#include <G4DNABrownianTransportation.hh>

Inheritance diagram for G4DNABrownianTransportation:

Collaboration diagram for G4DNABrownianTransportation:

Classes
struct	G4ITBrownianState

Public Member Functions
	G4DNABrownianTransportation (const G4String &aName="DNABrownianTransportation", G4int verbosityLevel=0)

virtual	~G4DNABrownianTransportation ()

	G4DNABrownianTransportation (const G4DNABrownianTransportation &)

G4DNABrownianTransportation &	operator= (const G4DNABrownianTransportation &)

void	SetBrownianAction (G4BrownianAction *)

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 &)

void	UseMaximumTimeBeforeReachingBoundary (bool flag=true)

void	UseCumulativeDensitFunction (bool flag=true)

void	UseLimitingTimeSteps (bool flag=true)

void	SpeedLevel (int level)

Public Member Functions inherited from G4ITTransportation
	G4ITTransportation (const G4String &aName="ITTransportation", G4int verbosityLevel=0)

virtual	~G4ITTransportation ()

	G4ITTransportation (const G4ITTransportation &)

G4bool	IsStepLimitedByGeometry ()

virtual G4double	AtRestGetPhysicalInteractionLength (const G4Track &, G4ForceCondition *)

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

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

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

G4shared_ptr< G4ProcessState_Lock >	GetProcessState ()

void	SetProcessState (G4shared_ptr< G4ProcessState_Lock > aProcInfo)

void	ResetProcessState ()

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

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	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	EndTracking ()

virtual void	SetProcessManager (const G4ProcessManager *)

virtual const G4ProcessManager *	GetProcessManager ()

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

virtual void	SetMasterProcess (G4VProcess *masterP)

const G4VProcess *	GetMasterProcess () const

virtual void	BuildWorkerPhysicsTable (const G4ParticleDefinition &part)

virtual void	PrepareWorkerPhysicsTable (const G4ParticleDefinition &)

Protected Member Functions
G4double	ComputeGeomLimit (const G4Track &track, G4double &presafety, G4double limit)

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 ()

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 previousStepSize)

void	ClearNumberOfInteractionLengthLeft ()

Protected Attributes
G4bool	fUseMaximumTimeBeforeReachingBoundary

G4Material *	fNistWater

G4bool	fUseSchedulerMinTimeSteps

G4double	fInternalMinTimeStep

G4bool	fSpeedMeUp

const std::vector< G4double > *	fpWaterDensity

G4BrownianAction *	fpBrownianAction

Protected Attributes inherited from G4ITTransportation
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

G4ITSafetyHelper *	fpSafetyHelper

G4int	fVerboseLevel

Protected Attributes inherited from G4VITProcess
G4shared_ptr< 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

Definition at line 109 of file G4DNABrownianTransportation.hh.

Constructor & Destructor Documentation

G4DNABrownianTransportation::G4DNABrownianTransportation	(	const G4String &	aName = `"DNABrownianTransportation"`,
		G4int	verbosityLevel = `0`
	)

Definition at line 120 of file G4DNABrownianTransportation.cc.

                                                                           :
     G4ITTransportation(aName, verbosity)
 {
 
   fVerboseLevel = 0;
 
   fpState.reset(new G4ITBrownianState());
 
   //ctor
   SetProcessSubType(61);
 
   fNistWater = G4NistManager::Instance()->FindOrBuildMaterial("G4_WATER");
   fpWaterDensity = 0;
 
   fUseMaximumTimeBeforeReachingBoundary = true;
   fUseSchedulerMinTimeSteps = false;
   fSpeedMeUp = true;
 
   fInternalMinTimeStep = 1*picosecond;
   fpBrownianAction = 0;
 }

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G4DNABrownianTransportation::~G4DNABrownianTransportation ( )

virtual

Definition at line 143 of file G4DNABrownianTransportation.cc.

 {
   if(fpBrownianAction) delete fpBrownianAction;
 }

G4DNABrownianTransportation::G4DNABrownianTransportation ( const G4DNABrownianTransportation & right )

Definition at line 148 of file G4DNABrownianTransportation.cc.

                                                                                                  :
     G4ITTransportation(right)
 {
   //copy ctor
   SetProcessSubType(61);
   fUseMaximumTimeBeforeReachingBoundary = right
       .fUseMaximumTimeBeforeReachingBoundary;
   fUseSchedulerMinTimeSteps = right.fUseSchedulerMinTimeSteps;
   fNistWater = right.fNistWater;
   fpWaterDensity = right.fpWaterDensity;
   fInternalMinTimeStep = right.fInternalMinTimeStep;
   fSpeedMeUp = right.fSpeedMeUp;
   fpBrownianAction = right.fpBrownianAction;
 }

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Member Function Documentation

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

virtual

Reimplemented from G4ITTransportation.

Definition at line 791 of file G4DNABrownianTransportation.cc.

 {
 #ifdef DEBUG_MEM
   MemStat mem_first, mem_second, mem_diff;
 #endif
 
 #ifdef DEBUG_MEM
   mem_first = MemoryUsage();
 #endif
 
   if (GetIT(track)->GetTrackingInfo()->IsLeadingStep()
       && State(fComputeLastPosition))
   {
     //==========================================================================
     // DEBUG
     //
 //     assert(fabs(State(theInteractionTimeLeft)-
 //                G4VScheduler::Instance()->GetTimeStep()) < DBL_EPSILON);
     //==========================================================================
 
     double spaceStep = DBL_MAX;
 
     if(State(theInteractionTimeLeft) <= fInternalMinTimeStep)
     {
       spaceStep = State(fEndPointDistance);
       State(fGeometryLimitedStep) = true;
     }
     else
     {
       G4double diffusionCoefficient = GetMolecule(track)->
       GetDiffusionCoefficient();
 
       double sqrt_2Dt= sqrt(2 * diffusionCoefficient * State(theInteractionTimeLeft));
       G4double x = G4RandGauss::shoot(0, sqrt_2Dt);
       G4double y = G4RandGauss::shoot(0, sqrt_2Dt);
       G4double z = G4RandGauss::shoot(0, sqrt_2Dt);
 
       spaceStep = sqrt(x * x + y * y + z * z);
 
       if(spaceStep >= State(fEndPointDistance))
       {
         State(fGeometryLimitedStep) = true;
        if (
            //fSpeedMeUp == false&&
            fUseSchedulerMinTimeSteps == false
            && spaceStep >= State(fEndPointDistance))
        {
          spaceStep = State(fEndPointDistance);
        }
       }
       else
       {
         State(fGeometryLimitedStep) = false;
       }
     }
 
 //    assert( (spaceStep <  State(fEndPointDistance) && State(fGeometryLimitedStep) == false)
 //|| (spaceStep >= State(fEndPointDistance) && State(fGeometryLimitedStep)));
 
     // Calculate final position
     //
     State(fTransportEndPosition) = track.GetPosition()
                + spaceStep * track.GetMomentumDirection();
   }
 
   if(fVerboseLevel)
   {
     G4cout << GREEN_ON_BLUE
             << "G4DNABrownianTransportation::AlongStepDoIt: "
                 "GeometryLimitedStep = "
             << State(fGeometryLimitedStep)
             << RESET_COLOR
             << G4endl;
   }
 
 //  static G4ThreadLocal G4int noCalls = 0;
 //  noCalls++;
 
 //  fParticleChange.Initialize(track);
 
   G4ITTransportation::AlongStepDoIt(track, step);
 
 #ifdef DEBUG_MEM
   MemStat mem_intermediaire = MemoryUsage();
   mem_diff = mem_intermediaire-mem_first;
   G4cout << "\t\t\t >> || MEM || After calling G4ITTransportation::"
   "AlongStepDoIt for "<< track.GetTrackID() << ", diff is : "
   << mem_diff << G4endl;
 #endif
 
   if(track.GetStepLength() != 0 // && State(fGeometryLimitedStep)
       //========================================================================
       // TODO: avoid changing direction after too small time steps
 //    && (G4VScheduler::Instance()->GetTimeStep() > fInternalMinTimeStep
 //        || fSpeedMeUp == false)
       //========================================================================
         )
   {
     Diffusion(track);
   }
   //else
   //{
   //  fParticleChange.ProposeMomentumDirection(State(fTransportEndMomentumDir));
   //}
 /*
   if (State(fParticleIsLooping))
   {
     if ((State(fNoLooperTrials)>= fThresholdTrials))
     {
       fParticleChange.ProposeTrackStatus(fStopAndKill);
       State(fNoLooperTrials) = 0;
 #ifdef G4VERBOSE
       if ((fVerboseLevel > 1))
       {
         G4cout
             << " G4DNABrownianTransportation is killing track that is looping or stuck "
             << G4endl;
         G4cout << "   Number of trials = " << State(fNoLooperTrials)
         << "   No of calls to AlongStepDoIt = " << noCalls
         << G4endl;
       }
 #endif
     }
     else
     {
       State(fNoLooperTrials)++;
     }
   }
   else
   {
     State(fNoLooperTrials)=0;
   }
 */
 #ifdef DEBUG_MEM
   mem_intermediaire = MemoryUsage();
   mem_diff = mem_intermediaire-mem_first;
   G4cout << "\t\t\t >> || MEM || After calling G4DNABrownianTransportation::"
   "Diffusion for "<< track.GetTrackID() << ", diff is : "
   << mem_diff << G4endl;
 #endif
 
   return &fParticleChange;
 }

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

virtual

Reimplemented from G4ITTransportation.

Definition at line 582 of file G4DNABrownianTransportation.cc.

 {
 #ifdef G4VERBOSE
   if(fVerboseLevel)
   {
     G4cout << " G4DNABrownianTransportation::AlongStepGetPhysicalInteractionLength - track ID: "
            << track.GetTrackID() << G4endl;
     G4cout << "In volume : " << track.GetVolume()->GetName()
            << " position : " << G4BestUnit(track.GetPosition() , "Length") << G4endl;
   }
 #endif
 
   G4double geometryStepLength =
       G4ITTransportation::AlongStepGetPhysicalInteractionLength(
           track, previousStepSize, currentMinimumStep, currentSafety,
           selection);
 
   if(geometryStepLength==0)
   { 
 //    G4cout << "geometryStepLength==0" << G4endl;
     if(State(fGeometryLimitedStep))
     {
 //      G4cout << "if(State(fGeometryLimitedStep))" << G4endl;
       G4TouchableHandle newTouchable = new G4TouchableHistory;
 
       newTouchable->UpdateYourself(State(fCurrentTouchableHandle)->GetVolume(),
                                    State(fCurrentTouchableHandle)->GetHistory());
 
        fLinearNavigator->SetGeometricallyLimitedStep();
        fLinearNavigator->LocateGlobalPointAndUpdateTouchableHandle(
            track.GetPosition(), track.GetMomentumDirection(),
            newTouchable, true);
 
        if(newTouchable->GetVolume() == 0)
        {
           return 0;
        }
 
        State(fCurrentTouchableHandle) = newTouchable;
 
        //=======================================================================
        // TODO: speed up navigation update
 //       geometryStepLength = fLinearNavigator->ComputeStep(track.GetPosition(),
 //                                     track.GetMomentumDirection(),
 //                                     currentMinimumStep,
 //                                     currentSafety);
        //=======================================================================
 
 
        //=======================================
        // Longer but safer ...
        geometryStepLength =
              G4ITTransportation::AlongStepGetPhysicalInteractionLength(
                  track, previousStepSize, currentMinimumStep, currentSafety,
                  selection);
 
       }
   }
 
   //============================================================================
   // DEBUG
  // G4cout << "geometryStepLength: " << G4BestUnit(geometryStepLength, "Length")
  //        << " | trackID: " << track.GetTrackID()
  //        << G4endl;
   //============================================================================
 
   G4double diffusionCoefficient = 0;
 
   /*
   G4Material* material = track.GetMaterial();
   G4double waterDensity = (*fpWaterDensity)[material->GetIndex()];
 
   if (waterDensity == 0.0)
   {
     if(fpBrownianAction)
     {
       diffusionCoefficient = fpBrownianAction->GetDiffusionCoefficient(material,
                                                                        GetMolecule(track));
     }
 
     if(diffusionCoefficient <= 0)
     {
       State(fGeometryLimitedStep) = false;
       State(theInteractionTimeLeft) = 0;
       State(fTransportEndPosition) = track.GetPosition();
       return 0;
     }
 
   }
   else
     */
   //{
     diffusionCoefficient = GetMolecule(track)->GetDiffusionCoefficient();
   //}
 
   State(fComputeLastPosition) = false;
   State(fTimeStepReachedLimit) = false;
 
   if (State(fGeometryLimitedStep))
   {
     // 95 % of the space step distribution is lower than
     // d_95 = 2 * sqrt(2*D*t)
     // where t is the corresponding time step
     // so by inversion :
     if (fUseMaximumTimeBeforeReachingBoundary)
     {
       if(fSpeedMeUp)
       {
       State(theInteractionTimeLeft) = (geometryStepLength * geometryStepLength)
           / (diffusionCoefficient); // d_50 - use straight line
       }
       else
       {
          State(theInteractionTimeLeft) = (currentSafety * currentSafety)
                   / (diffusionCoefficient); // d_50 - use safety
 
          //=====================================================================
          // State(theInteractionTimeLeft) = (currentSafety * currentSafety)
          //          / (8 * diffusionCoefficient); // d_95
          //=====================================================================
       }
       State(fComputeLastPosition) = true;
     }
     else
     // Will use a random time - this is precise but long to compute in certain
     // circumstances (many particles - small volumes)
     {
       State(fRandomNumber) = G4UniformRand();
       State(theInteractionTimeLeft) = 1 / (4 * diffusionCoefficient)
           * pow(geometryStepLength / InvErfc(State(fRandomNumber)),2);
 
       State(fTransportEndPosition) = geometryStepLength*
           track.GetMomentumDirection() + track.GetPosition();
     }
 
     if (fUseSchedulerMinTimeSteps)
     {
       double minTimeStepAllowed = G4VScheduler::Instance()->GetLimitingTimeStep();
       //========================================================================
       // TODO
 //      double currentMinTimeStep = G4VScheduler::Instance()->GetTimeStep();
       //========================================================================
 
       if (State(theInteractionTimeLeft) < minTimeStepAllowed)
       {
         State(theInteractionTimeLeft) = minTimeStepAllowed;
         State(fTimeStepReachedLimit) = true;
         State(fComputeLastPosition) = true;
       }
     }
     else if(State(theInteractionTimeLeft) < fInternalMinTimeStep)
       // TODO: find a better way when fForceLimitOnMinTimeSteps is not used
     {
       State(fTimeStepReachedLimit) = true;
       State(theInteractionTimeLeft) = fInternalMinTimeStep;
       if (fUseMaximumTimeBeforeReachingBoundary)
       {
         State(fComputeLastPosition) = true;
       }
     }
 
     State(fCandidateEndGlobalTime) =
         track.GetGlobalTime() + State(theInteractionTimeLeft);
 
     State(fEndGlobalTimeComputed) = true; // MK: ADDED ON 20/11/2014
 
     State(fPathLengthWasCorrected) = false;
   }
   else
   {
     // Transform geometrical step
     geometryStepLength = 2
         * sqrt(diffusionCoefficient * State(theInteractionTimeLeft))
         * InvErf(G4UniformRand());
     State(fPathLengthWasCorrected) = true;
     //State(fEndPointDistance) = geometryStepLength;
     State(fTransportEndPosition) = geometryStepLength*
               track.GetMomentumDirection() + track.GetPosition();
   }
 
 #ifdef G4VERBOSE
   //    DEBUG
   if (fVerboseLevel > 1)
   {
   G4cout << GREEN_ON_BLUE
          << "G4DNABrownianTransportation::AlongStepGetPhysicalInteractionLength = "
          << G4BestUnit(geometryStepLength, "Length")
          << " | trackID = "
          << track.GetTrackID()
          << RESET_COLOR
          << G4endl;
   }
 #endif
 
 // assert(geometryStepLength <  State(fEndPointDistance)
 //  || (geometryStepLength >= State(fEndPointDistance) && State(fGeometryLimitedStep)));
 
   return geometryStepLength;
 }

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void G4DNABrownianTransportation::BuildPhysicsTable ( const G4ParticleDefinition & particle )

virtual

Reimplemented from G4ITTransportation.

Definition at line 188 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"));
 
   fpSafetyHelper->InitialiseHelper();
   G4ITTransportation::BuildPhysicsTable(particle);
 }

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G4double G4DNABrownianTransportation::ComputeGeomLimit	(	const G4Track &	track,
		G4double &	presafety,
		G4double	limit
	)

protected

Definition at line 563 of file G4DNABrownianTransportation.cc.

 {
   G4double res = DBL_MAX;
   if(track.GetVolume() != fpSafetyHelper->GetWorldVolume())
   {
     G4TrackStateManager& trackStateMan = GetIT(track)->GetTrackingInfo()
     ->GetTrackStateManager();
     fpSafetyHelper->LoadTrackState(trackStateMan);
     res = fpSafetyHelper->CheckNextStep(
         track.GetStep()->GetPreStepPoint()->GetPosition(),
         track.GetMomentumDirection(),
         limit, presafety);
     fpSafetyHelper->ResetTrackState();
   }
   return res;
 }

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

virtual

Reimplemented from G4ITTransportation.

Definition at line 204 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;
 
   G4Molecule* molecule = GetMolecule(track);
 
   if(timeStep > 0)
   {
     spaceStep = DBL_MAX;
 
     // TODO : generalize this process to all kind of Brownian objects
     G4double diffCoeff = molecule->GetDiffusionCoefficient(track.GetMaterial(),
                                                            track.GetMaterial()->GetTemperature());
 
     static double sqrt_2 = sqrt(2.);
     double sqrt_Dt = sqrt(diffCoeff*timeStep);
     double sqrt_2Dt = sqrt_2*sqrt_Dt;
 
     if(State(fTimeStepReachedLimit)== true)
     {
       //========================================================================
       State(fGeometryLimitedStep) = true;// important
       //========================================================================
       spaceStep = State(fEndPointDistance);
    //   G4cout << "State(fTimeStepReachedLimit)== true" << G4endl;
     }
     else
     {
       G4double x = G4RandGauss::shoot(0,sqrt_2Dt);
       G4double y = G4RandGauss::shoot(0,sqrt_2Dt);
       G4double z = G4RandGauss::shoot(0,sqrt_2Dt);
 
       spaceStep = sqrt(x*x + y*y + z*z);
 
       if(spaceStep >= State(fEndPointDistance))
       {
         //G4cout << "spaceStep >= State(fEndPointDistance)" << G4endl;
         //======================================================================
         State(fGeometryLimitedStep) = true;// important
         //======================================================================
 /*
         if(fSpeedMeUp)
         {
           G4cout << "SpeedMeUp" << G4endl;
         }
         else
 */
         if(fUseSchedulerMinTimeSteps == false)// jump over barrier NOT used
         {
 #ifdef G4VERBOSE
           if (fVerboseLevel > 1)
           {
             G4cout << GREEN_ON_BLUE
             << "G4ITBrownianTransportation::ComputeStep() : "
             << "Step was limited to boundary"
             << RESET_COLOR
             << G4endl;
           }
 #endif
           //TODO
           if(State(fRandomNumber)>=0) // CDF is used
           {
             /*
              //=================================================================
              State(fGeometryLimitedStep) = true;// important
              //=================================================================
              spaceStep = State(fEndPointDistance);
              */
 
             //==================================================================
             // BE AWARE THAT THE TECHNIQUE USED BELOW IS A 1D APPROXIMATION
             // Cumulative density function for the 3D case is not yet
             // implemented
             //==================================================================
 //            G4cout << GREEN_ON_BLUE
 //                   << "G4ITBrownianTransportation::ComputeStep() : "
 //                   << "A random number was selected"
 //                   << RESET_COLOR
 //                   << G4endl;
             double value = State(fRandomNumber)+(1-State(fRandomNumber))*G4UniformRand();
             double invErfc = InvErfc(value);
             spaceStep = invErfc*2*sqrt_Dt;
 
             if(State(fTimeStepReachedLimit)== false)
             {
               //================================================================
               State(fGeometryLimitedStep) = false;// important
               //================================================================
             }
             //==================================================================
             // DEBUG
 //            if(spaceStep > State(fEndPointDistance))
 //            {
 //              G4cout << "value = " << value << G4endl;
 //              G4cout << "invErfc = " << invErfc << G4endl;
 //              G4cout << "spaceStep = " << G4BestUnit(spaceStep, "Length")
 //              << G4endl;
 //              G4cout << "end point distance= " << G4BestUnit(State(fEndPointDistance), "Length")
 //              << G4endl;
 //            }
 //
 //            assert(spaceStep <= State(fEndPointDistance));
             //==================================================================
 
           }
           else if(fUseMaximumTimeBeforeReachingBoundary == false) // CDF is used
           {
             double min_randomNumber = Erfc(State(fEndPointDistance)/2*sqrt_Dt);
             double value = min_randomNumber+(1-min_randomNumber)*G4UniformRand();
             double invErfc = InvErfc(value);
             spaceStep = invErfc*2*sqrt_Dt;
             if(spaceStep >= State(fEndPointDistance))
             {
               //================================================================
               State(fGeometryLimitedStep) = true;// important
               //================================================================
             }
             else if(State(fTimeStepReachedLimit)== false)
             {
               //================================================================
               State(fGeometryLimitedStep) = false;// important
               //================================================================
             }
           }
           else // CDF is NOT used
           {
             //==================================================================
             State(fGeometryLimitedStep) = true;// important
             //==================================================================
             spaceStep = State(fEndPointDistance);
             //TODO
 
             /*
             //==================================================================
             // 1D approximation to place the brownian between its starting point
             // and the geometry boundary
             //==================================================================
             double min_randomNumber = Erfc(State(fEndPointDistance)/2*sqrt_Dt);
             double value = State(fRandomNumber)+(1-State(fRandomNumber))*G4UniformRand();
             double invErfc = InvErfc(value*G4UniformRand());
             spaceStep = invErfc*2*sqrt_Dt;
             State(fGeometryLimitedStep) = false;
             */
           }
         }
 
         State(fTransportEndPosition)= spaceStep*
 //             step.GetPostStepPoint()->GetMomentumDirection() 
              track.GetMomentumDirection()
              + track.GetPosition();
       }
       else
       {
         //======================================================================
         State(fGeometryLimitedStep) = false;// important
         //======================================================================
         State(fTransportEndPosition)= spaceStep*step.GetPostStepPoint()->
         GetMomentumDirection() + track.GetPosition();
       }
     }
   }
   else
   {
     spaceStep = 0.;
     State(fTransportEndPosition) = track.GetPosition();
     State(fGeometryLimitedStep) = false;
   }
 
   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
            << "Initial position:" << G4BestUnit(track.GetPosition(), "Length")
            << G4endl
            << "Initial direction:" << track.GetMomentumDirection() << G4endl
            << "Final position:" << G4BestUnit(State(fTransportEndPosition), "Length")
            << G4endl
            << "Initial magnitude:" << G4BestUnit(track.GetPosition().mag(), "Length")
            << G4endl
            << "Final magnitude:" << G4BestUnit(State(fTransportEndPosition).mag(), "Length")
            << G4endl
            << "Diffusion length : "
            << G4BestUnit(spaceStep, "Length")
            << " within time step : " << G4BestUnit(timeStep,"Time")
            << G4endl
            << "State(fTimeStepReachedLimit)= " << State(fTimeStepReachedLimit) << G4endl
            << "State(fGeometryLimitedStep)=" << State(fGeometryLimitedStep) << G4endl
            << "End point distance was: " << G4BestUnit(State(fEndPointDistance), "Length")
            << G4endl
            << RESET_COLOR
            << G4endl<< G4endl;
   }
 #endif
 
 //==============================================================================
 // DEBUG
 //assert(spaceStep <  State(fEndPointDistance)
 //  || (spaceStep >= State(fEndPointDistance) && State(fGeometryLimitedStep)));
 //assert(track.GetMomentumDirection() == State(fTransportEndMomentumDir));
 //==============================================================================
 }

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void G4DNABrownianTransportation::Diffusion ( const G4Track & track )

protected

Definition at line 475 of file G4DNABrownianTransportation.cc.

 {
 
 #ifdef DEBUG_MEM
   MemStat mem_first = MemoryUsage();
 #endif
 
 #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_COLOR
            << G4endl
            << G4endl;
   }
 #endif
 
 /*
   fParticleChange.ProposePosition(State(fTransportEndPosition));
   //fParticleChange.ProposeEnergy(State(fTransportEndKineticEnergy));
   fParticleChange.SetMomentumChanged(State(fMomentumChanged));
 
   fParticleChange.ProposeGlobalTime(State(fCandidateEndGlobalTime));
   fParticleChange.ProposeLocalTime(State(fCandidateEndGlobalTime));
   fParticleChange.ProposeTrueStepLength(track.GetStepLength());
 */
   G4Material* material = track.GetMaterial();
 
   G4double waterDensity = (*fpWaterDensity)[material->GetIndex()];
 
   if (waterDensity == 0.0)
   {
     if(fpBrownianAction)
     {
       // Let the user Brownian action class decide what to do
       fpBrownianAction->Transport(track,
                                   fParticleChange);
       return;
     }
     else
     {
 #ifdef G4VERBOSE
       if(fVerboseLevel)
       {
         G4cout << "A track is outside water material : trackID = "
         << track.GetTrackID() << " (" << GetMolecule(track)->GetName() <<")"
         << G4endl;
         G4cout << "Local Time : " << G4BestUnit(track.GetGlobalTime(), "Time")
         << G4endl;
         G4cout << "Step Number :" << track.GetCurrentStepNumber() << G4endl;
       }
 #endif
       fParticleChange.ProposeEnergy(0.);
       fParticleChange.ProposeTrackStatus(fStopAndKill);
       return;// &fParticleChange is the final returned object
     }
   }
 
 
    #ifdef DEBUG_MEM
    MemStat mem_intermediaire = MemoryUsage();
    mem_diff = mem_intermediaire-mem_first;
    G4cout << "\t\t\t >> || MEM || In G4DNABrownianTransportation::Diffusion "
    "after dealing with waterDensity for "<< track.GetTrackID()
    << ", diff is : " << mem_diff << G4endl;
    #endif
 
   fParticleChange.ProposeMomentumDirection(G4RandomDirection());
   State(fMomentumChanged) = true;
   fParticleChange.SetMomentumChanged(true);
    //
    #ifdef DEBUG_MEM
    mem_intermediaire = MemoryUsage();
    mem_diff = mem_intermediaire-mem_first;
    G4cout << "\t\t\t >> || MEM || In G4DNABrownianTransportation::"
           "After proposing new direction to fParticleChange for "
           << track.GetTrackID() << ", diff is : " << mem_diff << G4endl;
    #endif
 
   return;// &fParticleChange is the final returned object
 }

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

Definition at line 163 of file G4DNABrownianTransportation.cc.

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

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

virtual

Reimplemented from G4ITTransportation.

Definition at line 451 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_COLOR
            << G4endl<< G4endl;
   }
 #endif
   return &fParticleChange;
 }

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void G4DNABrownianTransportation::SetBrownianAction ( G4BrownianAction * brownianAction )

inline

Definition at line 243 of file G4DNABrownianTransportation.hh.

 {
   fpBrownianAction = brownianAction;
 }

void G4DNABrownianTransportation::SpeedLevel ( int level )

inline

Definition at line 172 of file G4DNABrownianTransportation.hh.

   {
     if(level < 0) level =0;
     else if(level > 2) level = 2;
 
     switch(level)
     {
       case 0:
         fSpeedMeUp = false;
         fUseSchedulerMinTimeSteps = false;
         return;
 
       case 1:
         fSpeedMeUp = true;
         fUseSchedulerMinTimeSteps = false;
         return;
 
       case 2:
         //======================================================================
         // NB: BE AWARE THAT IF NO MIN TIME STEPS NO TIME STEPS HAVE BEEN
         // PROVIDED TO G4Scheduler THIS LEVEL MIGHT BE SLOWER THAN LEVEL 1
         //======================================================================
         fSpeedMeUp = true;
         fUseSchedulerMinTimeSteps = true;
         return;
     }
   }

void G4DNABrownianTransportation::StartTracking ( G4Track * aTrack )

virtual

Reimplemented from G4ITTransportation.

Definition at line 179 of file G4DNABrownianTransportation.cc.

 {
   fpState.reset(new G4ITBrownianState());
 //  G4cout << "G4DNABrownianTransportation::StartTracking : "
 //  "Initialised track State" << G4endl;
   SetInstantiateProcessState(false);
   G4ITTransportation::StartTracking(track);
 }

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void G4DNABrownianTransportation::UseCumulativeDensitFunction ( bool flag = true )

inline

Definition at line 156 of file G4DNABrownianTransportation.hh.

   {
     if(flag == true)
     {
       fUseMaximumTimeBeforeReachingBoundary = false;
       return;
     }
     fUseMaximumTimeBeforeReachingBoundary = true;
   }

void G4DNABrownianTransportation::UseLimitingTimeSteps ( bool flag = true )

inline

Definition at line 167 of file G4DNABrownianTransportation.hh.

   {
     fUseSchedulerMinTimeSteps = flag;
   }

void G4DNABrownianTransportation::UseMaximumTimeBeforeReachingBoundary ( bool flag = true )

inline

Definition at line 147 of file G4DNABrownianTransportation.hh.

   {
     fUseMaximumTimeBeforeReachingBoundary = flag;
   }

Member Data Documentation

G4double G4DNABrownianTransportation::fInternalMinTimeStep

protected

Definition at line 233 of file G4DNABrownianTransportation.hh.

G4Material* G4DNABrownianTransportation::fNistWater

protected

Definition at line 230 of file G4DNABrownianTransportation.hh.

G4BrownianAction* G4DNABrownianTransportation::fpBrownianAction

protected

Definition at line 239 of file G4DNABrownianTransportation.hh.

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

protected

Definition at line 237 of file G4DNABrownianTransportation.hh.

G4bool G4DNABrownianTransportation::fSpeedMeUp

protected

Definition at line 234 of file G4DNABrownianTransportation.hh.

G4bool G4DNABrownianTransportation::fUseMaximumTimeBeforeReachingBoundary

protected

Definition at line 229 of file G4DNABrownianTransportation.hh.

G4bool G4DNABrownianTransportation::fUseSchedulerMinTimeSteps

protected

Definition at line 232 of file G4DNABrownianTransportation.hh.

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

source/geant4.10.03.p03/source/processes/electromagnetic/dna/processes/include/G4DNABrownianTransportation.hh
source/geant4.10.03.p03/source/processes/electromagnetic/dna/processes/src/G4DNABrownianTransportation.cc

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation