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This commit is contained in:
Gabriele Cosmo
2016-12-09 12:35:28 +01:00
parent 4ec577e5c4
commit a3452e42ac
3514 changed files with 210500 additions and 89628 deletions
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source/processes/electromagnetic/dna/models/src/G4DNAOneStepThermalizationModel.cc
+150 -232
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@@ -23,9 +23,9 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// $Id: G4DNAOneStepThermalizationModel.cc 96861 2016-05-13 13:43:04Z gcosmo $
// $Id: G4DNAOneStepThermalizationModel.cc 101807 2016-11-30 13:42:28Z gunter $
//
// Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr)
// Author: Mathieu Karamitros
//
// WARNING : This class is released as a prototype.
// It might strongly evolve or even disapear in the next releases.
@@ -36,244 +36,162 @@
//
// -------------------------------------------------------------------
#include <algorithm>
#include "G4DNAOneStepThermalizationModel.hh"
#include "G4PhysicalConstants.hh"
#include "G4SystemOfUnits.hh"
#include "G4DNAWaterExcitationStructure.hh"
#include "G4ParticleChangeForGamma.hh"
#include "G4NistManager.hh"
#include "G4DNAChemistryManager.hh"
#include "G4DNAMolecularMaterial.hh"
#include "G4ITNavigator.hh"
#include "G4Navigator.hh"
#include "G4TransportationManager.hh"
#include "G4ITNavigator.hh"
#include "G4Exp.hh"
//#define MODEL_VERBOSE
G4DNAOneStepThermalizationModel::
G4DNAOneStepThermalizationModel(const G4ParticleDefinition*,
const G4String& nam) :
G4VEmModel(nam), fIsInitialised(false)
{
fVerboseLevel = 0;
SetLowEnergyLimit(0.);
G4DNAWaterExcitationStructure exStructure;
SetHighEnergyLimit(exStructure.ExcitationEnergy(0));
fParticleChangeForGamma = 0;
fpWaterDensity = 0;
fNavigator = 0;
}
#include "G4RandomDirection.hh"
//------------------------------------------------------------------------------
G4DNAOneStepThermalizationModel::~G4DNAOneStepThermalizationModel()
{
if(fNavigator)
{
if(fNavigator->GetNavigatorState())
delete fNavigator->GetNavigatorState();
delete fNavigator;
}
}
//------------------------------------------------------------------------------
void G4DNAOneStepThermalizationModel::
Initialise(const G4ParticleDefinition* particleDefinition,
const G4DataVector&)
{
#ifdef MODEL_VERBOSE
if(fVerboseLevel)
G4cout << "Calling G4DNAOneStepThermalizationModel::Initialise()" << G4endl;
#endif
if (particleDefinition->GetParticleName() != "e-")
{
G4ExceptionDescription errMsg;
errMsg << "G4DNAOneStepThermalizationModel can only be applied "
"to electrons";
G4Exception("G4DNAOneStepThermalizationModel::CrossSectionPerVolume",
"G4DNAOneStepThermalizationModel001",
FatalErrorInArgument,errMsg);
return;
}
if(!fIsInitialised)
{
fIsInitialised = true;
fParticleChangeForGamma = GetParticleChangeForGamma();
}
G4Navigator* navigator =
G4TransportationManager::GetTransportationManager()->
GetNavigatorForTracking();
fNavigator = new G4ITNavigator();
fNavigator->SetWorldVolume(navigator->GetWorldVolume());
fNavigator->NewNavigatorState();
fpWaterDensity =
G4DNAMolecularMaterial::Instance()->
GetNumMolPerVolTableFor(G4Material::GetMaterial("G4_WATER"));
}
//------------------------------------------------------------------------------
G4double G4DNAOneStepThermalizationModel::
CrossSectionPerVolume(const G4Material* material,
const G4ParticleDefinition*,
G4double ekin,
G4double,
G4double)
{
#ifdef MODEL_VERBOSE
if(fVerboseLevel > 1)
G4cout << "Calling CrossSectionPerVolume() of G4DNAOneStepThermalizationModel"
<< G4endl;
#endif
if(ekin > HighEnergyLimit())
{
return 0.0;
}
G4double waterDensity = (*fpWaterDensity)[material->GetIndex()];
if(waterDensity!= 0.0)
{
return DBL_MAX;
}
return 0.;
}
//------------------------------------------------------------------------------
G4ThreeVector G4DNAOneStepThermalizationModel::
RadialDistributionOfProducts(G4double expectationValue) const
{
G4double sigma = std::sqrt(1.57) / 2 * expectationValue;
G4double XValueForfMax = std::sqrt(2. * sigma * sigma);
G4double fMaxValue = std::sqrt(2. / 3.14)
* 1. / (sigma * sigma * sigma)
* (XValueForfMax * XValueForfMax)
* G4Exp(-1. / 2. * (XValueForfMax * XValueForfMax)
/ (sigma * sigma));
G4double R;
do
{
G4double aRandomfValue = fMaxValue * G4UniformRand();
G4double sign;
if(G4UniformRand() > 0.5)
{
sign = +1.;
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;
}
else
{
sign = -1;
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);
}
R = expectationValue + sign*3.*sigma* G4UniformRand();
G4double f = std::sqrt(2./3.14) * 1/std::pow(sigma, 3)
* R*R * G4Exp(-1./2. * R*R/(sigma*sigma));
if(aRandomfValue < f)
{
break;
else{
displacement=G4RandomDirection()*(1e-3*CLHEP::nanometer);
// rare events:
// prevent H2O and secondary electron to be at the spot
}
}
while(1);
//----------------------------------------------------------------------------
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
G4double costheta = (2. * G4UniformRand()-1.);
G4double theta = std::acos(costheta);
G4double phi = 2. * pi * G4UniformRand();
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];
// 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;
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;
G4double xDirection = R * std::cos(phi) * std::sin(theta);
G4double yDirection = R * std::sin(theta) * std::sin(phi);
G4double zDirection = R * costheta;
G4ThreeVector RandDirection = G4ThreeVector(xDirection,
yDirection,
zDirection);
return RandDirection;
}
//------------------------------------------------------------------------------
void G4DNAOneStepThermalizationModel::
SampleSecondaries(std::vector<G4DynamicParticle*>*,
const G4MaterialCutsCouple*,
const G4DynamicParticle* particle,
G4double,
G4double)
{
#ifdef MODEL_VERBOSE
if(fVerboseLevel)
G4cout << "Calling SampleSecondaries() of G4DNAOneStepThermalizationModel"
<< G4endl;
#endif
G4double k = particle->GetKineticEnergy();
if (k <= HighEnergyLimit())
{
G4double k_eV = k/eV;
fParticleChangeForGamma->ProposeTrackStatus(fStopAndKill);
fParticleChangeForGamma->ProposeLocalEnergyDeposit(k);
if(G4DNAChemistryManager::IsActivated())
{
G4double r_mean =
(-0.003*std::pow(k_eV,6)
+ 0.0749*std::pow(k_eV,5)
- 0.7197*std::pow(k_eV,4)
+ 3.1384*std::pow(k_eV,3)
- 5.6926*std::pow(k_eV,2)
+ 5.6237*k_eV
- 0.7883)*nanometer;
G4ThreeVector displacement = RadialDistributionOfProducts (r_mean);
//______________________________________________________________
const G4Track * theIncomingTrack =
fParticleChangeForGamma->GetCurrentTrack();
G4ThreeVector finalPosition(theIncomingTrack->GetPosition()+displacement);
fNavigator->SetWorldVolume(theIncomingTrack->GetTouchable()->
GetVolume(theIncomingTrack->GetTouchable()->
GetHistoryDepth()));
double displacementMag = displacement.mag();
double safety = DBL_MAX;
G4ThreeVector direction = displacement/displacementMag;
fNavigator->ResetHierarchyAndLocate(theIncomingTrack->GetPosition(),
direction,
*((G4TouchableHistory*)
theIncomingTrack->GetTouchable()));
fNavigator->ComputeStep(theIncomingTrack->GetPosition(),
displacement/displacementMag,
displacementMag,
safety);
if(safety <= displacementMag)
{
finalPosition = theIncomingTrack->GetPosition()
+ (displacement/displacementMag)*safety*0.80;
}
G4DNAChemistryManager::Instance()->CreateSolvatedElectron(theIncomingTrack,
&finalPosition);
fParticleChangeForGamma->SetProposedKineticEnergy(25.e-3*eV);
}
}
}
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;
}
}}