G4DNAWaterDissociationDisplacer.cc

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//
//
// Author: Mathieu Karamitros
//
// 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 "G4DNAWaterDissociationDisplacer.hh"
#include "G4PhysicalConstants.hh"
#include "G4SystemOfUnits.hh"
#include "G4H2O.hh"
#include "G4H2.hh"
#include "G4Hydrogen.hh"
#include "G4Oxygen.hh"
#include "G4OH.hh"
#include "G4H3O.hh"
#include "G4Electron_aq.hh"
#include "G4H2O2.hh"
#include "Randomize.hh"
#include "G4Molecule.hh"
#include "G4MolecularConfiguration.hh"
#include "G4RandomDirection.hh"
#include "G4Exp.hh"
#include "G4UnitsTable.hh"
#include "G4EmParameters.hh"
#include "G4DNAOneStepThermalizationModel.hh"
 
using namespace std;
 
//------------------------------------------------------------------------------
 
G4CT_COUNT_IMPL(G4DNAWaterDissociationDisplacer,
                Ionisation_DissociationDecay)
 
G4CT_COUNT_IMPL(G4DNAWaterDissociationDisplacer,
                A1B1_DissociationDecay)
 
G4CT_COUNT_IMPL(G4DNAWaterDissociationDisplacer,
                B1A1_DissociationDecay)
 
G4CT_COUNT_IMPL(G4DNAWaterDissociationDisplacer,
                B1A1_DissociationDecay2)
 
G4CT_COUNT_IMPL(G4DNAWaterDissociationDisplacer,
                AutoIonisation)
 
G4CT_COUNT_IMPL(G4DNAWaterDissociationDisplacer,
                DissociativeAttachment)
/*
//------------------------------------------------------------------------------
#ifdef _WATER_DISPLACER_USE_KREIPL_
// This function is used to generate the following density distribution:
//   f(r) := 4*r * exp(-2*r)
// reference:
//  Kreipl, M. S., Friedland, W. & Paretzke, H. G.
//  Time- and space-resolved Monte Carlo study of water radiolysis for photon,
//  electron and ion irradiation.
//  Radiat. Environ. Biophys. 48, 11–20 (2009).
G4double G4DNAWaterDissociationDisplacer::ElectronProbaDistribution(G4double r)
{
  return (2.*r+1.)*G4Exp(-2.*r);
}
#endif
 
//------------------------------------------------------------------------------
#ifdef _WATER_DISPLACER_USE_TERRISOL_
// This function is used to generate the following density distribution:
//   f(r) := 4*x^2/(sqrt(%pi)*(b)^3)*exp(-x^2/(b)^2)
// with b=27.22 for 7 eV
// reference
// Terrissol M, Beaudre A (1990) Simulation of space and time evolution
// of radiolytic species induced by electrons in water.
// Radiat Prot Dosimetry 31:171–175
 
G4double G4DNAWaterDissociationDisplacer::ElectronProbaDistribution(G4double r)
{
#define b 27.22 // nanometer
    static constexpr double sqrt_pi = 1.77245; // sqrt(CLHEP::pi);
    static constexpr double b_to3 = 20168.1; // pow(b,3.);
    static constexpr double b_to2 = 740.928; // pow(b,2.);
    static constexpr double inverse_b_to2 = 1. / b_to2;
 
    static constexpr double main_factor = 4. / (sqrt_pi * b_to3);
    static constexpr double factorA = sqrt_pi * b_to3 / 4.;
    static constexpr double factorB = b_to2 / 2.;
 
    return (main_factor *
            (factorA * erf(r / b)
             - factorB * r * G4Exp(-pow(r, 2.) * inverse_b_to2)));
}
 
#endif
//------------------------------------------------------------------------------
*/
G4DNAWaterDissociationDisplacer::G4DNAWaterDissociationDisplacer()
        :
        
        ke(1.7*eV)
/*#ifdef _WATER_DISPLACER_USE_KREIPL_
        fFastElectronDistrib(0., 5., 0.001)
#elif defined _WATER_DISPLACER_USE_TERRISOL_
        fFastElectronDistrib(0., 100., 0.001)
#endif*/
{/*
    fProba1DFunction =
            std::bind((G4double(*)(G4double))
                              &G4DNAWaterDissociationDisplacer::ElectronProbaDistribution,
                      std::placeholders::_1);
 
    size_t nBins = 500;
    fElectronThermalization.reserve(nBins);
    double eps = 1. / ((int) nBins);
    double proba = eps;
 
    fElectronThermalization.push_back(0.);
 
    for (size_t i = 1; i < nBins; ++i)
    {
        double r = fFastElectronDistrib.Revert(proba, fProba1DFunction);
        fElectronThermalization.push_back(r * nanometer);
        proba += eps;
//  G4cout << G4BestUnit(r*nanometer, "Length") << G4endl;
    }*/
    dnaSubType = G4EmParameters::Instance()->DNAeSolvationSubType();
//   SetVerbose(1);
}
G4DNAWaterDissociationDisplacer::G4DNAWaterDissociationDisplacer() {…}
 
//------------------------------------------------------------------------------
 
G4DNAWaterDissociationDisplacer::~G4DNAWaterDissociationDisplacer()
{
    ;
}
G4DNAWaterDissociationDisplacer::~G4DNAWaterDissociationDisplacer() {…}
 
//------------------------------------------------------------------------------
 
G4ThreeVector
G4DNAWaterDissociationDisplacer::
GetMotherMoleculeDisplacement(const G4MolecularDissociationChannel*
theDecayChannel) const
{
    G4int decayType = theDecayChannel->GetDisplacementType();
    G4double RMSMotherMoleculeDisplacement(0.);
 
    switch (decayType)
    {
        case Ionisation_DissociationDecay:
            RMSMotherMoleculeDisplacement = 2.0 * nanometer;
            break;
        case A1B1_DissociationDecay:
            RMSMotherMoleculeDisplacement = 0. * nanometer;
            break;
        case B1A1_DissociationDecay:
            RMSMotherMoleculeDisplacement = 0. * nanometer;
            break;
        case B1A1_DissociationDecay2:
            RMSMotherMoleculeDisplacement = 0. * nanometer;
            break;
        case AutoIonisation:
            RMSMotherMoleculeDisplacement = 2.0 * nanometer;
            break;
        case DissociativeAttachment:
            RMSMotherMoleculeDisplacement = 0. * nanometer;
            break;
    }
 
    if (RMSMotherMoleculeDisplacement == 0)
    {
        return G4ThreeVector(0, 0, 0);
    }
    auto RandDirection =
            radialDistributionOfProducts(RMSMotherMoleculeDisplacement);
 
    return RandDirection;
}
G4DNAWaterDissociationDisplacer:: {…}
 
//------------------------------------------------------------------------------
 
vector<G4ThreeVector>
G4DNAWaterDissociationDisplacer::
GetProductsDisplacement(const G4MolecularDissociationChannel* pDecayChannel) const
{
    G4int nbProducts = pDecayChannel->GetNbProducts();
    vector<G4ThreeVector> theProductDisplacementVector(nbProducts);
 
    typedef map<const G4MoleculeDefinition*, G4double> RMSmap;
    RMSmap theRMSmap;
 
    G4int decayType = pDecayChannel->GetDisplacementType();
 
    switch (decayType)
    {
        case Ionisation_DissociationDecay:
        {
            if (fVerbose != 0)
            {
                G4cout << "Ionisation_DissociationDecay" << G4endl;
                G4cout << "Channel's name: " << pDecayChannel->GetName() << G4endl;
            }
            G4double RdmValue = G4UniformRand();
 
            if (RdmValue < 0.5)
            {
                // H3O
                theRMSmap[G4H3O::Definition()] = 0. * nanometer;
                // OH
                theRMSmap[G4OH::Definition()] = 0.8 * nanometer;
            }
            else
            {
                // H3O
                theRMSmap[G4H3O::Definition()] = 0.8 * nanometer;
                // OH
                theRMSmap[G4OH::Definition()] = 0. * nanometer;
            }
 
            for (int i = 0; i < nbProducts; i++)
            {
                auto pProduct = pDecayChannel->GetProduct(i);
                G4double theRMSDisplacement = theRMSmap[pProduct->GetDefinition()];
 
                if (theRMSDisplacement == 0.)
                {
                    theProductDisplacementVector[i] = G4ThreeVector();
                }
                else
                {
                    auto RandDirection = radialDistributionOfProducts(theRMSDisplacement);
                    theProductDisplacementVector[i] = RandDirection;
                }
            }
            break;
        }
        case A1B1_DissociationDecay:
        {
            if (fVerbose != 0)
            {
                G4cout << "A1B1_DissociationDecay" << G4endl;
                G4cout << "Channel's name: " << pDecayChannel->GetName() << G4endl;
            }
            G4double theRMSDisplacement = 2.4 * nanometer;
            auto RandDirection =
                    radialDistributionOfProducts(theRMSDisplacement);
 
            for (G4int i = 0; i < nbProducts; i++)
            {
                auto pProduct = pDecayChannel->GetProduct(i);
 
                if (pProduct->GetDefinition() == G4OH::Definition())
                {
                    theProductDisplacementVector[i] = -1. / 18. * RandDirection;
                }
                else if (pProduct->GetDefinition() == G4Hydrogen::Definition())
                {
                    theProductDisplacementVector[i] = +17. / 18. * RandDirection;
                }
            }
            break;
        }
        case B1A1_DissociationDecay:
        {
            if (fVerbose != 0)
            {
                G4cout << "B1A1_DissociationDecay" << G4endl;
                G4cout << "Channel's name: " << pDecayChannel->GetName() << G4endl;
            }
 
            G4double theRMSDisplacement = 0.8 * nanometer;
            auto RandDirection =
                    radialDistributionOfProducts(theRMSDisplacement);
 
            G4int NbOfOH = 0;
            for (G4int i = 0; i < nbProducts; ++i)
            {
                auto pProduct = pDecayChannel->GetProduct(i);
                if (pProduct->GetDefinition() == G4H2::Definition())
                {
                    // In the paper of Kreipl (2009)
                    // theProductDisplacementVector[i] = -2. / 18. * RandDirection;
 
                    // Based on momentum conservation
                    theProductDisplacementVector[i] = -16. / 18. * RandDirection;
                }
                else if (pProduct->GetDefinition() == G4OH::Definition())
                {
                    // In the paper of Kreipl (2009)
                    // G4ThreeVector OxygenDisplacement = +16. / 18. * RandDirection;
 
                    // Based on momentum conservation
                    G4ThreeVector OxygenDisplacement = +2. / 18. * RandDirection;
                    G4double OHRMSDisplacement = 1.1 * nanometer;
 
                    auto OHDisplacement =
                            radialDistributionOfProducts(OHRMSDisplacement);
 
                    if (NbOfOH == 0)
                    {
                        OHDisplacement = 0.5 * OHDisplacement;
                    }
                    else
                    {
                        OHDisplacement = -0.5 * OHDisplacement;
                    }
 
                    theProductDisplacementVector[i] =
                            OHDisplacement + OxygenDisplacement;
 
                    ++NbOfOH;
                }
            }
            break;
        }
        case B1A1_DissociationDecay2:
        {
          if(fVerbose != 0){
            G4cout<<"B1A1_DissociationDecay2"<<G4endl;
            G4cout<<"Channel's name: "<<pDecayChannel->GetName()<<G4endl;
          }
 
          G4int NbOfH = 0;
          for(G4int i =0; i < nbProducts; ++i)
          {
            auto pProduct = pDecayChannel->GetProduct(i);
            if(pProduct->GetDefinition() == G4Oxygen::Definition()){
            // O(3p)
            theProductDisplacementVector[i] = G4ThreeVector(0,0,0);
          }
          else if(pProduct->GetDefinition() == G4Hydrogen::Definition()){
            // H
            G4double HRMSDisplacement = 1.6 * nanometer;
 
            auto HDisplacement =
            radialDistributionOfProducts(HRMSDisplacement);
 
            if(NbOfH==0) HDisplacement = 0.5*HDisplacement;
            else HDisplacement = -0.5*HDisplacement;
            theProductDisplacementVector[i] = HDisplacement;
 
            ++NbOfH;
          }
        }
        break;
        }
        case AutoIonisation:
        {
            if (fVerbose != 0)
            {
                G4cout << "AutoIonisation" << G4endl;
                G4cout << "Channel's name: " << pDecayChannel->GetName() << G4endl;
            }
 
            G4double RdmValue = G4UniformRand();
 
            if (RdmValue < 0.5)
            {
                // H3O
                theRMSmap[G4H3O::Definition()] = 0. * nanometer;
                // OH
                theRMSmap[G4OH::Definition()] = 0.8 * nanometer;
            }
            else
            {
                // H3O
                theRMSmap[G4H3O::Definition()] = 0.8 * nanometer;
                // OH
                theRMSmap[G4OH::Definition()] = 0. * nanometer;
            }
 
            for (G4int i = 0; i < nbProducts; i++)
            {
                auto pProduct = pDecayChannel->GetProduct(i);
                auto theRMSDisplacement = theRMSmap[pProduct->GetDefinition()];
 
                if (theRMSDisplacement == 0)
                {
                    theProductDisplacementVector[i] = G4ThreeVector();
                }
                else
                {
                    auto RandDirection =
                            radialDistributionOfProducts(theRMSDisplacement);
                    theProductDisplacementVector[i] = RandDirection;
                }
                if (pProduct->GetDefinition() == G4Electron_aq::Definition())
                {
                    theProductDisplacementVector[i] = radialDistributionOfElectron();
                }
            }
            break;
        }
        case DissociativeAttachment:
        {
            if (fVerbose != 0)
            {
                G4cout << "DissociativeAttachment" << G4endl;
                G4cout << "Channel's name: " << pDecayChannel->GetName() << G4endl;
            }
            G4double theRMSDisplacement = 0.8 * nanometer;
            auto RandDirection =
                    radialDistributionOfProducts(theRMSDisplacement);
 
            G4int NbOfOH = 0;
            for (G4int i = 0; i < nbProducts; ++i)
            {
                auto pProduct = pDecayChannel->GetProduct(i);
                if (pProduct->GetDefinition() == G4H2::Definition())
                {
                    // In the paper of Kreipl (2009)
                    // theProductDisplacementVector[i] = -2. / 18. * RandDirection;
 
                    // Based on momentum conservation
                    theProductDisplacementVector[i] = -16. / 18. * RandDirection;
                }
                else if (pProduct->GetDefinition() == G4OH::Definition())
                {
                    // In the paper of Kreipl (2009)
                    // G4ThreeVector OxygenDisplacement = +16. / 18. * RandDirection;
 
                    // Based on momentum conservation
                    G4ThreeVector OxygenDisplacement = +2. / 18. * RandDirection;
                    G4double OHRMSDisplacement = 1.1 * nanometer;
 
                    auto OHDisplacement =
                            radialDistributionOfProducts(OHRMSDisplacement);
 
                    if (NbOfOH == 0)
                    {
                        OHDisplacement = 0.5 * OHDisplacement;
                    }
                    else
                    {
                        OHDisplacement = -0.5 * OHDisplacement;
                    }
                    theProductDisplacementVector[i] = OHDisplacement +
                                                      OxygenDisplacement;
                    ++NbOfOH;
                }
            }
            break;
        }
    }
    return theProductDisplacementVector;
}
G4DNAWaterDissociationDisplacer:: {…}
 
//------------------------------------------------------------------------------
 
G4ThreeVector
G4DNAWaterDissociationDisplacer::
radialDistributionOfProducts(G4double Rrms) const
{
    static const double inverse_sqrt_3 = 1. / sqrt(3.);
    double sigma = Rrms * inverse_sqrt_3;
    double x = G4RandGauss::shoot(0., sigma);
    double y = G4RandGauss::shoot(0., sigma);
    double z = G4RandGauss::shoot(0., sigma);
    return G4ThreeVector(x, y, z);
}
G4DNAWaterDissociationDisplacer:: {…}
 
//------------------------------------------------------------------------------
 
G4ThreeVector
G4DNAWaterDissociationDisplacer::radialDistributionOfElectron() const
{/*
    G4double rand_value = G4UniformRand();
    size_t nBins = fElectronThermalization.size();
    size_t bin = size_t(floor(rand_value * nBins));
    size_t bin_p1 = min(bin + 1, nBins - 1);
 
    return (fElectronThermalization[bin] * (1. - rand_value)
            + fElectronThermalization[bin_p1] * rand_value) *
           G4RandomDirection();*/
 
    G4ThreeVector pdf = G4ThreeVector(0,0,0);
 
    if(dnaSubType == fRitchie1994eSolvation) DNA::Penetration::Ritchie1994::GetPenetration(ke,pdf);
    else if(dnaSubType == fTerrisol1990eSolvation) DNA::Penetration::Terrisol1990::GetPenetration(ke,pdf);
    else if(dnaSubType == fMeesungnoensolid2002eSolvation) DNA::Penetration::Meesungnoen2002_amorphous::GetPenetration(ke,pdf);
    else if(dnaSubType == fKreipl2009eSolvation) DNA::Penetration::Kreipl2009::GetPenetration(ke,pdf);
    else DNA::Penetration::Meesungnoen2002::GetPenetration(ke,pdf);
 
    return pdf;
}
G4DNAWaterDissociationDisplacer::radialDistributionOfElectron() const {…}