#include <G4DNAMolecularDissociation.hh>

Inheritance diagram for G4DNAMolecularDissociation:

Public Types
using	Species = const G4MoleculeDefinition

using	Displacer = G4VMolecularDissociationDisplacer

Public Member Functions
	G4DNAMolecularDissociation (const G4String &processName="DNAMolecularDecay", G4ProcessType type=fDecay)

	G4DNAMolecularDissociation ()=delete

	G4DNAMolecularDissociation (const G4DNAMolecularDissociation &right)=delete

G4DNAMolecularDissociation &	operator= (const G4DNAMolecularDissociation &right)=delete

	~G4DNAMolecularDissociation () override

G4bool	IsApplicable (const G4ParticleDefinition &) override

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

G4double	AtRestGetPhysicalInteractionLength (const G4Track &track, G4ForceCondition *condition) override

G4VParticleChange *	AtRestDoIt (const G4Track &track, const G4Step &step) override

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

void	SetVerbose (G4int)

void	SetUserBrownianAction (G4VUserBrownianAction *pBrownianAction)

void	SetDisplacer (Species , Displacer )

Displacer *	GetDisplacer (Species *)

Public Member Functions inherited from G4VITRestDiscreteProcess
	G4VITRestDiscreteProcess ()=delete

	G4VITRestDiscreteProcess (const G4String &, G4ProcessType aType=fNotDefined)

	G4VITRestDiscreteProcess (const G4VITRestDiscreteProcess &)=delete

G4VITRestDiscreteProcess &	operator= (const G4VITRestDiscreteProcess &right)=delete

	~G4VITRestDiscreteProcess () override

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

G4VParticleChange *	PostStepDoIt (const G4Track &, const G4Step &) override

G4double	AtRestGetPhysicalInteractionLength (const G4Track &, G4ForceCondition *) override

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

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

G4VParticleChange *	AlongStepDoIt (const G4Track &, const G4Step &) override

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

virtual	~G4VITProcess ()

	G4VITProcess (const G4VITProcess &other)

G4VITProcess &	operator= (const G4VITProcess &other)

G4bool	operator== (const G4VITProcess &right) const

G4bool	operator!= (const G4VITProcess &right) const

size_t	GetProcessID () const

G4shared_ptr< G4ProcessState_Lock >	GetProcessState ()

void	SetProcessState (G4shared_ptr< G4ProcessState_Lock > aProcInfo)

void	ResetProcessState ()

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 ()

G4VProcess &	operator= (const G4VProcess &)=delete

G4bool	operator== (const G4VProcess &right) const

G4bool	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 const G4VProcess *	GetCreatorProcess () const

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

virtual void	ProcessDescription (std::ostream &outfile) const

void	SetVerboseLevel (G4int value)

G4int	GetVerboseLevel () const

virtual void	SetMasterProcess (G4VProcess *masterP)

const G4VProcess *	GetMasterProcess () const

virtual void	BuildWorkerPhysicsTable (const G4ParticleDefinition &part)

virtual void	PrepareWorkerPhysicsTable (const G4ParticleDefinition &)

Protected Member Functions
virtual G4VParticleChange *	DecayIt (const G4Track &, const G4Step &)

G4double	GetMeanLifeTime (const G4Track &, G4ForceCondition *) override

G4double	GetMeanFreePath (const G4Track &, G4double, G4ForceCondition *) override

virtual G4double	GetMeanFreePath (const G4Track &aTrack, G4double previousStepSize, G4ForceCondition *condition)=0

virtual G4double	GetMeanLifeTime (const G4Track &aTrack, G4ForceCondition *condition)=0

Protected Member Functions inherited from G4VITProcess
void	RetrieveProcessInfo ()

void	CreateInfo ()

template<typename T >
T *	GetState ()

virtual void	SubtractNumberOfInteractionLengthLeft (G4double previousStepSize)

virtual void	ClearInteractionTimeLeft ()

virtual void	ClearNumberOfInteractionLengthLeft ()

void	SetInstantiateProcessState (G4bool flag)

G4bool	InstantiateProcessState ()

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

void	ClearNumberOfInteractionLengthLeft ()

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)

Protected Attributes inherited from G4VITProcess
G4shared_ptr< G4ProcessState >	fpState

G4bool	fProposesTimeStep

Protected Attributes inherited from G4VProcess
const G4ProcessManager *	aProcessManager = nullptr

G4VParticleChange *	pParticleChange = nullptr

G4ParticleChange	aParticleChange

G4double	theNumberOfInteractionLengthLeft = -1.0

G4double	currentInteractionLength = -1.0

G4double	theInitialNumberOfInteractionLength = -1.0

G4String	theProcessName

G4String	thePhysicsTableFileName

G4ProcessType	theProcessType = fNotDefined

G4int	theProcessSubType = -1

G4double	thePILfactor = 1.0

G4int	verboseLevel = 0

G4bool	enableAtRestDoIt = true

G4bool	enableAlongStepDoIt = true

G4bool	enablePostStepDoIt = true

Detailed Description

G4DNAMolecularDissociation should be called only for molecules. It will dissociate the molecules using the decay associated to this molecule and if a displacement scheme has been registered, it will place the products to the expected position.

Definition at line 63 of file G4DNAMolecularDissociation.hh.

Member Typedef Documentation

◆ Displacer

using G4DNAMolecularDissociation::Displacer = G4VMolecularDissociationDisplacer

Definition at line 74 of file G4DNAMolecularDissociation.hh.

◆ Species

using G4DNAMolecularDissociation::Species = const G4MoleculeDefinition

Definition at line 73 of file G4DNAMolecularDissociation.hh.

Constructor & Destructor Documentation

◆ G4DNAMolecularDissociation() [1/3]

G4DNAMolecularDissociation::G4DNAMolecularDissociation	(	const G4String &	processName = `"DNAMolecularDecay"`,
		G4ProcessType	type = `fDecay`
	)

Definition at line 50 of file G4DNAMolecularDissociation.cc.

   : G4VITRestDiscreteProcess(processName, type)
{
    // set Process Sub Type
    SetProcessSubType(fLowEnergyMolecularDecay); // DNA sub-type
    enableAlongStepDoIt = false;
    enablePostStepDoIt = true;
    enableAtRestDoIt = true;
 
    fVerbose = 0;
 
#ifdef G4VERBOSE
    if (verboseLevel > 1)
    {
        G4cout << "G4MolecularDissociationProcess constructor " << "  Name:"
               << processName << G4endl;
    }
#endif
 
    pParticleChange = &aParticleChange;
 
    fDecayAtFixedTime = true;
    fProposesTimeStep = true;
}

◆ G4DNAMolecularDissociation() [2/3]

G4DNAMolecularDissociation::G4DNAMolecularDissociation ( )

delete

◆ G4DNAMolecularDissociation() [3/3]

G4DNAMolecularDissociation::G4DNAMolecularDissociation ( const G4DNAMolecularDissociation & right )

delete

◆ ~G4DNAMolecularDissociation()

G4DNAMolecularDissociation::~G4DNAMolecularDissociation ( )

override

Definition at line 79 of file G4DNAMolecularDissociation.cc.

{
  delete fpBrownianAction;
}

Member Function Documentation

◆ AtRestDoIt()

G4VParticleChange * G4DNAMolecularDissociation::AtRestDoIt	(	const G4Track &	track,
		const G4Step &	step
	)

overridevirtual

Reimplemented from G4VITRestDiscreteProcess.

Definition at line 336 of file G4DNAMolecularDissociation.cc.

{
    ClearNumberOfInteractionLengthLeft();
    ClearInteractionTimeLeft();
    return DecayIt(track, step);
}

Referenced by PostStepDoIt().

◆ AtRestGetPhysicalInteractionLength()

G4double G4DNAMolecularDissociation::AtRestGetPhysicalInteractionLength	(	const G4Track &	track,
		G4ForceCondition *	condition
	)

overridevirtual

Reimplemented from G4VITRestDiscreteProcess.

Definition at line 346 of file G4DNAMolecularDissociation.cc.

{
    if (fDecayAtFixedTime)
    {
        return GetMeanLifeTime(track, condition);
    }
 
    return G4VITRestDiscreteProcess::AtRestGetPhysicalInteractionLength(track, condition);
}

◆ DecayIt()

G4VParticleChange * G4DNAMolecularDissociation::DecayIt	(	const G4Track &	track,
		const G4Step &
	)

protectedvirtual

Definition at line 119 of file G4DNAMolecularDissociation.cc.

{
    aParticleChange.Initialize(track);
    auto pMotherMolecule = GetMolecule(track);
    auto pMotherMoleculeDefinition = pMotherMolecule->GetDefinition();
 
    if (pMotherMoleculeDefinition->GetDecayTable())
    {
        const auto pDissociationChannels = pMotherMolecule->GetDissociationChannels();
 
        if (pDissociationChannels == nullptr)
        {
            G4ExceptionDescription exceptionDescription;
            pMotherMolecule->PrintState();
            exceptionDescription << "No decay channel was found for the molecule : "
                                 << pMotherMolecule->GetName() << G4endl;
            G4Exception("G4DNAMolecularDissociation::DecayIt",
                        "G4DNAMolecularDissociation::NoDecayChannel",
                        FatalException,
                        exceptionDescription);
            return &aParticleChange;
        }
 
        auto decayVectorSize = pDissociationChannels->size();
        G4double RdmValue = G4UniformRand();
 
        const G4MolecularDissociationChannel* pDecayChannel = nullptr;
        size_t i = 0;
        do
        {
            pDecayChannel = (*pDissociationChannels)[i];
            if (RdmValue < pDecayChannel->GetProbability())
            {
                break;
            }
            RdmValue -= pDecayChannel->GetProbability();
            i++;
        } while (i < decayVectorSize);
 
        G4double decayEnergy = pDecayChannel->GetEnergy();
        auto nbProducts = pDecayChannel->GetNbProducts();
 
        if (decayEnergy > 0.)
        {
            aParticleChange.ProposeLocalEnergyDeposit(pDecayChannel->GetEnergy());
        }
 
        if (nbProducts)
        {
            std::vector<G4ThreeVector> productsDisplacement(nbProducts);
            G4ThreeVector motherMoleculeDisplacement;
 
            auto it = fDisplacementMap.find(pMotherMoleculeDefinition);
 
            if (it != fDisplacementMap.end())
            {
                auto pDisplacer = it->second.get();
                productsDisplacement = pDisplacer->GetProductsDisplacement(pDecayChannel);
                motherMoleculeDisplacement =
                        pDisplacer->GetMotherMoleculeDisplacement(pDecayChannel);
            }
            else
            {
                G4ExceptionDescription errMsg;
                errMsg << "No G4MolecularDecayProcess::theDecayDisplacementMap["
                       << pMotherMolecule->GetName() + "]";
                G4Exception("G4MolecularDecayProcess::DecayIt",
                            "DNAMolecularDecay001",
                            FatalErrorInArgument,
                            errMsg);
            }
 
            aParticleChange.SetNumberOfSecondaries(nbProducts);
 
#ifdef G4VERBOSE
            if (fVerbose)
            {
                G4cout << "Decay Process : " << pMotherMolecule->GetName()
                       << " (trackID :" << track.GetTrackID() << ") "
                       << pDecayChannel->GetName() << G4endl;
            }
#endif
 
            auto pNavigator = G4ITTransportationManager::GetTransportationManager()->GetNavigatorForTracking();
 
            for (G4int j = 0; j < nbProducts; j++)
            {
                auto pProduct = new G4Molecule(pDecayChannel->GetProduct(j));
 
                G4ThreeVector displacement = motherMoleculeDisplacement + productsDisplacement[j];
                double mag_displacement = displacement.mag();
                G4ThreeVector displacement_direction = displacement / (mag_displacement + 1e-30);
 
                double prNewSafety = DBL_MAX;
 
                //double step =
                pNavigator->CheckNextStep(track.GetPosition(),
                                         displacement_direction,
                                         mag_displacement,
                                         prNewSafety);
 
                //if(prNewSafety < mag_displacement || step < mag_displacement)
                mag_displacement = std::min(prNewSafety * 0.8, mag_displacement);
 
                G4ThreeVector product_pos = track.GetPosition()
                                            + displacement_direction * mag_displacement;
 
                //Hoang: force changing position track::
                if(fpBrownianAction != nullptr)
                {
                  fpBrownianAction->Transport(product_pos);
                }
                //Hoang: force changing position track
 
                const G4AffineTransform& transform = pNavigator->GetGlobalToLocalTransform();
 
                G4ThreeVector localPoint = transform.TransformPoint(product_pos); //track.GetPosition());
                // warning if the decayed product is outside of the volume and
                // the mother volume has no water material  (the decayed product
                // is outside of the world volume will be killed in the next step)
                if (track.GetTouchable()->GetSolid()->Inside(localPoint) !=
                    EInside::kInside)
                {
                    auto WaterMaterial = G4Material::GetMaterial("G4_WATER");
                    auto Motherlogic = track.GetTouchable()->GetVolume()->
                                       GetMotherLogical();
                    if (Motherlogic != nullptr
                       && Motherlogic->GetMaterial() != WaterMaterial)
                    {
                        G4ExceptionDescription ED;
                        ED << "The decayed product is outside of the volume : "
                           << track.GetTouchable()->GetVolume()->GetName()
                           << " with material : "<< Motherlogic->GetMaterial()
                                                       ->GetName()<< G4endl;
                        G4Exception("G4DNAMolecularDissociation::DecayIt()",
                                    "OUTSIDE_OF_MOTHER_VOLUME",
                                    JustWarning, ED);
                    }
                }
 
                auto pSecondary = pProduct->BuildTrack(track.GetGlobalTime(), product_pos);
 
                pSecondary->SetTrackStatus(fAlive);
#ifdef G4VERBOSE
                if (fVerbose)
                {
                    G4cout << "Product : " << pProduct->GetName() << G4endl;
                }
#endif
                // add the secondary track in the List
                aParticleChange.G4VParticleChange::AddSecondary(pSecondary);
            }
#ifdef G4VERBOSE
            if (fVerbose)
            {
                G4cout << "-------------" << G4endl;
            }
#endif
        }
            //DEBUG
        else if (fVerbose && decayEnergy)
        {
            G4cout << "No products for this channel" << G4endl;
            G4cout << "-------------" << G4endl;
        }
        /*
         else if(!decayEnergy && !nbProducts)
         {
         G4ExceptionDescription errMsg;
         errMsg << "There is no products and no energy specified in the molecular "
         "dissociation channel";
         G4Exception("G4MolecularDissociationProcess::DecayIt",
         "DNAMolecularDissociation002",
         FatalErrorInArgument,
         errMsg);
         }
         */
    }
 
    aParticleChange.ProposeTrackStatus(fStopAndKill);
 
    return &aParticleChange;
}

Referenced by AtRestDoIt().

◆ GetDisplacer()

G4DNAMolecularDissociation::Displacer * G4DNAMolecularDissociation::GetDisplacer ( Species * pSpecies )

Definition at line 313 of file G4DNAMolecularDissociation.cc.

{
    return fDisplacementMap[pSpecies].get();
}

◆ GetMeanFreePath()

G4double G4DNAMolecularDissociation::GetMeanFreePath	(	const G4Track &	,
		G4double	,
		G4ForceCondition *
	)

overrideprotectedvirtual

Implements G4VITRestDiscreteProcess.

Definition at line 367 of file G4DNAMolecularDissociation.cc.

{
    return 0;
}

◆ GetMeanLifeTime()

G4double G4DNAMolecularDissociation::GetMeanLifeTime	(	const G4Track &	track,
		G4ForceCondition *
	)

overrideprotectedvirtual

Implements G4VITRestDiscreteProcess.

Definition at line 110 of file G4DNAMolecularDissociation.cc.

{
    G4double output = GetMolecule(track)->GetDecayTime() - track.GetProperTime();
    return output > 0. ? output : 0.;
}

Referenced by AtRestGetPhysicalInteractionLength().

◆ IsApplicable()

G4bool G4DNAMolecularDissociation::IsApplicable ( const G4ParticleDefinition & aParticleType )

overridevirtual

Reimplemented from G4VProcess.

Definition at line 86 of file G4DNAMolecularDissociation.cc.

{
    if (aParticleType.GetParticleType() == "Molecule")
    {
#ifdef G4VERBOSE
 
        if (fVerbose > 1)
        {
            G4cout << "G4MolecularDissociation::IsApplicable(";
            G4cout << aParticleType.GetParticleName() << ",";
            G4cout << aParticleType.GetParticleType() << ")" << G4endl;
        }
#endif
        return (true);
    }
    else
    {
        return false;
    }
}

◆ operator=()

G4DNAMolecularDissociation & G4DNAMolecularDissociation::operator= ( const G4DNAMolecularDissociation & right )

delete

◆ PostStepDoIt()

G4VParticleChange * G4DNAMolecularDissociation::PostStepDoIt	(	const G4Track &	track,
		const G4Step &	step
	)

overridevirtual

Reimplemented from G4VITRestDiscreteProcess.

Definition at line 359 of file G4DNAMolecularDissociation.cc.

{
    return AtRestDoIt(track, step);
}

◆ PostStepGetPhysicalInteractionLength()

G4double G4DNAMolecularDissociation::PostStepGetPhysicalInteractionLength	(	const G4Track &	track,
		G4double	previousStepSize,
		G4ForceCondition *	condition
	)

overridevirtual

Reimplemented from G4VITRestDiscreteProcess.

Definition at line 320 of file G4DNAMolecularDissociation.cc.

{
    return 0; //-1*(-log(1-G4UniformRand())*100*1e-15*s);
}

◆ SetDisplacer()

void G4DNAMolecularDissociation::SetDisplacer	(	Species *	pSpecies,
		Displacer *	pDisplacer
	)

Definition at line 306 of file G4DNAMolecularDissociation.cc.

{
    fDisplacementMap.emplace(pSpecies, std::unique_ptr<Displacer>(pDisplacer));
}

Referenced by G4EmDNAChemistry::ConstructProcess(), G4EmDNAChemistry_option1::ConstructProcess(), and G4EmDNAChemistry_option2::ConstructProcess().

◆ SetUserBrownianAction()

void G4DNAMolecularDissociation::SetUserBrownianAction ( G4VUserBrownianAction * pBrownianAction )

inline

Definition at line 91 of file G4DNAMolecularDissociation.hh.

    {
      fpBrownianAction = pBrownianAction;
    }

◆ SetVerbose()

void G4DNAMolecularDissociation::SetVerbose ( G4int verbose )

Definition at line 329 of file G4DNAMolecularDissociation.cc.

{
    fVerbose = verbose;
}

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

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Displacer

◆ Species

Constructor & Destructor Documentation

◆ G4DNAMolecularDissociation() [1/3]

◆ G4DNAMolecularDissociation() [2/3]

◆ G4DNAMolecularDissociation() [3/3]

◆ ~G4DNAMolecularDissociation()

Member Function Documentation

◆ AtRestDoIt()

◆ AtRestGetPhysicalInteractionLength()

◆ DecayIt()

◆ GetDisplacer()

◆ GetMeanFreePath()

◆ GetMeanLifeTime()

◆ IsApplicable()

◆ operator=()

◆ PostStepDoIt()

◆ PostStepGetPhysicalInteractionLength()

◆ SetDisplacer()

◆ SetUserBrownianAction()

◆ SetVerbose()