G4DNAPTBElasticModel Class Reference

The G4DNAPTBElasticModel class This class implements the elastic model for the DNA materials and precursors. More...

#include <G4DNAPTBElasticModel.hh>

Inheritance diagram for G4DNAPTBElasticModel:

Public Member Functions
	G4DNAPTBElasticModel (const G4String &applyToMaterial="all", const G4ParticleDefinition *p=0, const G4String &nam="DNAPTBElasticModel")
	G4DNAPTBElasticModel Constructor.
virtual	~G4DNAPTBElasticModel ()
	~G4DNAPTBElasticModel Destructor
virtual void	Initialise (const G4ParticleDefinition *particle, const G4DataVector &, G4ParticleChangeForGamma *fpChangeForGamme=nullptr)
	Initialise Mandatory method for every model class. The material/particle for which the model can be used have to be added here through the AddCrossSectionData method. Then the LoadCrossSectionData method must be called to trigger the load process. Scale factors to be applied to the cross section can be defined here.
virtual G4double	CrossSectionPerVolume (const G4Material *material, const G4String &materialName, const G4ParticleDefinition *p, G4double ekin, G4double emin, G4double emax)
	CrossSectionPerVolume This method is mandatory for any model class. It finds and return the cross section value for the current material, particle and energy values. The number of molecule per volume is not used here but in the G4DNAModelInterface class.
virtual void	SampleSecondaries (std::vector< G4DynamicParticle * > *, const G4MaterialCutsCouple *, const G4String &materialName, const G4DynamicParticle *, G4ParticleChangeForGamma *particleChangeForGamma, G4double tmin, G4double tmax)
	SampleSecondaries Method called after CrossSectionPerVolume if the process is the one which is selected (according to the sampling on the calculated path length). Here, the characteristics of the incident and created (if any) particle(s) are set (energy, momentum ...).
Public Member Functions inherited from G4VDNAModel
	G4VDNAModel (const G4String &nam, const G4String &applyToMaterial)
	G4VDNAModel Constructeur of the G4VDNAModel class.
virtual	~G4VDNAModel ()
	~G4VDNAModel
virtual void	Initialise (const G4ParticleDefinition *particle, const G4DataVector &cuts, G4ParticleChangeForGamma *fpChangeForGamme=nullptr)=0
	Initialise Each model must implement an Initialize method.
virtual G4double	CrossSectionPerVolume (const G4Material *material, const G4String &materialName, const G4ParticleDefinition *p, G4double ekin, G4double emin, G4double emax)=0
	CrossSectionPerVolume Every model must implement its own CrossSectionPerVolume method. It is used by the process to determine the step path and must return a cross section times a number of molecules per volume unit.
virtual void	SampleSecondaries (std::vector< G4DynamicParticle * > *, const G4MaterialCutsCouple *, const G4String &materialName, const G4DynamicParticle *, G4ParticleChangeForGamma *particleChangeForGamma, G4double tmin=0, G4double tmax=DBL_MAX)=0
	SampleSecondaries Each model must implement SampleSecondaries to decide if a particle will be created after the ModelInterface or if any charateristic of the incident particle will change.
G4bool	IsMaterialDefine (const G4String &materialName)
	IsMaterialDefine Check if the given material is defined in the simulation.
G4bool	IsMaterialExistingInModel (const G4String &materialName)
	IsMaterialExistingInModel Check if the given material is defined in the current model class.
G4bool	IsParticleExistingInModelForMaterial (const G4String &particleName, const G4String &materialName)
	IsParticleExistingInModelForMaterial To check two things: 1- is the material existing in model ? 2- if yes, is the particle defined for that material ?
G4String	GetName ()
	GetName.
G4double	GetHighELimit (const G4String &material, const G4String &particle)
	GetHighEnergyLimit.
G4double	GetLowELimit (const G4String &material, const G4String &particle)
	GetLowEnergyLimit.
void	SetHighELimit (const G4String &material, const G4String &particle, G4double lim)
	SetHighEnergyLimit.
void	SetLowELimit (const G4String &material, const G4String &particle, G4double lim)
	SetLowEnergyLimit.

Additional Inherited Members
Protected Types inherited from G4VDNAModel
typedef std::map< G4String, std::map< G4String, G4DNACrossSectionDataSet *, std::less< G4String > > >	TableMapData
typedef std::map< G4String, std::map< G4String, G4double > >	RatioMapData
typedef std::map< G4String, G4double >::const_iterator	ItCompoMapData
Protected Member Functions inherited from G4VDNAModel
TableMapData *	GetTableData ()
	GetTableData.
std::vector< G4String >	BuildApplyToMatVect (const G4String &materials)
	BuildApplyToMatVect Build the material name vector which is used to know the materials the user want to include in the model.
void	ReadAndSaveCSFile (const G4String &materialName, const G4String &particleName, const G4String &file, G4double scaleFactor)
	ReadAndSaveCSFile Read and save a "simple" cross section file : use of G4DNACrossSectionDataSet->loadData()
G4int	RandomSelectShell (G4double k, const G4String &particle, const G4String &materialName)
	RandomSelectShell Method to randomely select a shell from the data table uploaded. The size of the table (number of columns) is used to determine the total number of possible shells.
void	AddCrossSectionData (G4String materialName, G4String particleName, G4String fileCS, G4String fileDiffCS, G4double scaleFactor)
	AddCrossSectionData Method used during the initialization of the model class to add a new material. It adds a material to the model and fills vectors with informations.
void	AddCrossSectionData (G4String materialName, G4String particleName, G4String fileCS, G4double scaleFactor)
	AddCrossSectionData Method used during the initialization of the model class to add a new material. It adds a material to the model and fills vectors with informations. Not every model needs differential cross sections.
void	LoadCrossSectionData (const G4String &particleName)
	LoadCrossSectionData Method to loop on all the registered materials in the model and load the corresponding data.
virtual void	ReadDiffCSFile (const G4String &materialName, const G4String &particleName, const G4String &path, const G4double scaleFactor)
	ReadDiffCSFile Virtual method that need to be implemented if one wish to use the differential cross sections. The read method for that kind of information is not standardized yet.
void	EnableForMaterialAndParticle (const G4String &materialName, const G4String &particleName)
	EnableMaterialAndParticle.

Detailed Description

The G4DNAPTBElasticModel class This class implements the elastic model for the DNA materials and precursors.

Definition at line 48 of file G4DNAPTBElasticModel.hh.

Constructor & Destructor Documentation

G4DNAPTBElasticModel()

G4DNAPTBElasticModel::G4DNAPTBElasticModel	(	const G4String &	applyToMaterial = "all",
		const G4ParticleDefinition *	p = 0,
		const G4String &	nam = "DNAPTBElasticModel"
	)

G4DNAPTBElasticModel Constructor.

Parameters

applyToMaterial
p
nam

Definition at line 38 of file G4DNAPTBElasticModel.cc.

    : G4VDNAModel(nam, applyToMaterial)
{
    fKillBelowEnergy = 10*eV; // will be override by the limits defined for each material
 
    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
 
    if( verboseLevel>0 )
    {
        G4cout << "PTB Elastic model is constructed " << G4endl;
    }
}

~G4DNAPTBElasticModel()

G4DNAPTBElasticModel::~G4DNAPTBElasticModel ( )

virtual

~G4DNAPTBElasticModel Destructor

Definition at line 60 of file G4DNAPTBElasticModel.cc.

{
 
}

Member Function Documentation

CrossSectionPerVolume()

G4double G4DNAPTBElasticModel::CrossSectionPerVolume ( const G4Material *  material, const G4String &  materialName, const G4ParticleDefinition *  p, G4double  ekin, G4double  emin, G4double  emax  )

virtual

CrossSectionPerVolume This method is mandatory for any model class. It finds and return the cross section value for the current material, particle and energy values. The number of molecule per volume is not used here but in the G4DNAModelInterface class.

Parameters

material
materialName
p
ekin
emin
emax

Returns

the cross section value

Implements G4VDNAModel.

Definition at line 305 of file G4DNAPTBElasticModel.cc.

{
    if (verboseLevel > 3)
        G4cout << "Calling CrossSectionPerVolume() of G4DNAPTBElasticModel" << G4endl;
 
    // Get the name of the current particle
    const G4String& particleName = p->GetParticleName();
 
    // set killBelowEnergy value for current material
    fKillBelowEnergy = GetLowELimit(materialName, particleName);
 
    // initialise the return value (cross section) to zero
    G4double sigma(0);
 
    // check if we are below the high energy limit
    if (ekin < GetHighELimit(materialName, particleName) )
    {
        // This is used to kill the particle if its kinetic energy is below fKillBelowEnergy.
        // If the energy is lower then we return a maximum cross section and thus the SampleSecondaries method will be called for sure.
        // SampleSecondaries will remove the particle from the simulation.
        //
        //SI : XS must not be zero otherwise sampling of secondaries method ignored
        if (ekin < fKillBelowEnergy) return DBL_MAX;
 
        // Get the tables with the cross section data
        TableMapData* tableData = GetTableData();
 
        // Retrieve the cross section value
        sigma = (*tableData)[materialName][particleName]->FindValue(ekin);
    }
 
    if (verboseLevel > 2)
    {
        G4cout << "__________________________________" << G4endl;
        G4cout << "°°° G4DNAPTBElasticModel - XS INFO START" << G4endl;
        G4cout << "°°° Kinetic energy(eV)=" << ekin/eV << " particle : " << particleName << G4endl;
        G4cout << "°°° Cross section per molecule (cm^2)=" << sigma/cm/cm << G4endl;
        G4cout << "°°° G4DNAPTBElasticModel - XS INFO END" << G4endl;
    }
 
    // Return the cross section
    return sigma;
}

Initialise()

void G4DNAPTBElasticModel::Initialise ( const G4ParticleDefinition *  particle, const G4DataVector &  , G4ParticleChangeForGamma *  fpChangeForGamme = nullptr  )

virtual

Initialise Mandatory method for every model class. The material/particle for which the model can be used have to be added here through the AddCrossSectionData method. Then the LoadCrossSectionData method must be called to trigger the load process. Scale factors to be applied to the cross section can be defined here.

Implements G4VDNAModel.

Definition at line 67 of file G4DNAPTBElasticModel.cc.

{
    if (verboseLevel > 3)
        G4cout << "Calling G4DNAPTBElasticModel::Initialise()" << G4endl;
 
    G4double scaleFactor = 1e-16*cm*cm;
 
    G4ParticleDefinition* electronDef = G4Electron::ElectronDefinition();
 
    //*******************************************************
    // Cross section data
    //*******************************************************
 
    if(particle == electronDef)
    {
        G4String particleName = particle->GetParticleName();
 
        // MPietrzak, adding paths for N2
        AddCrossSectionData("N2",
                            particleName,
                            "dna/sigma_elastic_e-_PTB_N2",
                            "dna/sigmadiff_cumulated_elastic_e-_PTB_N2",
                            scaleFactor);
        SetLowELimit("N2", particleName, 10*eV);
        SetHighELimit("N2", particleName, 1.02*MeV);
        // MPietrzak
 
        AddCrossSectionData("THF",
                            particleName,
                            "dna/sigma_elastic_e-_PTB_THF",
                            "dna/sigmadiff_cumulated_elastic_e-_PTB_THF",
                            scaleFactor);
        SetLowELimit("THF", particleName, 10*eV);
        SetHighELimit("THF", particleName, 1*keV);
 
        AddCrossSectionData("PY",
                            particleName,
                            "dna/sigma_elastic_e-_PTB_PY",
                            "dna/sigmadiff_cumulated_elastic_e-_PTB_PY",
                            scaleFactor);
        SetLowELimit("PY", particleName, 10*eV);
        SetHighELimit("PY", particleName, 1*keV);
 
        AddCrossSectionData("PU",
                            particleName,
                            "dna/sigma_elastic_e-_PTB_PU",
                            "dna/sigmadiff_cumulated_elastic_e-_PTB_PU",
                            scaleFactor);
        SetLowELimit("PU", particleName, 10*eV);
        SetHighELimit("PU", particleName, 1*keV);
 
        AddCrossSectionData("TMP",
                            particleName,
                            "dna/sigma_elastic_e-_PTB_TMP",
                            "dna/sigmadiff_cumulated_elastic_e-_PTB_TMP",
                            scaleFactor);
        SetLowELimit("TMP", particleName, 10*eV);
        SetHighELimit("TMP", particleName, 1*keV);
 
        AddCrossSectionData("G4_WATER",
                            particleName,
                            "dna/sigma_elastic_e_champion",
                            "dna/sigmadiff_cumulated_elastic_e_champion",
                            scaleFactor);
        SetLowELimit("G4_WATER", particleName, 10*eV);
        SetHighELimit("G4_WATER", particleName, 1*keV);
 
        // DNA materials
        //
        AddCrossSectionData("backbone_THF",
                            particleName,
                            "dna/sigma_elastic_e-_PTB_THF",
                            "dna/sigmadiff_cumulated_elastic_e-_PTB_THF",
                            scaleFactor*33./30);
        SetLowELimit("backbone_THF", particleName, 10*eV);
        SetHighELimit("backbone_THF", particleName, 1*keV);
 
        AddCrossSectionData("cytosine_PY",
                            particleName,
                            "dna/sigma_elastic_e-_PTB_PY",
                            "dna/sigmadiff_cumulated_elastic_e-_PTB_PY",
                            scaleFactor*42./30);
        SetLowELimit("cytosine_PY", particleName, 10*eV);
        SetHighELimit("cytosine_PY", particleName, 1*keV);
 
        AddCrossSectionData("thymine_PY",
                            particleName,
                            "dna/sigma_elastic_e-_PTB_PY",
                            "dna/sigmadiff_cumulated_elastic_e-_PTB_PY",
                            scaleFactor*48./30);
        SetLowELimit("thymine_PY", particleName, 10*eV);
        SetHighELimit("thymine_PY", particleName, 1*keV);
 
        AddCrossSectionData("adenine_PU",
                            particleName,
                            "dna/sigma_elastic_e-_PTB_PU",
                            "dna/sigmadiff_cumulated_elastic_e-_PTB_PU",
                            scaleFactor*50./44);
        SetLowELimit("adenine_PU", particleName, 10*eV);
        SetHighELimit("adenine_PU", particleName, 1*keV);
 
        AddCrossSectionData("guanine_PU",
                            particleName,
                            "dna/sigma_elastic_e-_PTB_PU",
                            "dna/sigmadiff_cumulated_elastic_e-_PTB_PU",
                            scaleFactor*56./44);
        SetLowELimit("guanine_PU", particleName, 10*eV);
        SetHighELimit("guanine_PU", particleName, 1*keV);
 
        AddCrossSectionData("backbone_TMP",
                            particleName,
                            "dna/sigma_elastic_e-_PTB_TMP",
                            "dna/sigmadiff_cumulated_elastic_e-_PTB_TMP",
                            scaleFactor*33./50);
        SetLowELimit("backbone_TMP", particleName, 10*eV);
        SetHighELimit("backbone_TMP", particleName, 1*keV);
    }
 
    //*******************************************************
    // Load the data
    //*******************************************************
 
    LoadCrossSectionData(particle->GetParticleName() );
 
    //*******************************************************
    // Verbose output
    //*******************************************************
 
    if (verboseLevel > 2)
        G4cout << "Loaded cross section files for PTB Elastic model" << G4endl;
 
    if( verboseLevel>0 )
    {
        G4cout << "PTB Elastic model is initialized " << G4endl;
    }
}

SampleSecondaries()

void G4DNAPTBElasticModel::SampleSecondaries ( std::vector< G4DynamicParticle * > *  , const G4MaterialCutsCouple *  , const G4String &  materialName, const G4DynamicParticle *  aDynamicElectron, G4ParticleChangeForGamma *  particleChangeForGamma, G4double  tmin, G4double  tmax  )

virtual

SampleSecondaries Method called after CrossSectionPerVolume if the process is the one which is selected (according to the sampling on the calculated path length). Here, the characteristics of the incident and created (if any) particle(s) are set (energy, momentum ...).

Parameters

materialName
particleChangeForGamma
tmin
tmax

Implements G4VDNAModel.

Definition at line 356 of file G4DNAPTBElasticModel.cc.

{
    if (verboseLevel > 3)
        G4cout << "Calling SampleSecondaries() of G4DNAPTBElasticModel" << G4endl;
 
    G4double electronEnergy0 = aDynamicElectron->GetKineticEnergy();
 
    const G4String& particleName = aDynamicElectron->GetParticleDefinition()->GetParticleName();
 
    // set killBelowEnergy value for material
    fKillBelowEnergy = GetLowELimit(materialName, particleName);
 
    // If the particle (electron here) energy is below the kill limit then we remove it from the simulation
    if (electronEnergy0 < fKillBelowEnergy)
    {
        particleChangeForGamma->SetProposedKineticEnergy(0.);
        particleChangeForGamma->ProposeTrackStatus(fStopAndKill);
        particleChangeForGamma->ProposeLocalEnergyDeposit(electronEnergy0);
    }
    // If we are above the kill limite and below the high limit then we proceed
    else if (electronEnergy0>= fKillBelowEnergy && electronEnergy0 < GetHighELimit(materialName, particleName) )
    {
        // Random sampling of the cosTheta
        G4double cosTheta = RandomizeCosTheta(electronEnergy0, materialName);
 
        // Random sampling of phi
        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);
 
        // Particle direction after ModelInterface
        G4ThreeVector zPrikeVers((xDir*xVers + yDir*yVers + cosTheta*zVers));
 
        // Give the new direction
        particleChangeForGamma->ProposeMomentumDirection(zPrikeVers.unit()) ;
 
        // Update the energy which does not change here
        particleChangeForGamma->SetProposedKineticEnergy(electronEnergy0);
    }
}

---

The documentation for this class was generated from the following files:

• G4DNAPTBElasticModel.hh
• G4DNAPTBElasticModel.cc