{ The transportation method implemented is the one from Ermak-McCammon : J. Chem. Phys. 69, 1352 (1978)} More...

#include <G4DNABrownianTransportation.hh>

Inheritance diagram for G4DNABrownianTransportation:

Classes
struct	G4ITBrownianState

Public Member Functions
	G4DNABrownianTransportation (const G4String &aName="DNABrownianTransportation", G4int verbosityLevel=1)

virtual	~G4DNABrownianTransportation ()

	G4DNABrownianTransportation (const G4DNABrownianTransportation &other)

G4DNABrownianTransportation &	operator= (const G4DNABrownianTransportation &other)

virtual void	BuildPhysicsTable (const G4ParticleDefinition &)

virtual void	StartTracking (G4Track *aTrack)

virtual void	ComputeStep (const G4Track &, const G4Step &, const double, double &)

virtual G4double	AlongStepGetPhysicalInteractionLength (const G4Track &, G4double, G4double, G4double &, G4GPILSelection *)

virtual G4VParticleChange *	PostStepDoIt (const G4Track &track, const G4Step &)

virtual G4VParticleChange *	AlongStepDoIt (const G4Track &track, const G4Step &)

Public Member Functions inherited from G4ITTransportation
	G4ITTransportation (const G4String &aName="ITTransportation", G4int verbosityLevel=1)

virtual	~G4ITTransportation ()

	G4ITTransportation (const G4ITTransportation &)

virtual void	BuildPhysicsTable (const G4ParticleDefinition &)

virtual void	ComputeStep (const G4Track &, const G4Step &, const double timeStep, double &spaceStep)

virtual void	StartTracking (G4Track *aTrack)

virtual G4double	AtRestGetPhysicalInteractionLength (const G4Track &, G4ForceCondition *)

virtual G4VParticleChange *	AtRestDoIt (const G4Track &, const G4Step &)

virtual G4double	AlongStepGetPhysicalInteractionLength (const G4Track &track, G4double, G4double currentMinimumStep, G4double &currentSafety, G4GPILSelection *selection)

virtual G4double	PostStepGetPhysicalInteractionLength (const G4Track &, G4double, G4ForceCondition *pForceCond)

virtual G4VParticleChange *	AlongStepDoIt (const G4Track &track, const G4Step &stepData)

virtual G4VParticleChange *	PostStepDoIt (const G4Track &track, const G4Step &)

G4PropagatorInField *	GetPropagatorInField ()

void	SetPropagatorInField (G4PropagatorInField *pFieldPropagator)

void	SetVerboseLevel (G4int verboseLevel)

G4int	GetVerboseLevel () const

G4double	GetThresholdWarningEnergy () const

G4double	GetThresholdImportantEnergy () const

G4int	GetThresholdTrials () const

void	SetThresholdWarningEnergy (G4double newEnWarn)

void	SetThresholdImportantEnergy (G4double newEnImp)

void	SetThresholdTrials (G4int newMaxTrials)

G4double	GetMaxEnergyKilled () const

G4double	GetSumEnergyKilled () const

void	ResetKilledStatistics (G4int report=1)

void	EnableShortStepOptimisation (G4bool optimise=true)

Public Member Functions inherited from G4VITProcess
	G4VITProcess (const G4String &name, G4ProcessType type=fNotDefined)

virtual	~G4VITProcess ()

	G4VITProcess (const G4VITProcess &other)

G4VITProcess &	operator= (const G4VITProcess &other)

G4int	operator== (const G4VITProcess &right) const

G4int	operator!= (const G4VITProcess &right) const

size_t	GetProcessID () const

G4ProcessState_Lock *	GetProcessState ()

void	SetProcessState (G4ProcessState_Lock *aProcInfo)

virtual void	StartTracking (G4Track *)

virtual void	BuildPhysicsTable (const G4ParticleDefinition &)

G4double	GetInteractionTimeLeft ()

virtual void	ResetNumberOfInteractionLengthLeft ()

G4bool	ProposesTimeStep () const

Public Member Functions inherited from G4VProcess
	G4VProcess (const G4String &aName="NoName", G4ProcessType aType=fNotDefined)

	G4VProcess (const G4VProcess &right)

virtual	~G4VProcess ()

G4int	operator== (const G4VProcess &right) const

G4int	operator!= (const G4VProcess &right) const

virtual G4VParticleChange *	PostStepDoIt (const G4Track &track, const G4Step &stepData)=0

virtual G4VParticleChange *	AlongStepDoIt (const G4Track &track, const G4Step &stepData)=0

virtual G4VParticleChange *	AtRestDoIt (const G4Track &track, const G4Step &stepData)=0

virtual G4double	AlongStepGetPhysicalInteractionLength (const G4Track &track, G4double previousStepSize, G4double currentMinimumStep, G4double &proposedSafety, G4GPILSelection *selection)=0

virtual G4double	AtRestGetPhysicalInteractionLength (const G4Track &track, G4ForceCondition *condition)=0

virtual G4double	PostStepGetPhysicalInteractionLength (const G4Track &track, G4double previousStepSize, G4ForceCondition *condition)=0

G4double	GetCurrentInteractionLength () const

void	SetPILfactor (G4double value)

G4double	GetPILfactor () const

G4double	AlongStepGPIL (const G4Track &track, G4double previousStepSize, G4double currentMinimumStep, G4double &proposedSafety, G4GPILSelection *selection)

G4double	AtRestGPIL (const G4Track &track, G4ForceCondition *condition)

G4double	PostStepGPIL (const G4Track &track, G4double previousStepSize, G4ForceCondition *condition)

virtual G4bool	IsApplicable (const G4ParticleDefinition &)

virtual void	BuildPhysicsTable (const G4ParticleDefinition &)

virtual void	PreparePhysicsTable (const G4ParticleDefinition &)

virtual G4bool	StorePhysicsTable (const G4ParticleDefinition *, const G4String &, G4bool)

virtual G4bool	RetrievePhysicsTable (const G4ParticleDefinition *, const G4String &, G4bool)

const G4String &	GetPhysicsTableFileName (const G4ParticleDefinition *, const G4String &directory, const G4String &tableName, G4bool ascii=false)

const G4String &	GetProcessName () const

G4ProcessType	GetProcessType () const

void	SetProcessType (G4ProcessType)

G4int	GetProcessSubType () const

void	SetProcessSubType (G4int)

virtual void	StartTracking (G4Track *)

virtual void	EndTracking ()

virtual void	SetProcessManager (const G4ProcessManager *)

virtual const G4ProcessManager *	GetProcessManager ()

virtual void	ResetNumberOfInteractionLengthLeft ()

G4double	GetNumberOfInteractionLengthLeft () const

G4double	GetTotalNumberOfInteractionLengthTraversed () const

G4bool	isAtRestDoItIsEnabled () const

G4bool	isAlongStepDoItIsEnabled () const

G4bool	isPostStepDoItIsEnabled () const

virtual void	DumpInfo () const

void	SetVerboseLevel (G4int value)

G4int	GetVerboseLevel () const

Protected Member Functions
void	Diffusion (const G4Track &track)

Protected Member Functions inherited from G4ITTransportation
G4bool	DoesGlobalFieldExist ()

void	SetInstantiateProcessState (G4bool flag)

G4bool	InstantiateProcessState ()

Protected Member Functions inherited from G4VITProcess
void	RetrieveProcessInfo ()

void	CreateInfo ()

virtual void	ClearInteractionTimeLeft ()

virtual void	SubtractNumberOfInteractionLengthLeft (G4double previousStepSize)

virtual void	ClearNumberOfInteractionLengthLeft ()

void	SetInstantiateProcessState (G4bool flag)

G4bool	InstantiateProcessState ()

Protected Member Functions inherited from G4VProcess
void	SubtractNumberOfInteractionLengthLeft (G4double previousStepSize)

void	ClearNumberOfInteractionLengthLeft ()

Protected Attributes
G4ITBrownianState *const &	fpBrownianState

G4bool	fUseMaximumTimeBeforeReachingBoundary

G4Material *	fNistWater

const std::vector< G4double > *	fpWaterDensity

Protected Attributes inherited from G4ITTransportation
G4ITTransportationState *const &	fTransportationState

G4ITNavigator *	fLinearNavigator

G4PropagatorInField *	fFieldPropagator

G4ParticleChangeForTransport	fParticleChange

G4double	fThreshold_Warning_Energy

G4double	fThreshold_Important_Energy

G4int	fThresholdTrials

G4double	fUnimportant_Energy

G4double	fSumEnergyKilled

G4double	fMaxEnergyKilled

G4bool	fShortStepOptimisation

G4SafetyHelper *	fpSafetyHelper

G4int	fVerboseLevel

Protected Attributes inherited from G4VITProcess
G4ProcessState *	fpState

G4bool	fProposesTimeStep

Protected Attributes inherited from G4VProcess
const G4ProcessManager *	aProcessManager

G4VParticleChange *	pParticleChange

G4ParticleChange	aParticleChange

G4double	theNumberOfInteractionLengthLeft

G4double	currentInteractionLength

G4double	theInitialNumberOfInteractionLength

G4String	theProcessName

G4String	thePhysicsTableFileName

G4ProcessType	theProcessType

G4int	theProcessSubType

G4double	thePILfactor

G4bool	enableAtRestDoIt

G4bool	enableAlongStepDoIt

G4bool	enablePostStepDoIt

G4int	verboseLevel

Additional Inherited Members
Static Public Member Functions inherited from G4VITProcess
static const size_t &	GetMaxProcessIndex ()

Static Public Member Functions inherited from G4VProcess
static const G4String &	GetProcessTypeName (G4ProcessType)

Detailed Description

{ The transportation method implemented is the one from Ermak-McCammon : J. Chem. Phys. 69, 1352 (1978)}

Definition at line 49 of file G4DNABrownianTransportation.hh.

Constructor & Destructor Documentation

◆ G4DNABrownianTransportation() [1/2]

G4DNABrownianTransportation::G4DNABrownianTransportation	(	const G4String &	aName = `"DNABrownianTransportation"`,
		G4int	verbosityLevel = `1`
	)

Definition at line 83 of file G4DNABrownianTransportation.cc.

                                                                                               :
    G4ITTransportation(aName, verbosity),
    InitProcessState(fpBrownianState, fTransportationState)
{
    //ctor
    SetProcessSubType(61);
    verboseLevel = 1;
    fUseMaximumTimeBeforeReachingBoundary = true;
    fNistWater = G4NistManager::Instance()->FindOrBuildMaterial("G4_WATER");
    fpWaterDensity  = 0;
}

◆ ~G4DNABrownianTransportation()

G4DNABrownianTransportation::~G4DNABrownianTransportation ( )

virtual

Definition at line 95 of file G4DNABrownianTransportation.cc.

96{;}

◆ G4DNABrownianTransportation() [2/2]

G4DNABrownianTransportation::G4DNABrownianTransportation ( const G4DNABrownianTransportation & other )

Definition at line 98 of file G4DNABrownianTransportation.cc.

                                                                                                 :
    G4ITTransportation(right),
    InitProcessState(fpBrownianState, fTransportationState)
{
    //copy ctor
    SetProcessSubType(61);
    verboseLevel = right.verboseLevel;
    fUseMaximumTimeBeforeReachingBoundary = right.fUseMaximumTimeBeforeReachingBoundary;
    fNistWater = right.fNistWater;
    fpWaterDensity  = right.fpWaterDensity ;
}

Member Function Documentation

◆ AlongStepDoIt()

G4VParticleChange * G4DNABrownianTransportation::AlongStepDoIt	(	const G4Track &	track,
		const G4Step &	step
	)

virtual

Reimplemented from G4ITTransportation.

Definition at line 362 of file G4DNABrownianTransportation.cc.

{
    G4ITTransportation::AlongStepDoIt(track,step);
    Diffusion(track);
    return &fParticleChange;
}

◆ AlongStepGetPhysicalInteractionLength()

G4double G4DNABrownianTransportation::AlongStepGetPhysicalInteractionLength	(	const G4Track &	track,
		G4double	previousStepSize,
		G4double	currentMinimumStep,
		G4double &	currentSafety,
		G4GPILSelection *	selection
	)

virtual

Reimplemented from G4ITTransportation.

Definition at line 314 of file G4DNABrownianTransportation.cc.

{
    G4double geometryStepLength = G4ITTransportation::AlongStepGetPhysicalInteractionLength(track,
                                                                                            previousStepSize,
                                                                                            currentMinimumStep,
                                                                                            currentSafety,
                                                                                            selection);
 
    G4double diffusionCoefficient = GetMolecule(track)->GetDiffusionCoefficient();
    //    G4double diffusionCoefficient = GetITBrownianObject(track)->GetDiffusionCoefficient(track.GetMaterial());
 
    if(State(fGeometryLimitedStep))
    {
        // 99 % of the space step distribution is lower than
        // d_99 = 8 * sqrt(D*t)
        // where t is the corresponding time step
        // so by inversion :
        if(fUseMaximumTimeBeforeReachingBoundary)
        {
            State(theInteractionTimeLeft)     = (geometryStepLength*geometryStepLength)/(64 * diffusionCoefficient);
        }
        else // Will use a random time
        {
            State(theInteractionTimeLeft) = 1/(4*diffusionCoefficient) * pow(geometryStepLength/InvErfc(G4UniformRand()),2);
        }
 
        State(fCandidateEndGlobalTime) = track.GetGlobalTime() + State(theInteractionTimeLeft);
        State(fPathLengthWasCorrected) = false;
    }
    else
    {
        geometryStepLength  = 2*sqrt(diffusionCoefficient*State(theInteractionTimeLeft) ) *InvErf(G4UniformRand());
        State(fPathLengthWasCorrected) = true;
        State(endpointDistance) = geometryStepLength;
    }
 
    return geometryStepLength ;
}

◆ BuildPhysicsTable()

void G4DNABrownianTransportation::BuildPhysicsTable ( const G4ParticleDefinition & particle )

virtual

Reimplemented from G4ITTransportation.

Definition at line 129 of file G4DNABrownianTransportation.cc.

{
    if(verboseLevel > 0)
    {
        G4cout << G4endl << GetProcessName() << ":   for  "
               << setw(24) << particle.GetParticleName()
               << "\tSubType= " << GetProcessSubType()   << G4endl;
    }
 
    // Initialize water density pointer
    fpWaterDensity = G4DNAMolecularMaterial::Instance()->GetDensityTableFor(G4Material::GetMaterial("G4_WATER"));
}

◆ ComputeStep()

void G4DNABrownianTransportation::ComputeStep	(	const G4Track &	track,
		const G4Step &	step,
		const double	timeStep,
		double &	spaceStep
	)

virtual

Reimplemented from G4ITTransportation.

Definition at line 142 of file G4DNABrownianTransportation.cc.

{
    // G4cout << "G4ITBrownianTransportation::ComputeStep" << G4endl;
 
    // If this method is called, this step
    // cannot be geometry limited.
    // In case the step is limited by the geometry,
    // this method should not be called.
    // The fTransportEndPosition calculated in
    // the method AlongStepIL should be taken
    // into account.
    // In order to do so, the flag IsLeadingStep
    // is on. Meaning : this track has the minimum
    // interaction length over all others.
    if(GetIT(track)->GetTrackingInfo()->IsLeadingStep())
    {
        const G4VITProcess* ITProc = ((const G4VITProcess*) step.GetPostStepPoint()->GetProcessDefinedStep());
        bool makeException = true;
 
        if(ITProc && ITProc->ProposesTimeStep()) makeException = false;
 
        if(makeException)
        {
 
        G4ExceptionDescription exceptionDescription ;
        exceptionDescription << "ComputeStep is called while the track has the minimum interaction time";
        exceptionDescription << " so it should not recompute a timeStep ";
        G4Exception("G4DNABrownianTransportation::ComputeStep","G4DNABrownianTransportation001",
                    FatalErrorInArgument,exceptionDescription);
        }
    }
 
    State(fGeometryLimitedStep) = false;
    // TODO : generalize this process to all kind of brownian objects
    //    G4ITBrownianObject* ITBrown = GetITBrownianObject(track) ;
    //    G4double diffCoeff = ITBrown->GetDiffusionCoefficient(track.GetMaterial());
    G4Molecule* molecule = GetMolecule(track) ;
    G4double diffCoeff = molecule->GetDiffusionCoefficient();
 
    if(timeStep > 0)
    {
        spaceStep = DBL_MAX;
 
        while(spaceStep > State(endpointDistance))
            // Probably inefficient when the track is close close to boundaries
            // it goes with fUserMaximumTimeBeforeReachingBoundary == false
            // fUserMaximumTimeBeforeReachingBoundary == true, it should never loop
        {
            G4double x = G4RandGauss::shoot(0,sqrt(2*diffCoeff*timeStep));
            G4double y = G4RandGauss::shoot(0,sqrt(2*diffCoeff*timeStep));
            G4double z = G4RandGauss::shoot(0,sqrt(2*diffCoeff*timeStep));
 
            spaceStep = sqrt(x*x + y*y + z*z);
        }
        //        State(fTransportEndPosition).set(x + track.GetPosition().x(),
        //                                         y + track.GetPosition().y(),
        //                                         z + track.GetPosition().z());
 
        State(fTransportEndPosition)= spaceStep*step.GetPostStepPoint()->GetMomentumDirection() + track.GetPosition();
    }
    else
    {
        spaceStep = 0. ;
        State(fTransportEndPosition) =  track.GetPosition() ;
    }
 
    State(fCandidateEndGlobalTime) = step.GetPreStepPoint()->GetGlobalTime() + timeStep ;
    State(fEndGlobalTimeComputed) = true ;
 
#ifdef G4VERBOSE
    //    DEBUG
    if(fVerboseLevel>1)
    {
        G4cout<< GREEN_ON_BLUE
              << "G4ITBrownianTransportation::ComputeStep() : "
              << " trackID : "         << track.GetTrackID()
              << " : Molecule name: "  << molecule-> GetName()
              << G4endl
              << "Diffusion length : " << G4BestUnit(spaceStep, "Length")
              << " within time step : "  << G4BestUnit(timeStep,"Time")
              << RESET
              << G4endl<< G4endl;
    }
#endif
}

◆ Diffusion()

void G4DNABrownianTransportation::Diffusion ( const G4Track & track )

protected

Definition at line 253 of file G4DNABrownianTransportation.cc.

{
 
#ifdef G4VERBOSE
    // DEBUG
    if (fVerboseLevel>1)
    {
        G4cout<< GREEN_ON_BLUE
              << setw(18)<< "G4DNABrownianTransportation::Diffusion :"
              << setw(8) <<  GetIT(track)->GetName()
              << "\t trackID:"      << track.GetTrackID() <<"\t"
              << " Global Time = "  << G4BestUnit(track.GetGlobalTime(),"Time")
              << RESET
              << G4endl<< G4endl;
    }
#endif
 
    G4Material* material = track.GetMaterial();
//    if (material != fNistWater && material->GetBaseMaterial() != fNistWater)
 
   G4double waterDensity = (*fpWaterDensity)[material->GetIndex()];
 
   if(waterDensity == 0.0)
//  if (material == nistwater || material->GetBaseMaterial() == nistwater)
    {
        G4cout << "A track is outside water material : trackID"<< track.GetTrackID() << " (" << GetMolecule(track)->GetName()  <<")" << G4endl;
        G4cout << "Local Time : "<<  (track.GetLocalTime()) /s<<G4endl;
        G4cout<< "Step Number :" << track.GetCurrentStepNumber() <<G4endl;
 
        fParticleChange.ProposeEnergy(0.) ;
        fParticleChange.ProposeTrackStatus(fStopButAlive);
 
        // Got pb with :
        // fParticleChange.ProposeTrackStatus(fStopAndKill);
        // It makes the tracks going straight without killing them
 
        return ; // &fParticleChange is the final returned object
    }
 
    G4double costheta = (2*G4UniformRand()-1);
    G4double theta = acos (costheta);
    G4double phi = 2*pi*G4UniformRand();
 
    G4double xMomentum = cos(phi)* sin(theta);
    G4double yMomentum = sin(theta)*sin(phi);
    G4double zMomentum = costheta;
 
    fParticleChange.ProposeMomentumDirection(xMomentum, yMomentum, zMomentum);
    State(fMomentumChanged) = true;
    fParticleChange.SetMomentumChanged(true) ;
 
    //    G4cout << "BROWN : Propose new direction :" << G4ThreeVector(xMomentum, yMomentum, zMomentum) << G4endl;
 
    // Alternative
    //fParticleChange.ProposeMomentumDirection(G4RandomDirection());
 
    return; // &fParticleChange is the final returned object
}

Referenced by AlongStepDoIt().

◆ operator=()

G4DNABrownianTransportation & G4DNABrownianTransportation::operator= ( const G4DNABrownianTransportation & other )

Definition at line 110 of file G4DNABrownianTransportation.cc.

{
    if (this == &rhs) return *this; // handle self assignment
    //assignment operator
    return *this;
}

◆ PostStepDoIt()

G4VParticleChange * G4DNABrownianTransportation::PostStepDoIt	(	const G4Track &	track,
		const G4Step &	step
	)

virtual

Reimplemented from G4ITTransportation.

Definition at line 231 of file G4DNABrownianTransportation.cc.

{
    G4ITTransportation::PostStepDoIt(track,step);
 
#ifdef G4VERBOSE
    //    DEBUG
    if(fVerboseLevel>1)
    {
        G4cout<< GREEN_ON_BLUE
              << "G4ITBrownianTransportation::PostStepDoIt() :"
              << " trackID : "        << track.GetTrackID()
              << " Molecule name: "   << GetMolecule(track)-> GetName() << G4endl;
        G4cout<< "Diffusion length : "<< G4BestUnit(step.GetStepLength(),"Length") <<" within time step : "
              << G4BestUnit(step.GetDeltaTime(),"Time") << "\t"
              << " Current global time : " << G4BestUnit(track.GetGlobalTime(),"Time")
              << RESET
              << G4endl<< G4endl;
    }
#endif
    return &fParticleChange ;
}

◆ StartTracking()

void G4DNABrownianTransportation::StartTracking ( G4Track * aTrack )

virtual

Reimplemented from G4ITTransportation.

Definition at line 122 of file G4DNABrownianTransportation.cc.

{
    fpState = new G4ITBrownianState();
    SetInstantiateProcessState(false);
    G4ITTransportation::StartTracking(track);
}

Member Data Documentation

◆ fNistWater

G4Material* G4DNABrownianTransportation::fNistWater

protected

Definition at line 92 of file G4DNABrownianTransportation.hh.

Referenced by G4DNABrownianTransportation().

◆ fpBrownianState

G4ITBrownianState* const& G4DNABrownianTransportation::fpBrownianState

protected

Definition at line 89 of file G4DNABrownianTransportation.hh.

◆ fpWaterDensity

const std::vector<G4double>* G4DNABrownianTransportation::fpWaterDensity

protected

Definition at line 95 of file G4DNABrownianTransportation.hh.

Referenced by BuildPhysicsTable(), and G4DNABrownianTransportation().

◆ fUseMaximumTimeBeforeReachingBoundary

G4bool G4DNABrownianTransportation::fUseMaximumTimeBeforeReachingBoundary

protected

Definition at line 91 of file G4DNABrownianTransportation.hh.

Referenced by AlongStepGetPhysicalInteractionLength(), and G4DNABrownianTransportation().

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

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ G4DNABrownianTransportation() [1/2]

◆ ~G4DNABrownianTransportation()

◆ G4DNABrownianTransportation() [2/2]

Member Function Documentation

◆ AlongStepDoIt()

◆ AlongStepGetPhysicalInteractionLength()

◆ BuildPhysicsTable()

◆ ComputeStep()

◆ Diffusion()

◆ operator=()

◆ PostStepDoIt()

◆ StartTracking()

Member Data Documentation

◆ fNistWater

◆ fpBrownianState

◆ fpWaterDensity

◆ fUseMaximumTimeBeforeReachingBoundary