Gabriele Cosmo
318 lines
10 KiB
C++
318 lines
10 KiB
C++
//
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// ********************************************************************
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// * License and Disclaimer *
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// * *
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// * The Geant4 software is copyright of the Copyright Holders of *
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// * the Geant4 Collaboration. It is provided under the terms and *
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// * conditions of the Geant4 Software License, included in the file *
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// * LICENSE and available at http://cern.ch/geant4/license . These *
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// * include a list of copyright holders. *
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// * *
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// * Neither the authors of this software system, nor their employing *
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// * institutes,nor the agencies providing financial support for this *
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// * work make any representation or warranty, express or implied, *
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// * regarding this software system or assume any liability for its *
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// * use. Please see the license in the file LICENSE and URL above *
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// * for the full disclaimer and the limitation of liability. *
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// * *
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// * This code implementation is the result of the scientific and *
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// * technical work of the GEANT4 collaboration. *
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// * By using, copying, modifying or distributing the software (or *
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// * any work based on the software) you agree to acknowledge its *
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// * use in resulting scientific publications, and indicate your *
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// * acceptance of all terms of the Geant4 Software license. *
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// ********************************************************************
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//
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//
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// Author: Mathieu Karamitros
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//
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// WARNING : This class is released as a prototype.
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// It might strongly evolve or even disapear in the next releases.
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//
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// History:
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// -----------
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// 10 Oct 2011 M.Karamitros created
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//
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// -------------------------------------------------------------------
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#include <algorithm>
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#include "G4DNAOneStepThermalizationModel.hh"
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#include "globals.hh"
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#include "G4Exp.hh"
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#include "G4RandomDirection.hh"
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#include "G4Electron.hh"
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#include "G4EmParameters.hh"
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//------------------------------------------------------------------------------
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namespace DNA {
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namespace Penetration {
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const double
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Meesungnoen2002::gCoeff[13] =
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{ -4.06217193e-08, 3.06848412e-06, -9.93217814e-05,
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1.80172797e-03, -2.01135480e-02, 1.42939448e-01,
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-6.48348714e-01, 1.85227848e+00, -3.36450378e+00,
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4.37785068e+00, -4.20557339e+00, 3.81679083e+00,
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-2.34069784e-01 };
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// fit from Meesungnoen, 2002
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const double
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Meesungnoen2002_amorphous::gCoeff[7] =
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{ 7.3144e-05, -2.2474e-03, 3.4555e-02,
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-4.3574e-01, 2.8954e+00, -1.0381e+00,
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1.4300e+00 };
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// fit from Meesungnoen, 2002
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const double
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Terrisol1990::gEnergies_T1990[11] =
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{ 0.2, 0.5, 1, 2, 3, 4, 5, 6, 7,
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// The two last are not in the dataset
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8, 9}; // eV
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const double
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Terrisol1990::gStdDev_T1990[11] =
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{ 17.68*CLHEP::angstrom,
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22.3*CLHEP::angstrom,
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28.49*CLHEP::angstrom,
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45.35*CLHEP::angstrom,
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70.03*CLHEP::angstrom,
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98.05*CLHEP::angstrom,
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120.56*CLHEP::angstrom,
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132.73*CLHEP::angstrom,
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142.60*CLHEP::angstrom,
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// the above value as given in the paper's table does not match
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// b=27.22 nm nor the mean value. 129.62*CLHEP::angstrom could be
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// a better fit.
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//
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// The two last are made up
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137.9*CLHEP::angstrom,
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120.7*CLHEP::angstrom
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}; // angstrom
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//----------------------------------------------------------------------------
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double Meesungnoen2002::GetRmean(double k){
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G4double k_eV = k/eV;
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if(k_eV>0.1){ // data until 0.2 eV
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G4double r_mean = 0;
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for(int8_t i=12; i!=-1 ; --i){
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r_mean+=gCoeff[12-i]*std::pow(k_eV,i);
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}
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r_mean*=CLHEP::nanometer;
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return r_mean;
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}
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return 0;
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}
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double Meesungnoen2002_amorphous::GetRmean(double k){
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G4double k_eV = k/eV;
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if(k_eV>0.1){ // data until 0.2 eV
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G4double r_mean = 0;
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for(int8_t i=6; i!=-1 ; --i){
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r_mean+=gCoeff[6-i]*std::pow(k_eV,i);
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}
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r_mean*=CLHEP::nanometer;
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return r_mean;
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}
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return 0;
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}
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void GetGaussianPenetrationFromRmean3D(G4double r_mean,
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G4ThreeVector& displacement)
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{
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if(r_mean == 0)
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{
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// rare events:
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// prevent H2O and secondary electron from being placed at the same position
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displacement = G4RandomDirection() * (1e-3*CLHEP::nanometer);
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return;
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}
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static constexpr double convertRmean3DToSigma1D = 0.62665706865775006;
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// = sqrt(CLHEP::pi)/pow(2,3./2.)
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// Use r_mean to build a 3D gaussian
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const double sigma1D = r_mean * convertRmean3DToSigma1D;
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displacement = G4ThreeVector(G4RandGauss::shoot(0, sigma1D),
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G4RandGauss::shoot(0, sigma1D),
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G4RandGauss::shoot(0, sigma1D));
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}
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void Meesungnoen2002::GetPenetration(G4double k,
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G4ThreeVector& displacement)
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{
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GetGaussianPenetrationFromRmean3D(GetRmean(k), displacement);
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}
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void Meesungnoen2002_amorphous::GetPenetration(G4double k,
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G4ThreeVector& displacement)
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{
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GetGaussianPenetrationFromRmean3D(GetRmean(k), displacement);
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}
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void Kreipl2009::GetPenetration(G4double k,
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G4ThreeVector& displacement)
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{
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G4double r_mean = Meesungnoen2002::GetRmean(k);
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if(r_mean == 0)
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{
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// rare events:
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// prevent H2O and secondary electron from being placed at the same position
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displacement = G4RandomDirection() * (1e-3*CLHEP::nanometer);
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return;
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}
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double r = G4RandGamma::shoot(2,2);
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displacement = G4RandomDirection() * r * r_mean;
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}
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//----------------------------------------------------------------------------
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void Ritchie1994::GetPenetration(G4double k,
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G4ThreeVector& displacement)
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{
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GetGaussianPenetrationFromRmean3D(k/eV * 1.8 * nm, // r_mean
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displacement);
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}
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//----------------------------------------------------------------------------
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double Terrisol1990::Get3DStdDeviation(double energy){
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G4double k_eV = energy/eV;
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if(k_eV < 0.2){
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// rare events:
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// prevent H2O and secondary electron to be at the spot
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return 1e-3*CLHEP::nanometer;
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}
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if(k_eV == 9.){
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return gStdDev_T1990[10];
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}
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if(k_eV > 9.){
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G4ExceptionDescription description;
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description << "Terrisol1990 is not tabulated for energies greater than 9eV";
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G4Exception("Terrisol1990::Get3DStdDeviation",
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"INVALID_ARGUMENT",
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FatalErrorInArgument,
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description);
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}
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size_t lowBin, upBin;
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if(k_eV >= 1.){
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lowBin=std::floor(k_eV)+1;
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upBin=std::min(lowBin+1, size_t(10));
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}
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else{
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auto it=std::lower_bound(&gEnergies_T1990[0],
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&gEnergies_T1990[2],
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k_eV);
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lowBin = it-&gEnergies_T1990[0];
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upBin = lowBin+1;
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}
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double lowE = gEnergies_T1990[lowBin];
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double upE = gEnergies_T1990[upBin];
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double lowS = gStdDev_T1990[lowBin];
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double upS = gStdDev_T1990[upBin];
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double tanA = (lowS-upS)/(lowE-upE);
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double sigma3D = lowS + (k_eV-lowE)*tanA;
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return sigma3D;
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}
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double Terrisol1990::GetRmean(double energy){
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double sigma3D=Get3DStdDeviation(energy);
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static constexpr double s2r=1.595769121605731; // = pow(2,3./2.)/sqrt(CLHEP::pi)
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double r_mean=sigma3D*s2r;
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return r_mean;
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}
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void Terrisol1990::GetPenetration(G4double energy,
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G4ThreeVector& displacement){
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double sigma3D = Get3DStdDeviation(energy);
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static constexpr double factor = 2.20496999539; // = 1./(3. - 8./CLHEP::pi);
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double sigma1D = std::sqrt(std::pow(sigma3D, 2.)*factor);
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displacement = G4ThreeVector(G4RandGauss::shoot(0, sigma1D),
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G4RandGauss::shoot(0, sigma1D),
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G4RandGauss::shoot(0, sigma1D));
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}
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} // Penetration
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} // DNA
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//------------------------------------------------------------------------------
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G4VEmModel* G4DNASolvationModelFactory::Create(const G4String& penetrationModel)
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{
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G4String modelNamePrefix("DNAOneStepThermalizationModel_");
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if(penetrationModel == "Terrisol1990")
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{
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return new G4TDNAOneStepThermalizationModel<DNA::Penetration::Terrisol1990>(G4Electron::Definition(), modelNamePrefix + penetrationModel);
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}
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if(penetrationModel == "Meesungnoen2002")
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{
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return new G4TDNAOneStepThermalizationModel<DNA::Penetration::Meesungnoen2002>(G4Electron::Definition(), modelNamePrefix + penetrationModel);
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}
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if(penetrationModel == "Meesungnoen2002_amorphous")
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{
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return new G4TDNAOneStepThermalizationModel<DNA::Penetration::Meesungnoen2002_amorphous>(G4Electron::Definition(), modelNamePrefix + penetrationModel);
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}
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if(penetrationModel == "Kreipl2009")
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{
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return new G4TDNAOneStepThermalizationModel<DNA::Penetration::Kreipl2009>(G4Electron::Definition(), modelNamePrefix + penetrationModel);
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}
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if(penetrationModel == "Ritchie1994")
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{
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return new G4TDNAOneStepThermalizationModel<DNA::Penetration::Ritchie1994>(G4Electron::Definition(), modelNamePrefix + penetrationModel);
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}
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G4ExceptionDescription description;
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description << penetrationModel + " is not a valid model name.";
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G4Exception("G4DNASolvationModelFactory::Create",
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"INVALID_ARGUMENT",
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FatalErrorInArgument,
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description,
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"Options are: Terrisol1990, Meesungnoen2002, Ritchie1994.");
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return nullptr;
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}
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//------------------------------------------------------------------------------
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G4VEmModel* G4DNASolvationModelFactory::GetMacroDefinedModel()
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{
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auto dnaSubType = G4EmParameters::Instance()->DNAeSolvationSubType();
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switch(dnaSubType)
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{
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case fRitchie1994eSolvation:
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return Create("Ritchie1994");
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case fTerrisol1990eSolvation:
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return Create("Terrisol1990");
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case fKreipl2009eSolvation:
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return Create("Kreipl2009");
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case fMeesungnoensolid2002eSolvation:
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return Create("Meesungnoen2002_amorphous");
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case fMeesungnoen2002eSolvation:
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case fDNAUnknownModel:
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return Create("Meesungnoen2002");
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default:
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G4Exception("G4DNASolvationModelFactory::GetMacroDefinedModel",
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"DnaSubType",
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FatalErrorInArgument,
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"The solvation parameter stored in G4EmParameters is unknown. Supported types are: fRitchie1994eSolvation, fTerrisol1990eSolvation, fMeesungnoen2002eSolvation.");
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}
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return nullptr;
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}
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