G4DNASmoluchowskiReactionModel Class Reference

#include <G4DNASmoluchowskiReactionModel.hh>

Inheritance diagram for G4DNASmoluchowskiReactionModel:

Collaboration diagram for G4DNASmoluchowskiReactionModel:

Public Member Functions
	G4DNASmoluchowskiReactionModel ()
virtual	~G4DNASmoluchowskiReactionModel ()
	G4DNASmoluchowskiReactionModel (const G4DNASmoluchowskiReactionModel &)
virtual void	Initialise (G4MolecularConfiguration *, const G4Track &)
virtual void	InitialiseToPrint (G4MolecularConfiguration *)
virtual G4double	GetReactionRadius (G4MolecularConfiguration *, G4MolecularConfiguration *)
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 ()

Private Member Functions
G4DNASmoluchowskiReactionModel &	operator= (const G4DNASmoluchowskiReactionModel &)

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

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 67 of file G4DNASmoluchowskiReactionModel.hh.

Constructor & Destructor Documentation

G4DNASmoluchowskiReactionModel() [1/2]

G4DNASmoluchowskiReactionModel::G4DNASmoluchowskiReactionModel

(

)

Definition at line 36 of file G4DNASmoluchowskiReactionModel.cc.

                                                               :
    G4VDNAReactionModel()
{
  fReactionData = 0;
}

~G4DNASmoluchowskiReactionModel()

G4DNASmoluchowskiReactionModel::~G4DNASmoluchowskiReactionModel ( )

virtual

Definition at line 55 of file G4DNASmoluchowskiReactionModel.cc.

{
  fReactionData = 0;
}

G4DNASmoluchowskiReactionModel() [2/2]

G4DNASmoluchowskiReactionModel::G4DNASmoluchowskiReactionModel

(

const G4DNASmoluchowskiReactionModel &

__right

)

Definition at line 42 of file G4DNASmoluchowskiReactionModel.cc.

                                                                                                            :
    G4VDNAReactionModel(__right)
{
  fReactionData = 0;
}

Member Function Documentation

FindReaction()

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

virtual

Implements G4VDNAReactionModel.

Definition at line 88 of file G4DNASmoluchowskiReactionModel.cc.

{
  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();

    //===================================
    // Brownian bridge


//    if(G4Scheduler::Instance()->GetTimeStep() != __trackB.GetStep()->GetDeltaTime())
//    {
//      G4cout << G4Scheduler::Instance()->GetTimeStep() << G4endl;
//      G4cout << __trackB.GetStep()->GetDeltaTime() << G4endl;
//      assert(G4Scheduler::Instance()->GetTimeStep() == __trackB.GetStep()->GetDeltaTime());
//    }

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

    if (__selectedPOE <= __probabiltyOfEncounter) return true;
    //===================================
  }

  return false;
}

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GetReactionRadius() [1/2]

G4double G4DNASmoluchowskiReactionModel::GetReactionRadius ( G4MolecularConfiguration *  __mol1, G4MolecularConfiguration *  __mol2  )

virtual

Implements G4VDNAReactionModel.

Definition at line 74 of file G4DNASmoluchowskiReactionModel.cc.

{
  G4double __output = fReactionTable->GetReactionData(__mol1, __mol2)
      ->GetEffectiveReactionRadius();
  return __output;
}

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GetReactionRadius() [2/2]

G4double G4DNASmoluchowskiReactionModel::GetReactionRadius ( const G4int  __i )

virtual

Implements G4VDNAReactionModel.

Definition at line 82 of file G4DNASmoluchowskiReactionModel.cc.

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

Initialise()

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

virtual

Reimplemented from G4VDNAReactionModel.

Definition at line 60 of file G4DNASmoluchowskiReactionModel.cc.

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

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InitialiseToPrint()

void G4DNASmoluchowskiReactionModel::InitialiseToPrint ( G4MolecularConfiguration *  __molecule )

virtual

Implements G4VDNAReactionModel.

Definition at line 68 of file G4DNASmoluchowskiReactionModel.cc.

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

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operator=()

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

private

Definition at line 48 of file G4DNASmoluchowskiReactionModel.cc.

{
  if (this == &right) return *this;
  fReactionData = 0;
  return *this;
}

Member Data Documentation

fReactionData

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

private

Definition at line 90 of file G4DNASmoluchowskiReactionModel.hh.

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

• G4DNASmoluchowskiReactionModel.hh
• G4DNASmoluchowskiReactionModel.cc