecule(trackB);
 
#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);
 
            productTrack->SetTrackStatus(fAlive);
 
            fpChanges->AddSecondary(productTrack);
            G4ITManager<G4Molecule>::Instance()->Push(productTrack);
        }
    }
 
    fpChanges->KillParents(true);
 
    return fpChanges;
}