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This commit is contained in:
Gabriele Cosmo
2018-06-29 10:58:11 +02:00
parent fe81a77428
commit 6aa23be517
1581 changed files with 124288 additions and 83758 deletions
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source/processes/electromagnetic/dna/models/src/G4DNAOneStepThermalizationModel.cc
+212 -146
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@@ -23,7 +23,7 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// $Id: G4DNAOneStepThermalizationModel.cc 101807 2016-11-30 13:42:28Z gunter $
// $Id: G4DNAOneStepThermalizationModel.cc 110873 2018-06-22 13:11:22Z gcosmo $
//
// Author: Mathieu Karamitros
//
@@ -38,160 +38,226 @@
#include <algorithm>
#include "G4DNAOneStepThermalizationModel.hh"
#include "globals.hh"
#include "G4Exp.hh"
#include "G4RandomDirection.hh"
#include "G4Electron.hh"
#include "G4EmParameters.hh"
//------------------------------------------------------------------------------
namespace DNA{ namespace Penetration{
namespace DNA {
namespace Penetration {
const double
Meesungnoen2002::gCoeff[13] =
{ -4.06217193e-08, 3.06848412e-06, -9.93217814e-05,
1.80172797e-03, -2.01135480e-02, 1.42939448e-01,
-6.48348714e-01, 1.85227848e+00, -3.36450378e+00,
4.37785068e+00, -4.20557339e+00, 3.81679083e+00,
-2.34069784e-01 };
// fit from Meesungnoen, 2002
const double
Terrisol1990::gEnergies_T1990[11] =
{ 0.2, 0.5, 1, 2, 3, 4, 5, 6, 7,
// The two last are not in the dataset
8, 9}; // eV
const double
Terrisol1990::gStdDev_T1990[11] =
{ 17.68*CLHEP::angstrom,
22.3*CLHEP::angstrom,
28.49*CLHEP::angstrom,
45.35*CLHEP::angstrom,
70.03*CLHEP::angstrom,
98.05*CLHEP::angstrom,
120.56*CLHEP::angstrom,
132.73*CLHEP::angstrom,
142.60*CLHEP::angstrom,
// the above value as given in the paper's table does not match
// b=27.22 nm nor the mean value. 129.62*CLHEP::angstrom could be
// a better fit.
//
// The two last are made up
137.9*CLHEP::angstrom,
120.7*CLHEP::angstrom
}; // angstrom
//----------------------------------------------------------------------------
double Meesungnoen2002::GetRmean(double k){
G4double k_eV = k/eV;
if(k_eV>0.1){ // data until 0.2 eV
G4double r_mean = 0;
for(int8_t i=12; i!=-1 ; --i){
r_mean+=gCoeff[12-i]*std::pow(k_eV,i);
}
r_mean*=CLHEP::nanometer;
return r_mean;
}
return 0;
}
void Meesungnoen2002::GetPenetration(G4double k,
G4ThreeVector& displacement){
displacement=G4ThreeVector(0,0,0);
G4double k_eV = k/eV;
if(k_eV>0.1){ // data until 0.2 eV
G4double r_mean = 0;
for(int8_t i=12; i!=-1 ; --i){
r_mean+=gCoeff[12-i]*std::pow(k_eV,i);
}
r_mean*=nanometer;
//G4cout << "rmean = " << r_mean << G4endl;
static constexpr double r2s=0.62665706865775006; //sqrt(CLHEP::pi)/pow(2,3./2.)
// Use r_mean to build a 3D gaussian
double sigma3D = r_mean*r2s;
double x = G4RandGauss::shoot(0,sigma3D);
double y = G4RandGauss::shoot(0,sigma3D);
double z = G4RandGauss::shoot(0,sigma3D);
displacement=G4ThreeVector(x,y,z);
}
else{
displacement=G4RandomDirection()*(1e-3*CLHEP::nanometer);
// rare events:
// prevent H2O and secondary electron to be at the spot
}
}
//----------------------------------------------------------------------------
double Terrisol1990::Get3DStdDeviation(double energy){
G4double k_eV = energy/eV;
if(k_eV < 0.2) return 1e-3*CLHEP::nanometer;
// rare events:
// prevent H2O and secondary electron to be at the spot
if(k_eV == 9.) return gStdDev_T1990[10];
// TODO if k_eV > 9
const double
Meesungnoen2002::gCoeff[13] =
{ -4.06217193e-08, 3.06848412e-06, -9.93217814e-05,
1.80172797e-03, -2.01135480e-02, 1.42939448e-01,
-6.48348714e-01, 1.85227848e+00, -3.36450378e+00,
4.37785068e+00, -4.20557339e+00, 3.81679083e+00,
-2.34069784e-01 };
// fit from Meesungnoen, 2002
size_t lowBin, upBin;
if(k_eV >= 1.){
lowBin=std::floor(k_eV)+1;
upBin=std::min(lowBin+1, size_t(10));
const double
Terrisol1990::gEnergies_T1990[11] =
{ 0.2, 0.5, 1, 2, 3, 4, 5, 6, 7,
// The two last are not in the dataset
8, 9}; // eV
const double
Terrisol1990::gStdDev_T1990[11] =
{ 17.68*CLHEP::angstrom,
22.3*CLHEP::angstrom,
28.49*CLHEP::angstrom,
45.35*CLHEP::angstrom,
70.03*CLHEP::angstrom,
98.05*CLHEP::angstrom,
120.56*CLHEP::angstrom,
132.73*CLHEP::angstrom,
142.60*CLHEP::angstrom,
// the above value as given in the paper's table does not match
// b=27.22 nm nor the mean value. 129.62*CLHEP::angstrom could be
// a better fit.
//
// The two last are made up
137.9*CLHEP::angstrom,
120.7*CLHEP::angstrom
}; // angstrom
//----------------------------------------------------------------------------
double Meesungnoen2002::GetRmean(double k){
G4double k_eV = k/eV;
if(k_eV>0.1){ // data until 0.2 eV
G4double r_mean = 0;
for(int8_t i=12; i!=-1 ; --i){
r_mean+=gCoeff[12-i]*std::pow(k_eV,i);
}
else{
auto it=std::lower_bound(&gEnergies_T1990[0],
&gEnergies_T1990[2],
k_eV);
lowBin = it-&gEnergies_T1990[0];
upBin = lowBin+1;
}
double lowE = gEnergies_T1990[lowBin];
double upE = gEnergies_T1990[upBin];
// G4cout << lowE << " " << upE << G4endl;
double lowS = gStdDev_T1990[lowBin];
double upS = gStdDev_T1990[upBin];
double tanA = (lowS-upS)/(lowE-upE);
double sigma3D = lowS + (k_eV-lowE)*tanA;
return sigma3D;
}
double Terrisol1990::GetRmean(double energy){
double sigma3D=Get3DStdDeviation(energy);
static constexpr double s2r=1.595769121605731;
// pow(2,3./2.)/sqrt(CLHEP::pi)
double r_mean=sigma3D*s2r;
r_mean*=CLHEP::nanometer;
return r_mean;
}
void Terrisol1990::GetPenetration(G4double energy,
G4ThreeVector& displacement){
double sigma3D=Get3DStdDeviation(energy);
// G4cout << "sigma3D = " << sigma3D/CLHEP::nanometer << G4endl;
static constexpr double factor = 2.20496999539;
// 1./(3. - 8./CLHEP::pi);
double sigma1D = std::sqrt(std::pow(sigma3D, 2.)*factor);
// G4cout << "sigma1D = " << sigma1D/CLHEP::nanometer << G4endl;
return 0;
}
double x = G4RandGauss::shoot(0.,sigma1D);
double y = G4RandGauss::shoot(0.,sigma1D);
double z = G4RandGauss::shoot(0.,sigma1D);
displacement=G4ThreeVector(x,y,z);
// G4cout << "displacement[nm]: "
// << displacement.mag()/CLHEP::nanometer << G4endl;
void GetGaussianPenetrationFromRmean3D(G4double r_mean,
G4ThreeVector& displacement)
{
if(r_mean == 0)
{
// rare events:
// prevent H2O and secondary electron from being placed at the same position
displacement = G4RandomDirection() * (1e-3*CLHEP::nanometer);
return;
}
}}
static constexpr double convertRmean3DToSigma1D = 0.62665706865775006;
// = sqrt(CLHEP::pi)/pow(2,3./2.)
// Use r_mean to build a 3D gaussian
const double sigma1D = r_mean * convertRmean3DToSigma1D;
displacement = G4ThreeVector(G4RandGauss::shoot(0, sigma1D),
G4RandGauss::shoot(0, sigma1D),
G4RandGauss::shoot(0, sigma1D));
}
void Meesungnoen2002::GetPenetration(G4double k,
G4ThreeVector& displacement)
{
GetGaussianPenetrationFromRmean3D(GetRmean(k), displacement);
}
//----------------------------------------------------------------------------
void Ritchie1994::GetPenetration(G4double k,
G4ThreeVector& displacement)
{
GetGaussianPenetrationFromRmean3D(k/eV * 1.8 * nm, // r_mean
displacement);
}
//----------------------------------------------------------------------------
double Terrisol1990::Get3DStdDeviation(double energy){
G4double k_eV = energy/eV;
if(k_eV < 0.2){
// rare events:
// prevent H2O and secondary electron to be at the spot
return 1e-3*CLHEP::nanometer;
}
else if(k_eV == 9.){
return gStdDev_T1990[10];
}
else if(k_eV > 9.){
G4ExceptionDescription description;
description << "Terrisol1990 is not tabulated for energies greater than 9eV";
G4Exception("Terrisol1990::Get3DStdDeviation",
"INVALID_ARGUMENT",
FatalErrorInArgument,
description);
}
size_t lowBin, upBin;
if(k_eV >= 1.){
lowBin=std::floor(k_eV)+1;
upBin=std::min(lowBin+1, size_t(10));
}
else{
auto it=std::lower_bound(&gEnergies_T1990[0],
&gEnergies_T1990[2],
k_eV);
lowBin = it-&gEnergies_T1990[0];
upBin = lowBin+1;
}
double lowE = gEnergies_T1990[lowBin];
double upE = gEnergies_T1990[upBin];
double lowS = gStdDev_T1990[lowBin];
double upS = gStdDev_T1990[upBin];
double tanA = (lowS-upS)/(lowE-upE);
double sigma3D = lowS + (k_eV-lowE)*tanA;
return sigma3D;
}
double Terrisol1990::GetRmean(double energy){
double sigma3D=Get3DStdDeviation(energy);
static constexpr double s2r=1.595769121605731; // = pow(2,3./2.)/sqrt(CLHEP::pi)
double r_mean=sigma3D*s2r;
return r_mean;
}
void Terrisol1990::GetPenetration(G4double energy,
G4ThreeVector& displacement){
double sigma3D = Get3DStdDeviation(energy);
static constexpr double factor = 2.20496999539; // = 1./(3. - 8./CLHEP::pi);
double sigma1D = std::sqrt(std::pow(sigma3D, 2.)*factor);
displacement = G4ThreeVector(G4RandGauss::shoot(0, sigma1D),
G4RandGauss::shoot(0, sigma1D),
G4RandGauss::shoot(0, sigma1D));
}
} // Penetration
} // DNA
//------------------------------------------------------------------------------
G4VEmModel* G4DNASolvationModelFactory::Create(const G4String& penetrationModel)
{
G4String modelNamePrefix("DNAOneStepThermalizationModel_");
if(penetrationModel == "Terrisol1990")
{
return new G4TDNAOneStepThermalizationModel<DNA::Penetration::Terrisol1990>(G4Electron::Definition(), modelNamePrefix + penetrationModel);
}
else if(penetrationModel == "Meesungnoen2002")
{
return new G4TDNAOneStepThermalizationModel<DNA::Penetration::Meesungnoen2002>(G4Electron::Definition(), modelNamePrefix + penetrationModel);
}
else if(penetrationModel == "Ritchie1994")
{
return new G4TDNAOneStepThermalizationModel<DNA::Penetration::Ritchie1994>(G4Electron::Definition(), modelNamePrefix + penetrationModel);
}
else
{
G4ExceptionDescription description;
description << penetrationModel + " is not a valid model name.";
G4Exception("G4DNASolvationModelFactory::Create",
"INVALID_ARGUMENT",
FatalErrorInArgument,
description,
"Options are: Terrisol1990, Meesungnoen2002, Ritchie1994.");
}
return nullptr;
}
//------------------------------------------------------------------------------
G4VEmModel* G4DNASolvationModelFactory::GetMacroDefinedModel()
{
auto dnaSubType = G4EmParameters::Instance()->DNAeSolvationSubType();
switch(dnaSubType)
{
case fRitchie1994eSolvation:
return Create("Ritchie1994");
case fTerrisol1990eSolvation:
return Create("Terrisol1990");
case fMeesungnoen2002eSolvation:
case fDNAUnknownModel:
return Create("Meesungnoen2002");
default:
G4Exception("G4DNASolvationModelFactory::GetMacroDefinedModel",
"DnaSubType",
FatalErrorInArgument,
"The solvation parameter stored in G4EmParameters is unknown. Supported types are: fRitchie1994eSolvation, fTerrisol1990eSolvation, fMeesungnoen2002eSolvation.");
}
return nullptr;
}