G4DNASmoluchowskiReactionModel Class Reference

#include <G4DNASmoluchowskiReactionModel.hh>

Inheritance diagram for G4DNASmoluchowskiReactionModel:

Public Member Functions
virtual G4bool	FindReaction (const G4Track &, const G4Track &, G4double, G4double &, G4bool)
	G4DNASmoluchowskiReactionModel ()
	G4DNASmoluchowskiReactionModel (const G4DNASmoluchowskiReactionModel &)=delete
virtual G4double	GetReactionRadius (const G4int)
virtual G4double	GetReactionRadius (const G4MolecularConfiguration *, const G4MolecularConfiguration *)
const G4DNAMolecularReactionTable *	GetReactionTable ()
virtual void	Initialise (const G4MolecularConfiguration *, const G4Track &)
virtual void	InitialiseToPrint (const G4MolecularConfiguration *)
G4DNASmoluchowskiReactionModel &	operator= (const G4DNASmoluchowskiReactionModel &)=delete
void	SetReactionTable (const G4DNAMolecularReactionTable *)
virtual	~G4DNASmoluchowskiReactionModel ()

Protected Attributes
const G4DNAMolecularReactionTable *	fpReactionTable

Private Attributes
const std::vector< const G4DNAMolecularReactionData * > *	fpReactionData

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 63 of file G4DNASmoluchowskiReactionModel.hh.

Constructor & Destructor Documentation

G4DNASmoluchowskiReactionModel() [1/2]

G4DNASmoluchowskiReactionModel::G4DNASmoluchowskiReactionModel

(

)

Definition at line 35 of file G4DNASmoluchowskiReactionModel.cc.

    : G4VDNAReactionModel()
    , fpReactionData(nullptr)
{
}

~G4DNASmoluchowskiReactionModel()

G4DNASmoluchowskiReactionModel::~G4DNASmoluchowskiReactionModel ( )

virtualdefault

G4DNASmoluchowskiReactionModel() [2/2]

G4DNASmoluchowskiReactionModel::G4DNASmoluchowskiReactionModel ( const G4DNASmoluchowskiReactionModel &  )

delete

Member Function Documentation

FindReaction()

G4bool G4DNASmoluchowskiReactionModel::FindReaction ( const G4Track &  __trackA, const G4Track &  __trackB, G4double  __reactionRadius, G4double &  __separationDistance, G4bool  __alongStepReaction  )

virtual

Implements G4VDNAReactionModel.

Definition at line 67 of file G4DNASmoluchowskiReactionModel.cc.

{
    const G4double R2 = __reactionRadius * __reactionRadius;
    G4double postStepSeparation = 0.;
    bool do_break = false;
    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
        __separationDistance = std::sqrt(postStepSeparation);
        return true;
    }
    else if (__alongStepReaction == true)
    {
        //Along step check 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
        __separationDistance = (postStepSeparation = std::sqrt(postStepSeparation));
 
        auto pMoleculeA = GetMolecule(__trackA);
        auto pMoleculeB = GetMolecule(__trackB);
 
        G4double D = pMoleculeA->GetDiffusionCoefficient()
                     + pMoleculeB->GetDiffusionCoefficient();
 
        const auto& preStepPositionA = __trackA.GetStep()->GetPreStepPoint()->GetPosition();
        const auto& preStepPositionB = __trackB.GetStep()->GetPreStepPoint()->GetPosition();
 
        G4double preStepSeparation = (preStepPositionA - preStepPositionB).mag();
 
        //===================================
        // Brownian bridge
        G4double __probabiltyOfEncounter = G4Exp(-(preStepSeparation - __reactionRadius)
                                                    * (postStepSeparation - __reactionRadius)
                                                 / (D * (__trackB.GetStep()->GetDeltaTime()))
                                            );
        G4double __selectedPOE = G4UniformRand();
 
        if (__selectedPOE <= __probabiltyOfEncounter)
        {
            return true;
        }
        //===================================
    }
 
    return false;
}

References D(), G4Exp(), G4UniformRand, G4Step::GetDeltaTime(), GetMolecule(), G4StepPoint::GetPosition(), G4Track::GetPosition(), G4Step::GetPreStepPoint(), and G4Track::GetStep().

GetReactionRadius() [1/2]

G4double G4DNASmoluchowskiReactionModel::GetReactionRadius ( const G4int  __i )

virtual

Implements G4VDNAReactionModel.

Definition at line 61 of file G4DNASmoluchowskiReactionModel.cc.

{
    G4double __output = (*fpReactionData)[__i]->GetEffectiveReactionRadius();
    return __output;
}

GetReactionRadius() [2/2]

G4double G4DNASmoluchowskiReactionModel::GetReactionRadius ( const G4MolecularConfiguration *  pMol1, const G4MolecularConfiguration *  pMol2  )

virtual

Implements G4VDNAReactionModel.

Definition at line 54 of file G4DNASmoluchowskiReactionModel.cc.

{
    G4double __output = fpReactionTable->GetReactionData(pMol1, pMol2)->GetEffectiveReactionRadius();
    return __output;
}

References G4VDNAReactionModel::fpReactionTable, G4DNAMolecularReactionData::GetEffectiveReactionRadius(), and G4DNAMolecularReactionTable::GetReactionData().

GetReactionTable()

const G4DNAMolecularReactionTable * G4VDNAReactionModel::GetReactionTable ( )

inherited

Definition at line 41 of file G4VDNAReactionModel.cc.

{
    return fpReactionTable;
}

References G4VDNAReactionModel::fpReactionTable.

Referenced by G4DNAMolecularReactionTable::PrintTable().

Initialise()

void G4DNASmoluchowskiReactionModel::Initialise ( const G4MolecularConfiguration *  pMolecule, const G4Track &    )

virtual

Reimplemented from G4VDNAReactionModel.

Definition at line 43 of file G4DNASmoluchowskiReactionModel.cc.

{
    fpReactionData = fpReactionTable->GetReactionData(pMolecule);
}

References fpReactionData, G4VDNAReactionModel::fpReactionTable, and G4DNAMolecularReactionTable::GetReactionData().

InitialiseToPrint()

void G4DNASmoluchowskiReactionModel::InitialiseToPrint ( const G4MolecularConfiguration *  pMolecule )

virtual

Implements G4VDNAReactionModel.

Definition at line 49 of file G4DNASmoluchowskiReactionModel.cc.

{
    fpReactionData = fpReactionTable->GetReactionData(pMolecule);
}

References fpReactionData, G4VDNAReactionModel::fpReactionTable, and G4DNAMolecularReactionTable::GetReactionData().

operator=()

G4DNASmoluchowskiReactionModel & G4DNASmoluchowskiReactionModel::operator= ( const G4DNASmoluchowskiReactionModel &  )

delete

SetReactionTable()

void G4VDNAReactionModel::SetReactionTable ( const G4DNAMolecularReactionTable *  pReactionTable )

inherited

Definition at line 36 of file G4VDNAReactionModel.cc.

{
    fpReactionTable = pReactionTable;
}

References G4VDNAReactionModel::fpReactionTable.

Referenced by G4DNAMolecularReactionTable::PrintTable().

Field Documentation

fpReactionData

const std::vector<const G4DNAMolecularReactionData*>* G4DNASmoluchowskiReactionModel::fpReactionData

private

Definition at line 85 of file G4DNASmoluchowskiReactionModel.hh.

Referenced by Initialise(), and InitialiseToPrint().

fpReactionTable

const G4DNAMolecularReactionTable* G4VDNAReactionModel::fpReactionTable

protectedinherited

Definition at line 82 of file G4VDNAReactionModel.hh.

Referenced by GetReactionRadius(), G4DiffusionControlledReactionModel::GetReactionRadius(), G4VDNAReactionModel::GetReactionTable(), Initialise(), G4DiffusionControlledReactionModel::Initialise(), InitialiseToPrint(), G4DiffusionControlledReactionModel::InitialiseToPrint(), and G4VDNAReactionModel::SetReactionTable().

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

• source/processes/electromagnetic/dna/models/include/G4DNASmoluchowskiReactionModel.hh
• source/processes/electromagnetic/dna/models/src/G4DNASmoluchowskiReactionModel.cc