lars/geant4
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Import Geant4 10.5.0.beta source tree

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files
source/processes/electromagnetic/dna/models/include/G4DNAOneStepThermalizationModel.hh
+40 -7
View File
@@ -23,7 +23,7 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// $Id: G4DNAOneStepThermalizationModel.hh 108498 2018-02-15 15:33:07Z gcosmo $
// $Id: G4DNAOneStepThermalizationModel.hh 110873 2018-06-22 13:11:22Z gcosmo $
//
// Author: Mathieu Karamitros
@@ -47,6 +47,7 @@
#ifndef G4DNAOneStepThermalizationModel_hh
#define G4DNAOneStepThermalizationModel_hh
#include <memory>
#include "G4VEmModel.hh"
class G4ITNavigator;
@@ -86,6 +87,21 @@ namespace DNA{
static const double gEnergies_T1990[11];
static const double gStdDev_T1990[11];
};
//-----------------------
/*
* Article: Ritchie RH, Hamm RN, Turner JE, Bolch WE (1994) Interaction of
* low-energy electrons with condensed matter: relevance for track
* structure.
* Computational approaches in molecular radiation biology, Plenum,
* New York, Vol. 63, pp. 155–166
* Note: also used in Ballarini et al., 2000
*/
struct Ritchie1994{
static void GetPenetration(G4double energy,
G4ThreeVector& displacement);
static double GetRmean(double energy);
};
}
}
@@ -102,7 +118,7 @@ class G4TDNAOneStepThermalizationModel : public G4VEmModel
public:
typedef MODEL Model;
G4TDNAOneStepThermalizationModel(const G4ParticleDefinition* p = 0,
const G4String& nam =
const G4String& nam =
"DNAOneStepThermalizationModel");
virtual ~G4TDNAOneStepThermalizationModel();
@@ -123,19 +139,19 @@ public:
inline void SetVerbose(int flag){
fVerboseLevel = flag;
}
void GetPenetration(G4double energy,
G4ThreeVector& displacement);
double GetRmean(double energy);
protected:
const std::vector<G4double>* fpWaterDensity;
G4ParticleChangeForGamma* fParticleChangeForGamma;
G4ParticleChangeForGamma* fpParticleChangeForGamma;
G4bool fIsInitialised;
G4int fVerboseLevel;
G4Navigator* fNavigator;
std::unique_ptr<G4Navigator> fpNavigator;
private:
G4TDNAOneStepThermalizationModel&
@@ -151,4 +167,21 @@ typedef G4TDNAOneStepThermalizationModel<DNA::Penetration::Meesungnoen2002> G4DN
// Note: if you use the above distribution, it would be
// better to follow the electrons down to 6 eV and only then apply
// the one step thermalization
class G4DNASolvationModelFactory
{
public:
/// @param penetrationType Available options:
/// Meesungnoen2002, Terrisol1990, Ritchie1994
static G4VEmModel* Create(const G4String& penetrationModel);
/// \brief One step thermalization model can be chosen via macro using
/// /process/dna/e-SolvationSubType Ritchie1994
/// \return Create the model defined via the command macro
/// /process/dna/e-SolvationSubType
/// In case the command is unused, it returns the default model set in
/// G4EmParameters.
static G4VEmModel* GetMacroDefinedModel();
};
#endif
source/processes/electromagnetic/dna/models/include/G4DNAOneStepThermalizationModel.hpp
+14 -19
View File
@@ -54,16 +54,15 @@
template<typename MODEL>
G4TDNAOneStepThermalizationModel<MODEL>::
G4TDNAOneStepThermalizationModel(const G4ParticleDefinition*,
const G4String& nam) :
const G4String& nam) :
G4VEmModel(nam), fIsInitialised(false)
{
fVerboseLevel = 0;
SetLowEnergyLimit(0.);
G4DNAWaterExcitationStructure exStructure;
SetHighEnergyLimit(exStructure.ExcitationEnergy(0));
fParticleChangeForGamma = 0;
fpParticleChangeForGamma = 0;
fpWaterDensity = 0;
fNavigator = 0;
}
//------------------------------------------------------------------------------
@@ -71,12 +70,8 @@ G4VEmModel(nam), fIsInitialised(false)
template<typename MODEL>
G4TDNAOneStepThermalizationModel<MODEL>::~G4TDNAOneStepThermalizationModel()
{
if(fNavigator)
{
// if(fNavigator->GetNavigatorState())
// delete fNavigator->GetNavigatorState();
delete fNavigator;
}
// if(fpNavigator && fpNavigator->GetNavigatorState())
// delete fpNavigator->GetNavigatorState();
}
//------------------------------------------------------------------------------
@@ -104,19 +99,19 @@ Initialise(const G4ParticleDefinition* particleDefinition,
if(!fIsInitialised)
{
fIsInitialised = true;
fParticleChangeForGamma = GetParticleChangeForGamma();
fpParticleChangeForGamma = GetParticleChangeForGamma();
}
G4Navigator* navigator =
G4TransportationManager::GetTransportationManager()->
GetNavigatorForTracking();
fNavigator = new G4Navigator();
fpNavigator.reset(new G4Navigator());
if(navigator){ // add these checks for testing mode
auto world=navigator->GetWorldVolume();
if(world){
fNavigator->SetWorldVolume(world);
fpNavigator->SetWorldVolume(world);
//fNavigator->NewNavigatorState();
}
}
@@ -188,8 +183,8 @@ SampleSecondaries(std::vector<G4DynamicParticle*>*,
if (k <= HighEnergyLimit())
{
fParticleChangeForGamma->ProposeTrackStatus(fStopAndKill);
fParticleChangeForGamma->ProposeLocalEnergyDeposit(k);
fpParticleChangeForGamma->ProposeTrackStatus(fStopAndKill);
fpParticleChangeForGamma->ProposeLocalEnergyDeposit(k);
if(G4DNAChemistryManager::IsActivated())
{
@@ -198,10 +193,10 @@ SampleSecondaries(std::vector<G4DynamicParticle*>*,
//______________________________________________________________
const G4Track * theIncomingTrack =
fParticleChangeForGamma->GetCurrentTrack();
fpParticleChangeForGamma->GetCurrentTrack();
G4ThreeVector finalPosition(theIncomingTrack->GetPosition()+displacement);
fNavigator->SetWorldVolume(theIncomingTrack->GetTouchable()->
fpNavigator->SetWorldVolume(theIncomingTrack->GetTouchable()->
GetVolume(theIncomingTrack->GetTouchable()->
GetHistoryDepth()));
@@ -229,12 +224,12 @@ SampleSecondaries(std::vector<G4DynamicParticle*>*,
// }
//--
fNavigator->ResetHierarchyAndLocate(theIncomingTrack->GetPosition(),
fpNavigator->ResetHierarchyAndLocate(theIncomingTrack->GetPosition(),
direction,
*((G4TouchableHistory*)
theIncomingTrack->GetTouchable()));
fNavigator->ComputeStep(theIncomingTrack->GetPosition(),
fpNavigator->ComputeStep(theIncomingTrack->GetPosition(),
displacement/displacementMag,
displacementMag,
safety);
@@ -248,7 +243,7 @@ SampleSecondaries(std::vector<G4DynamicParticle*>*,
G4DNAChemistryManager::Instance()->CreateSolvatedElectron(theIncomingTrack,
&finalPosition);
fParticleChangeForGamma->SetProposedKineticEnergy(25.e-3*eV);
fpParticleChangeForGamma->SetProposedKineticEnergy(25.e-3*eV);
}
}
}
source/processes/electromagnetic/dna/models/src/G4DNAOneStepThermalizationModel.cc
+212 -146
View File
@@ -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;
}
source/processes/electromagnetic/dna/models/src/G4LEPTSDiffXS.cc
+5 -5
View File
@@ -68,7 +68,7 @@ void G4LEPTSDiffXS::readDXS( ) {
//G4cout << "Reading2 " << fileName << G4endl;
//NumAng = 181;
fscanf(fp, "%d %d %s", &NumAng, &NumEn, DXSTypeName);
(void) fscanf(fp, "%d %d %s", &NumAng, &NumEn, DXSTypeName);
if( !strcmp(DXSTypeName, "KTC") ) DXSType = 2; // read DXS & calculate KT
else if( !strcmp(DXSTypeName, "KT") ) DXSType = 1; // read DXS & KT
else DXSType = 0;
@@ -77,7 +77,7 @@ void G4LEPTSDiffXS::readDXS( ) {
// << "DXSType " << DXSTypeName << " " << DXSType << G4endl;
for (G4int eBin=1; eBin<=NumEn; eBin++){
fscanf(fp,"%f ",&data);
(void) fscanf(fp,"%f ",&data);
Eb[eBin] = (G4double)data;
}
@@ -87,10 +87,10 @@ void G4LEPTSDiffXS::readDXS( ) {
if(DXSType==1) {
G4cout << "DXSTYpe 1" << G4endl;
for (G4int aBin=0;aBin<NumAng;aBin++){
fscanf(fp,"%f ",&data);
(void) fscanf(fp,"%f ",&data);
DXS[0][aBin]=(G4double)data;
for (G4int eBin=1;eBin<=NumEn;eBin++){
fscanf(fp,"%f %f ",&data2, &data);
(void) fscanf(fp,"%f %f ",&data2, &data);
DXS[eBin][aBin]=(G4double)data;
KT[eBin][aBin]=(G4double)data2;
}
@@ -99,7 +99,7 @@ void G4LEPTSDiffXS::readDXS( ) {
else {
for(G4int aBin=0; aBin<NumAng; aBin++){
for(G4int eBin=0; eBin<=NumEn; eBin++){
fscanf(fp,"%f ",&data);
(void) fscanf(fp,"%f ",&data);
DXS[eBin][aBin] = (G4double)data;
}
}
source/processes/electromagnetic/dna/models/src/G4LEPTSElossDistr.cc
+5 -5
View File
@@ -52,21 +52,21 @@ void G4LEPTSElossDistr::ReadFile()
G4int nEnergies;
G4int nAngles;
G4int nData;
fscanf(fp,"%i \n",&nEnergies);
(void) fscanf(fp,"%i \n",&nEnergies);
for( G4int ie = 0; ie < nEnergies; ie++ ){
float energySep;
fscanf(fp,"%f \n",&energySep);
fscanf(fp,"%i \n",&nAngles);
(void) fscanf(fp,"%f \n",&energySep);
(void) fscanf(fp,"%i \n",&nAngles);
for( G4int ia = 0; ia < nAngles; ia++ ){
float angleSep;
fscanf(fp,"%f \n",&angleSep);
(void) fscanf(fp,"%f \n",&angleSep);
G4LEPTSDistribution* dist = new G4LEPTSDistribution();
theNDistributions ++;
mddist angleDist;
angleDist[angleSep] = dist;
theDistributions[energySep] = angleDist;
fscanf(fp,"%i \n",&nData);
(void) fscanf(fp,"%i \n",&nData);
if( dist->ReadFile( fp, nData ) ) {
G4Exception("G4LEPTSElossDistr",
"",