G4DNASmoluchowskiReactionModel Class Reference

#include <G4DNASmoluchowskiReactionModel.hh>

Inheritance diagram for G4DNASmoluchowskiReactionModel:

Public Member Functions
	G4DNASmoluchowskiReactionModel ()
virtual	~G4DNASmoluchowskiReactionModel ()
	G4DNASmoluchowskiReactionModel (const G4DNASmoluchowskiReactionModel &)
virtual void	Initialise (const G4Molecule *, const G4Track &)
virtual void	InitialiseToPrint (const G4Molecule *)
virtual G4double	GetReactionRadius (const G4Molecule *, const G4Molecule *)
virtual G4double	GetReactionRadius (const G4int)
virtual G4bool	FindReaction (const G4Track &, const G4Track &, const G4double, G4double &, const G4bool)
Public Member Functions inherited from G4VDNAReactionModel
	G4VDNAReactionModel ()
	G4VDNAReactionModel (const G4VDNAReactionModel &)
virtual	~G4VDNAReactionModel ()
void	SetReactionTable (const G4DNAMolecularReactionTable *)
const G4DNAMolecularReactionTable *	GetReactionTable ()

Additional Inherited Members
Protected Member Functions inherited from G4VDNAReactionModel
G4VDNAReactionModel &	operator= (const G4VDNAReactionModel &)
Protected Attributes inherited from G4VDNAReactionModel
const G4DNAMolecularReactionTable *	fReactionTable

Detailed Description

G4DNASmoluchowskiReactionModel should be used for very fast reactions (high reaction rate) : the reactions between reactants occuring at encounter. When the time step is constrained this model uses brownian bridge : "Absorbing (Smoluchowski) boundary condition" Reference : On the simulation of diffusion processes close to boundaries, N. J. B. Green, Molecular Physics, 65: 6, 1399 — 1408(1988)

Definition at line 58 of file G4DNASmoluchowskiReactionModel.hh.

Constructor & Destructor Documentation

G4DNASmoluchowskiReactionModel::G4DNASmoluchowskiReactionModel

(

)

Definition at line 34 of file G4DNASmoluchowskiReactionModel.cc.

                                                               : G4VDNAReactionModel()
{
    fReactionData = 0 ;
}

G4DNASmoluchowskiReactionModel::~G4DNASmoluchowskiReactionModel ( )

virtual

Definition at line 52 of file G4DNASmoluchowskiReactionModel.cc.

{
    fReactionData = 0 ;
}

G4DNASmoluchowskiReactionModel::G4DNASmoluchowskiReactionModel

(

const G4DNASmoluchowskiReactionModel &

__right

)

Definition at line 39 of file G4DNASmoluchowskiReactionModel.cc.

                                                                                                            :
    G4VDNAReactionModel(__right)
{
    fReactionData = 0 ;
}

Member Function Documentation

G4bool G4DNASmoluchowskiReactionModel::FindReaction ( const G4Track &  __trackA, const G4Track &  __trackB, const G4double  __R, G4double &  __r, const G4bool  __alongStepReaction  )

virtual

Implements G4VDNAReactionModel.

Definition at line 80 of file G4DNASmoluchowskiReactionModel.cc.

References FatalErrorInArgument, G4BestUnit, G4endl, G4Exception(), G4UniformRand, G4Step::GetDeltaTime(), G4Molecule::GetDiffusionCoefficient(), GetMolecule(), G4Molecule::GetName(), G4StepPoint::GetPosition(), G4Track::GetPosition(), G4Step::GetPreStepPoint(), G4Track::GetStep(), and G4Track::GetTrackID().

{
    G4double __postStepSeparation = 0;
    bool __do_break = false ;
    G4double __R2 = __R*__R ;
    int k = 0 ;

    for(; k < 3 ; k++)
    {
        __postStepSeparation += std::pow(__trackA.GetPosition()[k] - __trackB.GetPosition()[k],2);

        if(__postStepSeparation > __R2)
        {
            __do_break = true  ;
            break ;
        }
    }

    if(__do_break == false)
    {
         // The loop was not break
         // => __r^2 < __R^2
        __r = std::sqrt(__postStepSeparation);
        return true;
    }
    else if(__alongStepReaction == true)
    {
        //G4cout << "alongStepReaction==true" << G4endl;
        //Along step cheack and
        // the loop has break

        // Continue loop
        for(; k < 3 ; k++)
        {
            __postStepSeparation += std::pow(__trackA.GetPosition()[k] - __trackB.GetPosition()[k],2);
        }
        // Use Green approach : the Brownian bridge
        __r = (__postStepSeparation = std::sqrt(__postStepSeparation) );

        G4Molecule* __moleculeA = GetMolecule(__trackA);
        G4Molecule* __moleculeB = GetMolecule(__trackB);

        G4double __D = __moleculeA->GetDiffusionCoefficient() + __moleculeB->GetDiffusionCoefficient();

        G4ThreeVector __preStepPositionA = __trackA.GetStep()->GetPreStepPoint() ->GetPosition();
        G4ThreeVector __preStepPositionB = __trackB.GetStep()->GetPreStepPoint() ->GetPosition();

        if(__preStepPositionA == __trackA.GetPosition())
        {
            G4ExceptionDescription exceptionDescription ;
            exceptionDescription << "The molecule : " <<  __moleculeA->GetName();
            exceptionDescription << " with track ID :" <<  __trackA.GetTrackID();
            exceptionDescription << " did not move since the previous step." << G4endl;
            exceptionDescription << "Current position : " << G4BestUnit(__trackA.GetPosition(),"Length") << G4endl;
            exceptionDescription << "Previous position : " << G4BestUnit(__preStepPositionA,"Length") << G4endl;
            G4Exception("G4DNASmoluchowskiReactionModel::FindReaction","G4DNASmoluchowskiReactionModel",
                        FatalErrorInArgument,exceptionDescription);
        }

        G4double __preStepSeparation = (__preStepPositionA - __preStepPositionB).mag();

        G4double __probabiltyOfEncounter =  std::exp(-(__preStepSeparation - __R)*(__postStepSeparation - __R)
                                        / (__D* (__trackB.GetStep()->GetDeltaTime())));
        G4double __selectedPOE = G4UniformRand();

        if(__selectedPOE<=__probabiltyOfEncounter)  return true;
    }

    return false ;
}

G4double G4DNASmoluchowskiReactionModel::GetReactionRadius ( const G4Molecule *  mol1, const G4Molecule *  mol2  )

virtual

Implements G4VDNAReactionModel.

Definition at line 67 of file G4DNASmoluchowskiReactionModel.cc.

References G4VDNAReactionModel::fReactionTable.

{
    G4double __output = fReactionTable -> GetReactionData(mol1,mol2)->GetReducedReactionRadius();
    return  __output ;
}

G4double G4DNASmoluchowskiReactionModel::GetReactionRadius ( const G4int  __i )

virtual

Implements G4VDNAReactionModel.

Definition at line 74 of file G4DNASmoluchowskiReactionModel.cc.

{
    G4double __output = (*fReactionData)[__i] -> GetReducedReactionRadius();
    return  __output ;
}

void G4DNASmoluchowskiReactionModel::Initialise ( const G4Molecule *  , const G4Track &    )

virtual

This macro is defined in AddClone_def

Reimplemented from G4VDNAReactionModel.

Definition at line 57 of file G4DNASmoluchowskiReactionModel.cc.

References G4VDNAReactionModel::fReactionTable, and G4DNAMolecularReactionTable::GetReactionData().

{
    fReactionData = fReactionTable->GetReactionData(__molecule);
}

void G4DNASmoluchowskiReactionModel::InitialiseToPrint ( const G4Molecule *  __molecule )

virtual

Implements G4VDNAReactionModel.

Definition at line 62 of file G4DNASmoluchowskiReactionModel.cc.

References G4VDNAReactionModel::fReactionTable, and G4DNAMolecularReactionTable::GetReactionData().

{
    fReactionData = fReactionTable->GetReactionData(__molecule);
}

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

• G4DNASmoluchowskiReactionModel.hh
• G4DNASmoluchowskiReactionModel.cc