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This commit is contained in:
Gabriele Cosmo
2019-12-06 15:12:28 +01:00
parent b2a62ae692
commit 5baee230e9
2997 changed files with 141580 additions and 98673 deletions
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source/processes/electromagnetic/dna/models/src/G4DNAELSEPAElasticModel.cc
Executable
+493
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@@ -0,0 +1,493 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// $Id: G4DNAELSEPAElasticModel.cc 97497 2016-06-03 11:41:57Z matkara $
//
#include "G4DNAELSEPAElasticModel.hh"
#include "G4PhysicalConstants.hh"
#include "G4SystemOfUnits.hh"
#include "G4DNAMolecularMaterial.hh"
#include "G4Exp.hh"
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
using namespace std;
#define ELSEPA_VERBOSE
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4DNAELSEPAElasticModel::
G4DNAELSEPAElasticModel(const G4ParticleDefinition*, const G4String& nam) :
G4VEmModel(nam), isInitialised(false)
{
SetLowEnergyLimit(10. * eV);
SetHighEnergyLimit(1. * MeV);
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
#ifdef ELSEPA_VERBOSE
if (verboseLevel > 0)
{
G4cout << "ELSEPA Elastic model is constructed "
<< G4endl
<< "Energy range: "
<< LowEnergyLimit() / eV << " eV - "
<< HighEnergyLimit() / MeV << " MeV"
<< G4endl;
}
#endif
fParticleChangeForGamma = 0;
fpMolWaterDensity = 0;
fpData = 0;
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4DNAELSEPAElasticModel::~G4DNAELSEPAElasticModel()
{
// For total cross section
if(fpData) delete fpData;
// For final state
eVecm.clear();
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
void G4DNAELSEPAElasticModel::Initialise(const G4ParticleDefinition* particle,
const G4DataVector& /*cuts*/)
{
#ifdef ELSEPA_VERBOSE
if (verboseLevel > 3)
{
G4cout << "Calling G4DNAELSEPAElasticModel::Initialise()" << G4endl;
}
#endif
if(particle->GetParticleName() != "e-")
{
G4Exception("G4DNAELSEPAElasticModel::Initialise",
"em0002",
FatalException,
"Model not applicable to particle type.");
}
// Energy limits
if (LowEnergyLimit() < 10*eV)
{
G4cout << "G4DNAELSEPAElasticModel: low energy limit increased from "
<< LowEnergyLimit()/eV << " eV to " << 10 << " eV"
<< G4endl;
SetLowEnergyLimit(10.*eV);
}
if (HighEnergyLimit() > 1.*MeV)
{
G4cout << "G4DNAELSEPAElasticModel: high energy limit decreased from "
<< HighEnergyLimit()/MeV << " MeV to " << 1. << " MeV"
<< G4endl;
SetHighEnergyLimit(1.*MeV);
}
if (isInitialised) { return; }
// *** ELECTRON
// For total cross section
// Reading of data files
G4double scaleFactor = 1*cm*cm;
G4String fileElectron("dna/sigma_elastic_e_elsepa_muffin");
// Alternative option
// G4String fileElectron("dna/sigma_elastic_e_elsepa_free");
fpData = new G4DNACrossSectionDataSet(new G4LogLogInterpolation(),
eV,
scaleFactor );
fpData->LoadData(fileElectron);
// For final state
char *path = getenv("G4LEDATA");
if (!path)
{
G4Exception("G4ELSEPAElasticModel::Initialise",
"em0006",
FatalException,
"G4LEDATA environment variable not set.");
return;
}
std::ostringstream eFullFileName;
// Alternative option
// eFullFileName << path << "/dna/sigmadiff_cumulated_elastic_e_elsepa_free.dat";
eFullFileName << path << "/dna/sigmadiff_cumulated_elastic_e_elsepa_muffin.dat";
std::ifstream eDiffCrossSection(eFullFileName.str().c_str());
if (!eDiffCrossSection)
{
G4ExceptionDescription errMsg;
errMsg << "Missing data file:/dna/sigmadiff_cumulated_elastic_e_elsepa_muffin.dat; "
<< "please use G4EMLOW7.8 and above.";
G4Exception("G4DNAELSEPAElasticModel::Initialise",
"em0003",
FatalException,
errMsg);
}
// March 25th, 2014 - Vaclav Stepan, Sebastien Incerti
// Added clear for MT
eTdummyVec.clear();
eVecm.clear();
eDiffCrossSectionData.clear();
//
eTdummyVec.push_back(0.);
while(!eDiffCrossSection.eof())
{
double tDummy;
double eDummy;
eDiffCrossSection >> tDummy >> eDummy;
// SI : mandatory eVecm initialization
if (tDummy != eTdummyVec.back())
{
eTdummyVec.push_back(tDummy);
eVecm[tDummy].push_back(0.);
}
eDiffCrossSection >> eDiffCrossSectionData[tDummy][eDummy];
if (eDummy != eVecm[tDummy].back()) eVecm[tDummy].push_back(eDummy);
}
// End final state
#ifdef ELSEPA_VERBOSE
if (verboseLevel>0)
{
if (verboseLevel > 2)
{
G4cout << "Loaded cross section files for ELSEPA Elastic model" << G4endl;
}
G4cout << "ELSEPA Elastic model is initialized " << G4endl
<< "Energy range: "
<< LowEnergyLimit() / eV << " eV - "
<< HighEnergyLimit() / MeV << " MeV"
<< G4endl;
}
#endif
// Initialize water density pointer
G4DNAMolecularMaterial::Instance()->Initialize();
fpMolWaterDensity = G4DNAMolecularMaterial::Instance()->
GetNumMolPerVolTableFor(G4Material::GetMaterial("G4_WATER"));
fParticleChangeForGamma = GetParticleChangeForGamma();
isInitialised = true;
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4double
G4DNAELSEPAElasticModel::
CrossSectionPerVolume(const G4Material* material,
#ifdef ELSEPA_VERBOSE
const G4ParticleDefinition* p,
#else
const G4ParticleDefinition*,
#endif
G4double ekin,
G4double,
G4double)
{
#ifdef ELSEPA_VERBOSE
if (verboseLevel > 3)
{
G4cout << "Calling CrossSectionPerVolume() of G4DNAELSEPAElasticModel"
<< G4endl;
}
#endif
// Calculate total cross section for model
G4double sigma = 0.;
G4double waterDensity = (*fpMolWaterDensity)[material->GetIndex()];
if(waterDensity!= 0.0)
{
if (ekin < HighEnergyLimit() && ekin >= LowEnergyLimit())
{
//SI : XS must not be zero otherwise sampling of secondaries method ignored
//
sigma = fpData->FindValue(ekin);
}
#ifdef ELSEPA_VERBOSE
if (verboseLevel > 2)
{
G4cout << "__________________________________" << G4endl;
G4cout << "=== G4DNAELSEPAElasticModel - XS INFO START" << G4endl;
G4cout << "=== Kinetic energy(eV)=" << ekin/eV << " particle : " << p->GetParticleName() << G4endl;
G4cout << "=== Cross section per water molecule (cm^2)=" << sigma/cm/cm << G4endl;
G4cout << "=== Cross section per water molecule (cm^-1)=" << sigma*waterDensity/(1./cm) << G4endl;
G4cout << "=== G4DNAELSEPAElasticModel - XS INFO END" << G4endl;
}
#endif
}
return sigma*waterDensity;
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
void G4DNAELSEPAElasticModel::SampleSecondaries(std::vector<G4DynamicParticle*>* /*fvect*/,
const G4MaterialCutsCouple* /*couple*/,
const G4DynamicParticle* aDynamicElectron,
G4double,
G4double)
{
#ifdef ELSEPA_VERBOSE
if (verboseLevel > 3)
{
G4cout << "Calling SampleSecondaries() of G4DNAELSEPAElasticModel" << G4endl;
}
#endif
G4double electronEnergy0 = aDynamicElectron->GetKineticEnergy();
// if (electronEnergy0 < HighEnergyLimit()) // necessaire ?
{
G4double cosTheta = RandomizeCosTheta(electronEnergy0);
G4double phi = 2. * pi * G4UniformRand();
G4ThreeVector zVers = aDynamicElectron->GetMomentumDirection();
G4ThreeVector xVers = zVers.orthogonal();
G4ThreeVector yVers = zVers.cross(xVers);
G4double xDir = std::sqrt(1. - cosTheta*cosTheta);
G4double yDir = xDir;
xDir *= std::cos(phi);
yDir *= std::sin(phi);
G4ThreeVector zPrimeVers((xDir*xVers + yDir*yVers + cosTheta*zVers));
fParticleChangeForGamma->ProposeMomentumDirection(zPrimeVers.unit());
fParticleChangeForGamma->SetProposedKineticEnergy(electronEnergy0);
// necessaire ?
}
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4double G4DNAELSEPAElasticModel::Theta(//G4ParticleDefinition * particleDefinition,
G4double k,
G4double integrDiff)
{
G4double theta = 0.;
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()) // necessaire ?
{
std::vector<double>::iterator t2 = std::upper_bound(eTdummyVec.begin(),
eTdummyVec.end(), k);
std::vector<double>::iterator t1 = t2 - 1;
std::vector<double>::iterator e12 = std::upper_bound(eVecm[(*t1)].begin(),
eVecm[(*t1)].end(),
integrDiff);
std::vector<double>::iterator e11 = e12 - 1;
std::vector<double>::iterator e22 = std::upper_bound(eVecm[(*t2)].begin(),
eVecm[(*t2)].end(),
integrDiff);
std::vector<double>::iterator e21 = e22 - 1;
valueT1 = *t1;
valueT2 = *t2;
valueE21 = *e21;
valueE22 = *e22;
valueE12 = *e12;
valueE11 = *e11;
xs11 = eDiffCrossSectionData[valueT1][valueE11];
xs12 = eDiffCrossSectionData[valueT1][valueE12];
xs21 = eDiffCrossSectionData[valueT2][valueE21];
xs22 = eDiffCrossSectionData[valueT2][valueE22];
}
if (xs11 == 0 && xs12 == 0 && xs21 == 0 && xs22 == 0) return (0.);
theta = QuadInterpolator(valueE11, valueE12, valueE21, valueE22, xs11, xs12,
xs21, xs22, valueT1, valueT2, k, integrDiff);
return theta;
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4double G4DNAELSEPAElasticModel::LinLogInterpolate(G4double e1,
G4double e2,
G4double e,
G4double xs1,
G4double xs2)
{
G4double d1 = std::log(xs1);
G4double d2 = std::log(xs2);
G4double value = G4Exp(d1 + (d2 - d1) * (e - e1) / (e2 - e1));
return value;
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4double G4DNAELSEPAElasticModel::LinLinInterpolate(G4double e1,
G4double e2,
G4double e,
G4double xs1,
G4double xs2)
{
G4double d1 = xs1;
G4double d2 = xs2;
G4double value = (d1 + (d2 - d1) * (e - e1) / (e2 - e1));
return value;
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4double G4DNAELSEPAElasticModel::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 G4DNAELSEPAElasticModel::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)
{
// Log-Log
/*
G4double interpolatedvalue1 = LogLogInterpolate(e11, e12, e, xs11, xs12);
G4double interpolatedvalue2 = LogLogInterpolate(e21, e22, e, xs21, xs22);
G4double value = LogLogInterpolate(t1, t2, t, interpolatedvalue1, interpolatedvalue2);
// Lin-Log
G4double interpolatedvalue1 = LinLogInterpolate(e11, e12, e, xs11, xs12);
G4double interpolatedvalue2 = LinLogInterpolate(e21, e22, e, xs21, xs22);
G4double value = LinLogInterpolate(t1, t2, t, interpolatedvalue1, interpolatedvalue2);
*/
// Lin-Lin
G4double interpolatedvalue1 = LinLinInterpolate(e11, e12, e, xs11, xs12);
G4double interpolatedvalue2 = LinLinInterpolate(e21, e22, e, xs21, xs22);
G4double value = LinLinInterpolate(t1, t2, t, interpolatedvalue1,
interpolatedvalue2);
return value;
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4double G4DNAELSEPAElasticModel::RandomizeCosTheta(G4double k)
{
G4double integrdiff = 0;
G4double uniformRand = G4UniformRand();
integrdiff = uniformRand;
G4double theta = 0.;
G4double cosTheta = 0.;
theta = Theta(//G4Electron::ElectronDefinition(),
k / eV, integrdiff);
cosTheta = std::cos(theta * pi / 180);
return cosTheta;
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
void G4DNAELSEPAElasticModel::SetKillBelowThreshold(G4double)
{
G4ExceptionDescription errMsg;
errMsg << "The method G4DNAELSEPAElasticModel::SetKillBelowThreshold is deprecated";
G4Exception("G4DNAELSEPAElasticModel::SetKillBelowThreshold",
"deprecated",
JustWarning,
errMsg);
}
source/processes/electromagnetic/dna/models/src/G4DNAMolecularReaction.cc
+2 -2
View File
@@ -95,8 +95,8 @@ std::unique_ptr<G4ITReactionChange> G4DNAMolecularReaction::MakeReaction(const G
{
const G4double D1 = pMoleculeA->GetDiffusionCoefficient();
const G4double D2 = pMoleculeB->GetDiffusionCoefficient();
const G4double sqrD1 = D1 == 0. ? 0. : sqrt(D1);
const G4double sqrD2 = D2 == 0. ? 0. : sqrt(D2);
const G4double sqrD1 = D1 == 0. ? 0. : std::sqrt(D1);
const G4double sqrD2 = D2 == 0. ? 0. : std::sqrt(D2);
const G4double inv_numerator = 1./(sqrD1 + sqrD2);
const G4ThreeVector reactionSite = sqrD2 * inv_numerator * trackA.GetPosition()
+ sqrD1 * inv_numerator * trackB.GetPosition();
source/processes/electromagnetic/dna/models/src/G4DNAOneStepThermalizationModel.cc
+57
View File
@@ -57,6 +57,13 @@ Meesungnoen2002::gCoeff[13] =
-2.34069784e-01 };
// fit from Meesungnoen, 2002
const double
Meesungnoen2002_amorphous::gCoeff[7] =
{ 7.3144e-05, -2.2474e-03, 3.4555e-02,
-4.3574e-01, 2.8954e+00, -1.0381e+00,
1.4300e+00 };
// fit from Meesungnoen, 2002
const double
Terrisol1990::gEnergies_T1990[11] =
{ 0.2, 0.5, 1, 2, 3, 4, 5, 6, 7,
@@ -99,6 +106,20 @@ double Meesungnoen2002::GetRmean(double k){
return 0;
}
double Meesungnoen2002_amorphous::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=6; i!=-1 ; --i){
r_mean+=gCoeff[6-i]*std::pow(k_eV,i);
}
r_mean*=CLHEP::nanometer;
return r_mean;
}
return 0;
}
void GetGaussianPenetrationFromRmean3D(G4double r_mean,
G4ThreeVector& displacement)
{
@@ -126,6 +147,30 @@ void Meesungnoen2002::GetPenetration(G4double k,
GetGaussianPenetrationFromRmean3D(GetRmean(k), displacement);
}
void Meesungnoen2002_amorphous::GetPenetration(G4double k,
G4ThreeVector& displacement)
{
GetGaussianPenetrationFromRmean3D(GetRmean(k), displacement);
}
void Kreipl2009::GetPenetration(G4double k,
G4ThreeVector& displacement)
{
G4double r_mean = Meesungnoen2002::GetRmean(k);
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;
}
double r = G4RandGamma::shoot(2,2);
displacement = G4RandomDirection() * r * r_mean;
}
//----------------------------------------------------------------------------
void Ritchie1994::GetPenetration(G4double k,
@@ -220,6 +265,14 @@ G4VEmModel* G4DNASolvationModelFactory::Create(const G4String& penetrationModel)
{
return new G4TDNAOneStepThermalizationModel<DNA::Penetration::Meesungnoen2002>(G4Electron::Definition(), modelNamePrefix + penetrationModel);
}
else if(penetrationModel == "Meesungnoen2002_amorphous")
{
return new G4TDNAOneStepThermalizationModel<DNA::Penetration::Meesungnoen2002_amorphous>(G4Electron::Definition(), modelNamePrefix + penetrationModel);
}
else if(penetrationModel == "Kreipl2009")
{
return new G4TDNAOneStepThermalizationModel<DNA::Penetration::Kreipl2009>(G4Electron::Definition(), modelNamePrefix + penetrationModel);
}
else if(penetrationModel == "Ritchie1994")
{
return new G4TDNAOneStepThermalizationModel<DNA::Penetration::Ritchie1994>(G4Electron::Definition(), modelNamePrefix + penetrationModel);
@@ -248,6 +301,10 @@ G4VEmModel* G4DNASolvationModelFactory::GetMacroDefinedModel()
return Create("Ritchie1994");
case fTerrisol1990eSolvation:
return Create("Terrisol1990");
case fKreipl2009eSolvation:
return Create("Kreipl2009");
case fMeesungnoensolid2002eSolvation:
return Create("Meesungnoen2002_amorphous");
case fMeesungnoen2002eSolvation:
case fDNAUnknownModel:
return Create("Meesungnoen2002");
source/processes/electromagnetic/dna/models/src/G4DNAPTBElasticModel.cc
Executable → Regular
+1 -1
View File
@@ -203,7 +203,7 @@ void G4DNAPTBElasticModel::ReadDiffCSFile(const G4String& materialName,
// This method is not yet standard.
// get the path of the G4LEDATA data folder
char *path = getenv("G4LEDATA");
char *path = std::getenv("G4LEDATA");
// if it is not found then quit and print error message
if(!path)
{
source/processes/electromagnetic/dna/models/src/G4DNAPTBIonisationModel.cc
Executable → Regular
+1 -1
View File
@@ -437,7 +437,7 @@ void G4DNAPTBIonisationModel::ReadDiffCSFile(const G4String& materialName,
// To read and save the informations contained within the differential cross section files
// get the path of the G4LEDATA data folder
char *path = getenv("G4LEDATA");
char *path = std::getenv("G4LEDATA");
// if it is not found then quit and print error message
if(!path)
{
source/processes/electromagnetic/dna/models/src/G4VLEPTSModel.cc
+1 -1
View File
@@ -87,7 +87,7 @@ G4double G4VLEPTSModel::GetMeanFreePath(const G4Material* aMaterial,
void G4VLEPTSModel::BuildPhysicsTable(const G4ParticleDefinition& aParticleType)
{
//CHECK IF PATH VARIABLE IS DEFINED
char* path = getenv("G4LEDATA");
char* path = std::getenv("G4LEDATA");
if( !path ) {
G4Exception("G4VLEPTSModel",
"",