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// $Id: G4DNABornIonisationModel.cc,v 1.16 2010/03/26 18:10:43 sincerti Exp $
// GEANT4 tag $Name: geant4-09-04-beta-cand-01 $
//

#include "G4DNABornIonisationModel.hh"
//#include "G4DynamicMolecule.hh"

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....

using namespace std;

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....

G4DNABornIonisationModel::G4DNABornIonisationModel(const G4ParticleDefinition*,
                                             const G4String& nam)
:G4VEmModel(nam),isInitialised(false)
{
  verboseLevel= 0;
  // Verbosity scale:
  // 0 = nothing 
  // 1 = warning for energy non-conservation 
  // 2 = details of energy budget
  // 3 = calculation of cross sections, file openings, sampling of atoms
  // 4 = entering in methods
  
  if( verboseLevel>0 ) 
  { 
    G4cout << "Born ionisation model is constructed " << G4endl;
  }
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....

G4DNABornIonisationModel::~G4DNABornIonisationModel()
{  
  // Cross section
  
  std::map< G4String,G4DNACrossSectionDataSet*,std::less<G4String> >::iterator pos;
  for (pos = tableData.begin(); pos != tableData.end(); ++pos)
  {
    G4DNACrossSectionDataSet* table = pos->second;
    delete table;
  }
  
  // Final state
  
  eVecm.clear();
  pVecm.clear();

}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....

void G4DNABornIonisationModel::Initialise(const G4ParticleDefinition* particle,
                                       const G4DataVector& /*cuts*/)
{

  if (verboseLevel > 3)
    G4cout << "Calling G4DNABornIonisationModel::Initialise()" << G4endl;

  // Energy limits

  G4String fileElectron("dna/sigma_ionisation_e_born");
  G4String fileProton("dna/sigma_ionisation_p_born");

  G4ParticleDefinition* electronDef = G4Electron::ElectronDefinition();
  G4ParticleDefinition* protonDef = G4Proton::ProtonDefinition();

  G4String electron;
  G4String proton;
  
  G4double scaleFactor = (1.e-22 / 3.343) * m*m;

  char *path = getenv("G4LEDATA");

  if (electronDef != 0)
  {
    electron = electronDef->GetParticleName();

    tableFile[electron] = fileElectron;

    lowEnergyLimit[electron] = 11. * eV; 
    highEnergyLimit[electron] = 1. * MeV;

    // Cross section
    
    G4DNACrossSectionDataSet* tableE = new G4DNACrossSectionDataSet(new G4LogLogInterpolation, eV,scaleFactor );
    tableE->LoadData(fileElectron);
      
    tableData[electron] = tableE;
    
    // Final state
    
    std::ostringstream eFullFileName;
    eFullFileName << path << "/dna/sigmadiff_ionisation_e_born.dat";
    std::ifstream eDiffCrossSection(eFullFileName.str().c_str());

    if (!eDiffCrossSection)
    { 
      G4Exception("G4DNABornIonisationModel::ERROR OPENING electron DATA FILE");
    }
      
    eTdummyVec.push_back(0.);
    while(!eDiffCrossSection.eof())
    {
      double tDummy;
      double eDummy;
      eDiffCrossSection>>tDummy>>eDummy;
      if (tDummy != eTdummyVec.back()) eTdummyVec.push_back(tDummy);
      for (int j=0; j<5; j++)
      {
        eDiffCrossSection>>eDiffCrossSectionData[j][tDummy][eDummy];

        // SI - only if eof is not reached !
        if (!eDiffCrossSection.eof()) eDiffCrossSectionData[j][tDummy][eDummy]*=scaleFactor;

        eVecm[tDummy].push_back(eDummy);

      }
    }

    //
  }
  else
  {
    G4Exception("G4DNABornIonisationModel::Initialise(): electron is not defined");
  }

  if (protonDef != 0)
  {
    proton = protonDef->GetParticleName();

    tableFile[proton] = fileProton;

    lowEnergyLimit[proton] = 500. * keV;
    highEnergyLimit[proton] = 100. * MeV;

    // Cross section
    
    G4DNACrossSectionDataSet* tableP = new G4DNACrossSectionDataSet(new G4LogLogInterpolation, eV,scaleFactor );
    tableP->LoadData(fileProton);
      
    tableData[proton] = tableP;
    
    // Final state

    std::ostringstream pFullFileName;
    pFullFileName << path << "/dna/sigmadiff_ionisation_p_born.dat";
    std::ifstream pDiffCrossSection(pFullFileName.str().c_str());
    
    if (!pDiffCrossSection)
    { 
      G4Exception("G4DNABornIonisationModel::ERROR OPENING proton DATA FILE");
    }
      
    pTdummyVec.push_back(0.);
    while(!pDiffCrossSection.eof())
    {
      double tDummy;
      double eDummy;
      pDiffCrossSection>>tDummy>>eDummy;
      if (tDummy != pTdummyVec.back()) pTdummyVec.push_back(tDummy);
      for (int j=0; j<5; j++)
      {
        pDiffCrossSection>>pDiffCrossSectionData[j][tDummy][eDummy];

        // SI - only if eof is not reached !
        if (!pDiffCrossSection.eof()) pDiffCrossSectionData[j][tDummy][eDummy]*=scaleFactor;

        pVecm[tDummy].push_back(eDummy);
      }
    }
  
  }
  else
  {
    G4Exception("G4DNABornIonisationModel::Initialise(): proton is not defined");
  }

  if (particle==electronDef) 
  {
    SetLowEnergyLimit(lowEnergyLimit[electron]);
    SetHighEnergyLimit(highEnergyLimit[electron]);
  }

  if (particle==protonDef) 
  {
    SetLowEnergyLimit(lowEnergyLimit[proton]);
    SetHighEnergyLimit(highEnergyLimit[proton]);
  }

  if( verboseLevel>0 ) 
  { 
    G4cout << "Born ionisation model is initialized " << G4endl
           << "Energy range: "
           << LowEnergyLimit() / eV << " eV - "
           << HighEnergyLimit() / keV << " keV for "
           << particle->GetParticleName()
           << G4endl;
  }
  
  //
  
  if(!isInitialised) 
  {
    isInitialised = true;
  
    if(pParticleChange)
      fParticleChangeForGamma = reinterpret_cast<G4ParticleChangeForGamma*>(pParticleChange);
    else
      fParticleChangeForGamma = new G4ParticleChangeForGamma();
  }    

  // InitialiseElementSelectors(particle,cuts);

}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....

G4double G4DNABornIonisationModel::CrossSectionPerVolume(const G4Material* material,
					   const G4ParticleDefinition* particleDefinition,
					   G4double ekin,
					   G4double,
					   G4double)
{
  if (verboseLevel > 3)
    G4cout << "Calling CrossSectionPerVolume() of G4DNABornIonisationModel" << G4endl;

  if (
      particleDefinition != G4Proton::ProtonDefinition()
      &&
      particleDefinition != G4Electron::ElectronDefinition()
     )
   	    
    return 0;
  
  // Calculate total cross section for model

  G4double lowLim = 0;
  G4double highLim = 0;
  G4double sigma=0;

  if (material->GetName() == "G4_WATER")
  {
    const G4String& particleName = particleDefinition->GetParticleName();
 
    std::map< G4String,G4double,std::less<G4String> >::iterator pos1;
    pos1 = lowEnergyLimit.find(particleName);
    if (pos1 != lowEnergyLimit.end())
    {
      lowLim = pos1->second;
    }
  
    std::map< G4String,G4double,std::less<G4String> >::iterator pos2;
    pos2 = highEnergyLimit.find(particleName);
    if (pos2 != highEnergyLimit.end())
    {
      highLim = pos2->second;
    }

    if (ekin >= lowLim && ekin < highLim)
    {
      std::map< G4String,G4DNACrossSectionDataSet*,std::less<G4String> >::iterator pos;
      pos = tableData.find(particleName);
	
      if (pos != tableData.end())
      {
        G4DNACrossSectionDataSet* table = pos->second;
        if (table != 0)
        {
	  sigma = table->FindValue(ekin);
        }
      }
      else
      {
        G4Exception("G4DNABornIonisationModel::CrossSectionPerVolume: attempting to calculate cross section for wrong particle");
      }
    }

    if (verboseLevel > 3)
    {
      G4cout << "---> Kinetic energy(eV)=" << ekin/eV << G4endl;
      G4cout << " - Cross section per water molecule (cm^2)=" << sigma/cm/cm << G4endl;
      G4cout << " - Cross section per water molecule (cm^-1)=" << sigma*material->GetAtomicNumDensityVector()[1]/(1./cm) << G4endl;
    } 
 
  } // if (waterMaterial)
 
 return sigma*material->GetAtomicNumDensityVector()[1];		   

}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....

void G4DNABornIonisationModel::SampleSecondaries(std::vector<G4DynamicParticle*>* fvect,
					      const G4MaterialCutsCouple* /*couple*/,
					      const G4DynamicParticle* particle,
					      G4double,
					      G4double)
{

  if (verboseLevel > 3)
    G4cout << "Calling SampleSecondaries() of G4DNABornIonisationModel" << G4endl;

  G4double lowLim = 0;
  G4double highLim = 0;

  G4double k = particle->GetKineticEnergy();

  const G4String& particleName = particle->GetDefinition()->GetParticleName();

  std::map< G4String,G4double,std::less<G4String> >::iterator pos1;
  pos1 = lowEnergyLimit.find(particleName);

  if (pos1 != lowEnergyLimit.end())
  {
    lowLim = pos1->second;
  }

  std::map< G4String,G4double,std::less<G4String> >::iterator pos2;
  pos2 = highEnergyLimit.find(particleName);

  if (pos2 != highEnergyLimit.end())
  {
    highLim = pos2->second;
  }

  if (k >= lowLim && k < highLim)
  {
    G4ParticleMomentum primaryDirection = particle->GetMomentumDirection();
    G4double particleMass = particle->GetDefinition()->GetPDGMass();
    G4double totalEnergy = k + particleMass;
    G4double pSquare = k * (totalEnergy + particleMass);
    G4double totalMomentum = std::sqrt(pSquare);

    G4int ionizationShell = RandomSelect(k,particleName);
  
    G4double secondaryKinetic = RandomizeEjectedElectronEnergy(particle->GetDefinition(),k,ionizationShell);
  
    G4double bindingEnergy = waterStructure.IonisationEnergy(ionizationShell);

    G4double cosTheta = 0.;
    G4double phi = 0.; 
    RandomizeEjectedElectronDirection(particle->GetDefinition(), k,secondaryKinetic, cosTheta, phi);

    G4double sinTheta = std::sqrt(1.-cosTheta*cosTheta);
    G4double dirX = sinTheta*std::cos(phi);
    G4double dirY = sinTheta*std::sin(phi);
    G4double dirZ = cosTheta;
    G4ThreeVector deltaDirection(dirX,dirY,dirZ);
    deltaDirection.rotateUz(primaryDirection);

    G4double deltaTotalMomentum = std::sqrt(secondaryKinetic*(secondaryKinetic + 2.*electron_mass_c2 ));

    G4double finalPx = totalMomentum*primaryDirection.x() - deltaTotalMomentum*deltaDirection.x();
    G4double finalPy = totalMomentum*primaryDirection.y() - deltaTotalMomentum*deltaDirection.y();
    G4double finalPz = totalMomentum*primaryDirection.z() - deltaTotalMomentum*deltaDirection.z();
    G4double finalMomentum = std::sqrt(finalPx*finalPx + finalPy*finalPy + finalPz*finalPz);
    finalPx /= finalMomentum;
    finalPy /= finalMomentum;
    finalPz /= finalMomentum;
    
    G4ThreeVector direction;
    direction.set(finalPx,finalPy,finalPz);
    
    fParticleChangeForGamma->ProposeMomentumDirection(direction.unit()) ;
    fParticleChangeForGamma->SetProposedKineticEnergy(k-bindingEnergy-secondaryKinetic);
    fParticleChangeForGamma->ProposeLocalEnergyDeposit(bindingEnergy);

    G4DynamicParticle* dp = new G4DynamicParticle (G4Electron::Electron(),deltaDirection,secondaryKinetic) ;
    fvect->push_back(dp);

  }

}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

G4double G4DNABornIonisationModel::RandomizeEjectedElectronEnergy(G4ParticleDefinition* particleDefinition, 
G4double k, G4int shell)
{
  if (particleDefinition == G4Electron::ElectronDefinition()) 
  {
    G4double maximumEnergyTransfer=0.;
    if ((k+waterStructure.IonisationEnergy(shell))/2. > k) maximumEnergyTransfer=k;
    else maximumEnergyTransfer = (k+waterStructure.IonisationEnergy(shell))/2.;
    
// SI : original method
/*
    G4double crossSectionMaximum = 0.;
    for(G4double value=waterStructure.IonisationEnergy(shell); value<=maximumEnergyTransfer; value+=0.1*eV)
    {
      G4double differentialCrossSection = DifferentialCrossSection(particleDefinition, k/eV, value/eV, shell);
      if(differentialCrossSection >= crossSectionMaximum) crossSectionMaximum = differentialCrossSection;
    }
*/

 
// SI : alternative method

    G4double crossSectionMaximum = 0.;

    G4double minEnergy = waterStructure.IonisationEnergy(shell);
    G4double maxEnergy = maximumEnergyTransfer;
    G4int nEnergySteps = 50;

    G4double value(minEnergy);
    G4double stpEnergy(std::pow(maxEnergy/value, 1./static_cast<G4double>(nEnergySteps-1)));
    G4int step(nEnergySteps);
    while (step>0)
    {
      step--;
      G4double differentialCrossSection = DifferentialCrossSection(particleDefinition, k/eV, value/eV, shell);
      if(differentialCrossSection >= crossSectionMaximum) crossSectionMaximum = differentialCrossSection;
      value*=stpEnergy;
    }
//
 
    G4double secondaryElectronKineticEnergy=0.;
    do 
    {
      secondaryElectronKineticEnergy = G4UniformRand() * (maximumEnergyTransfer-waterStructure.IonisationEnergy(shell));
    } while(G4UniformRand()*crossSectionMaximum >
      DifferentialCrossSection(particleDefinition, k/eV,(secondaryElectronKineticEnergy+waterStructure.IonisationEnergy(shell))/eV,shell));

    return secondaryElectronKineticEnergy;
 
  }
  
  if (particleDefinition == G4Proton::ProtonDefinition()) 
  {
    G4double maximumKineticEnergyTransfer = 4.* (electron_mass_c2 / proton_mass_c2) * k;

    G4double crossSectionMaximum = 0.;
    for (G4double value = waterStructure.IonisationEnergy(shell); 
         value<=4.*waterStructure.IonisationEnergy(shell) ; 
         value+=0.1*eV)
    {
      G4double differentialCrossSection = DifferentialCrossSection(particleDefinition, k/eV, value/eV, shell);
      if (differentialCrossSection >= crossSectionMaximum) crossSectionMaximum = differentialCrossSection;
    }

    G4double secondaryElectronKineticEnergy = 0.;
    do
    {
      secondaryElectronKineticEnergy = G4UniformRand() * maximumKineticEnergyTransfer;
    } while(G4UniformRand()*crossSectionMaximum >= 
	      DifferentialCrossSection(particleDefinition, k/eV,(secondaryElectronKineticEnergy+waterStructure.IonisationEnergy(shell))/eV,shell));

    return secondaryElectronKineticEnergy;
  }

  return 0;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

void G4DNABornIonisationModel::RandomizeEjectedElectronDirection(G4ParticleDefinition* particleDefinition, 
								   G4double k, 
								   G4double secKinetic, 
								   G4double & cosTheta, 
								   G4double & phi )
{
  if (particleDefinition == G4Electron::ElectronDefinition()) 
  {
    phi = twopi * G4UniformRand();
    if (secKinetic < 50.*eV) cosTheta = (2.*G4UniformRand())-1.;
    else if (secKinetic <= 200.*eV) 	
    {
      if (G4UniformRand() <= 0.1) cosTheta = (2.*G4UniformRand())-1.;
      else cosTheta = G4UniformRand()*(std::sqrt(2.)/2);
    }
    else	
    {
      G4double sin2O = (1.-secKinetic/k) / (1.+secKinetic/(2.*electron_mass_c2));
      cosTheta = std::sqrt(1.-sin2O);
    }
  }
 
  if (particleDefinition == G4Proton::ProtonDefinition()) 
  {
    G4double maxSecKinetic = 4.* (electron_mass_c2 / proton_mass_c2) * k;
    phi = twopi * G4UniformRand();
    cosTheta = std::sqrt(secKinetic / maxSecKinetic);
  }			
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

double G4DNABornIonisationModel::DifferentialCrossSection(G4ParticleDefinition * particleDefinition, 
							    G4double k, 
							    G4double energyTransfer, 
							    G4int ionizationLevelIndex)
{
  G4double sigma = 0.;

  if (energyTransfer >= waterStructure.IonisationEnergy(ionizationLevelIndex))
  {
    G4double valueT1 = 0;
    G4double valueT2 = 0;
    G4double valueE21 = 0;
    G4double valueE22 = 0;
    G4double valueE12 = 0;
    G4double valueE11 = 0;

    G4double xs11 = 0;   
    G4double xs12 = 0; 
    G4double xs21 = 0; 
    G4double xs22 = 0; 

    if (particleDefinition == G4Electron::ElectronDefinition()) 
    {
      // k should be in eV and energy transfer eV also

      std::vector<double>::iterator t2 = std::upper_bound(eTdummyVec.begin(),eTdummyVec.end(), k);

      std::vector<double>::iterator t1 = t2-1;

      // SI : the following condition avoids situations where energyTransfer >last vector element
      if (energyTransfer <= eVecm[(*t1)].back() && energyTransfer <= eVecm[(*t2)].back() )
      {
        std::vector<double>::iterator e12 = std::upper_bound(eVecm[(*t1)].begin(),eVecm[(*t1)].end(), energyTransfer);
        std::vector<double>::iterator e11 = e12-1;

        std::vector<double>::iterator e22 = std::upper_bound(eVecm[(*t2)].begin(),eVecm[(*t2)].end(), energyTransfer);
        std::vector<double>::iterator e21 = e22-1;

        valueT1  =*t1;
        valueT2  =*t2;
        valueE21 =*e21;
        valueE22 =*e22;
        valueE12 =*e12;
        valueE11 =*e11;

        xs11 = eDiffCrossSectionData[ionizationLevelIndex][valueT1][valueE11];
        xs12 = eDiffCrossSectionData[ionizationLevelIndex][valueT1][valueE12];
        xs21 = eDiffCrossSectionData[ionizationLevelIndex][valueT2][valueE21];
        xs22 = eDiffCrossSectionData[ionizationLevelIndex][valueT2][valueE22];
      }

    }
  
   if (particleDefinition == G4Proton::ProtonDefinition()) 
   {
      // k should be in eV and energy transfer eV also
      std::vector<double>::iterator t2 = std::upper_bound(pTdummyVec.begin(),pTdummyVec.end(), k);
      std::vector<double>::iterator t1 = t2-1;
      
        std::vector<double>::iterator e12 = std::upper_bound(pVecm[(*t1)].begin(),pVecm[(*t1)].end(), energyTransfer);
        std::vector<double>::iterator e11 = e12-1;

        std::vector<double>::iterator e22 = std::upper_bound(pVecm[(*t2)].begin(),pVecm[(*t2)].end(), energyTransfer);
        std::vector<double>::iterator e21 = e22-1;
 
        valueT1  =*t1;
        valueT2  =*t2;
        valueE21 =*e21;
        valueE22 =*e22;
        valueE12 =*e12;
        valueE11 =*e11;

        xs11 = pDiffCrossSectionData[ionizationLevelIndex][valueT1][valueE11];
        xs12 = pDiffCrossSectionData[ionizationLevelIndex][valueT1][valueE12];
        xs21 = pDiffCrossSectionData[ionizationLevelIndex][valueT2][valueE21];
        xs22 = pDiffCrossSectionData[ionizationLevelIndex][valueT2][valueE22];

   }
  
   G4double xsProduct = xs11 * xs12 * xs21 * xs22;
   if (xsProduct != 0.)
   {
     sigma = QuadInterpolator(     valueE11, valueE12, 
				   valueE21, valueE22, 
				   xs11, xs12, 
				   xs21, xs22, 
				   valueT1, valueT2, 
				   k, energyTransfer);
   }
  
 }
  
  return sigma;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

G4double G4DNABornIonisationModel::LogLogInterpolate(G4double e1, 
						       G4double e2, 
						       G4double e, 
						       G4double xs1, 
						       G4double xs2)
{
  G4double a = (std::log10(xs2)-std::log10(xs1)) / (std::log10(e2)-std::log10(e1));
  G4double b = std::log10(xs2) - a*std::log10(e2);
  G4double sigma = a*std::log10(e) + b;
  G4double value = (std::pow(10.,sigma));
  return value;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

G4double G4DNABornIonisationModel::QuadInterpolator(G4double e11, G4double e12, 
						      G4double e21, G4double e22, 
						      G4double xs11, G4double xs12, 
						      G4double xs21, G4double xs22, 
						      G4double t1, G4double t2, 
						      G4double t, G4double e)
{
  G4double interpolatedvalue1 = LogLogInterpolate(e11, e12, e, xs11, xs12);
  G4double interpolatedvalue2 = LogLogInterpolate(e21, e22, e, xs21, xs22);
  G4double value = LogLogInterpolate(t1, t2, t, interpolatedvalue1, interpolatedvalue2);
  return value;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

G4int G4DNABornIonisationModel::RandomSelect(G4double k, const G4String& particle )
{   
  G4int level = 0;

  std::map< G4String,G4DNACrossSectionDataSet*,std::less<G4String> >::iterator pos;
  pos = tableData.find(particle);

  if (pos != tableData.end())
  {
    G4DNACrossSectionDataSet* table = pos->second;

    if (table != 0)
    {
      G4double* valuesBuffer = new G4double[table->NumberOfComponents()];
      const size_t n(table->NumberOfComponents());
      size_t i(n);
      G4double value = 0.;
	    
      while (i>0)
      { 
	i--;
	valuesBuffer[i] = table->GetComponent(i)->FindValue(k);
	value += valuesBuffer[i];
      }
	    
      value *= G4UniformRand();
    
      i = n;
	    
      while (i > 0)
      {
	i--;

	if (valuesBuffer[i] > value)
        {
          delete[] valuesBuffer;
          return i;
        }
	value -= valuesBuffer[i];
      }
	    
      if (valuesBuffer) delete[] valuesBuffer;
    
    }
  }
  else
  {
    G4Exception("G4DNABornIonisationModel::RandomSelect attempting to calculate cross section for wrong particle");
  }
      
  return level;
}

