#include <G4DNAScavengerProcess.hh>

Inheritance diagram for G4DNAScavengerProcess:

Classes
struct	G4DNAScavengerProcessState

Public Types
using	MolType = const G4MolecularConfiguration*

using	Data = const G4DNAMolecularReactionData

Public Member Functions
	G4DNAScavengerProcess (const G4String &aName, const G4DNABoundingBox &box, G4ProcessType type=fUserDefined)

	~G4DNAScavengerProcess () override

	G4DNAScavengerProcess (const G4DNAScavengerProcess &)=delete

G4DNAScavengerProcess &	operator= (const G4DNAScavengerProcess &)=delete

void	StartTracking (G4Track *) override

void	SetReaction (MolType, Data *pData)

void	BuildPhysicsTable (const G4ParticleDefinition &) 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)

	~G4VITProcess () override

	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 ()

void	StartTracking (G4Track *) override

void	BuildPhysicsTable (const G4ParticleDefinition &) override

G4double	GetInteractionTimeLeft ()

void	ResetNumberOfInteractionLengthLeft () override

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

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 const G4VProcess *	GetCreatorProcess () const

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

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 Attributes
G4bool	fIsInitialized

G4double	fReturnedValue

G4ParticleChange	fParticleChange

const G4MolecularConfiguration *	fpMolecularConfiguration

std::map< MolType, std::map< MolType, Data * > >	fConfMap

std::vector< MolType >	fpMaterialVector

MolType	fpMaterialConf

const G4DNABoundingBox *	fpBoundingBox

G4DNAScavengerMaterial *	fpScavengerMaterial {nullptr}

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

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 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 ()

Detailed Description

Definition at line 35 of file G4DNAScavengerProcess.hh.

Member Typedef Documentation

◆ Data

using G4DNAScavengerProcess::Data = const G4DNAMolecularReactionData

Definition at line 39 of file G4DNAScavengerProcess.hh.

◆ MolType

using G4DNAScavengerProcess::MolType = const G4MolecularConfiguration*

Definition at line 38 of file G4DNAScavengerProcess.hh.

Constructor & Destructor Documentation

◆ G4DNAScavengerProcess() [1/2]

G4DNAScavengerProcess::G4DNAScavengerProcess	(	const G4String &	aName,
		const G4DNABoundingBox &	box,
		G4ProcessType	type = fUserDefined )

explicit

Definition at line 45 of file G4DNAScavengerProcess.cc.

  : G4VITProcess(aName, type)
  , fpBoundingBox(&box)
{
  pParticleChange     = &fParticleChange;
  enableAtRestDoIt    = false;
  enableAlongStepDoIt = false;
  enablePostStepDoIt  = true;
  SetProcessSubType(66);
  G4VITProcess::SetInstantiateProcessState(false);
  fIsInitialized           = false;
  fpMolecularConfiguration = nullptr;
  fpMaterialConf           = nullptr;
  fProposesTimeStep        = true;
  fReturnedValue           = DBL_MAX;
  verboseLevel             = 0;
}

◆ ~G4DNAScavengerProcess()

G4DNAScavengerProcess::~G4DNAScavengerProcess ( )

override

Definition at line 65 of file G4DNAScavengerProcess.cc.

{
  for(auto& iter : fConfMap)
  {
    for(auto& iter2 : iter.second)
    {
      delete iter2.second;
    }
  }
}

◆ G4DNAScavengerProcess() [2/2]

G4DNAScavengerProcess::G4DNAScavengerProcess ( const G4DNAScavengerProcess & )

delete

Member Function Documentation

◆ AlongStepDoIt()

G4VParticleChange * G4DNAScavengerProcess::AlongStepDoIt	(	const G4Track &	,
		const G4Step &	)

inlineoverridevirtual

Implements G4VProcess.

Definition at line 78 of file G4DNAScavengerProcess.hh.

  {
    return nullptr;
  }

◆ AlongStepGetPhysicalInteractionLength()

G4double G4DNAScavengerProcess::AlongStepGetPhysicalInteractionLength	(	const G4Track &	,
		G4double	,
		G4double	,
		G4double &	,
		G4GPILSelection *	)

inlineoverridevirtual

Implements G4VProcess.

Definition at line 70 of file G4DNAScavengerProcess.hh.

  {
    return -1.0;
  }

◆ AtRestDoIt()

G4VParticleChange * G4DNAScavengerProcess::AtRestDoIt	(	const G4Track &	,
		const G4Step &	)

inlineoverridevirtual

Implements G4VProcess.

Definition at line 64 of file G4DNAScavengerProcess.hh.

  {
    return nullptr;
  }

◆ AtRestGetPhysicalInteractionLength()

G4double G4DNAScavengerProcess::AtRestGetPhysicalInteractionLength	(	const G4Track &	,
		G4ForceCondition *	)

inlineoverridevirtual

Implements G4VProcess.

Definition at line 58 of file G4DNAScavengerProcess.hh.

  {
    return -1.0;
  }

◆ BuildPhysicsTable()

void G4DNAScavengerProcess::BuildPhysicsTable ( const G4ParticleDefinition & )

overridevirtual

Reimplemented from G4VProcess.

Definition at line 81 of file G4DNAScavengerProcess.cc.

{
  fpScavengerMaterial = dynamic_cast<G4DNAScavengerMaterial*>(
    G4Scheduler::Instance()->GetScavengerMaterial());
  if(fpScavengerMaterial == nullptr)
  {
    return;
  }
  fIsInitialized = true;
}

◆ operator=()

G4DNAScavengerProcess & G4DNAScavengerProcess::operator= ( const G4DNAScavengerProcess & )

delete

◆ PostStepDoIt()

G4VParticleChange * G4DNAScavengerProcess::PostStepDoIt	(	const G4Track &	track,
		const G4Step &	)

overridevirtual

Implements G4VProcess.

Definition at line 247 of file G4DNAScavengerProcess.cc.

{
  G4Molecule* molecule = GetMolecule(track);
  auto molConf         = molecule->GetMolecularConfiguration();
  if(fpMolecularConfiguration != molConf)
  {
    fReturnedValue = DBL_MAX;
    fParticleChange.Initialize(track);
    State(fPreviousTimeAtPreStepPoint) = -1;
    return &fParticleChange;
  }
  std::vector<G4Track*> products;
#ifdef G4VERBOSE
  if(verboseLevel > 1)
  {
    G4cout << "___________" << G4endl;
    G4cout << ">>> Beginning of G4DNAScavengerProcess verbose" << G4endl;
    G4cout << ">>> Returned value : " << G4BestUnit(fReturnedValue, "Time")
           << G4endl;
    G4cout << ">>> Time Step : "
           << G4BestUnit(G4VScheduler::Instance()->GetTimeStep(), "Time")
           << G4endl;
    G4cout << ">>> Global Time : "
           << G4BestUnit(G4VScheduler::Instance()->GetGlobalTime(), "Time")
           << G4endl;
    G4cout << ">>> Global Time Track : "
           << G4BestUnit(track.GetGlobalTime(), "Time") << G4endl;
    G4cout << ">>> Track Position : " << track.GetPosition() << G4endl;
    G4cout << ">>> Reaction : " << molecule->GetName() << "("
           << track.GetTrackID() << ") + " << fpMaterialConf->GetName()
           << G4endl;
    G4cout << ">>> End of G4DNAScavengerProcess verbose <<<" << G4endl;
  }
#endif
 
  G4double reactionTime = track.GetGlobalTime();
  auto data = fConfMap[fpMolecularConfiguration][fpMaterialConf];
 
  auto nbSecondaries = data->GetNbProducts();
 
  for(G4int j = 0; j < nbSecondaries; ++j)
  {
    auto pProduct = new G4Molecule(data->GetProduct(j));
    auto pProductTrack =
      pProduct->BuildTrack(reactionTime, track.GetPosition());
    pProductTrack->SetTrackStatus(fAlive);
    G4ITTrackHolder::Instance()->Push(pProductTrack);
    G4MoleculeFinder::Instance()->Push(pProductTrack);
    products.push_back(pProductTrack);
  }
 
#ifdef G4VERBOSE
  if(verboseLevel != 0)
  {
    G4cout << "At time : " << std::setw(7) << G4BestUnit(reactionTime, "Time")
           << " Reaction : " << GetIT(track)->GetName() << " ("
           << track.GetTrackID() << ") + " << fpMaterialConf->GetName() << " ("
           << "B"
           << ") -> ";
  }
#endif
  if(nbSecondaries > 0)
  {
    for(G4int i = 0; i < nbSecondaries; ++i)
    {
#ifdef G4VERBOSE
      if((verboseLevel != 0) && i != 0)
      {
        G4cout << " + ";
      }
 
      if(verboseLevel != 0)
      {
        G4cout << GetIT(products.at(i))->GetName() << " ("
               << products.at(i)->GetTrackID() << ")";
      }
#endif
    }
  }
  else
  {
#ifdef G4VERBOSE
    if(verboseLevel != 0)
    {
      G4cout << "No product";
    }
#endif
  }
#ifdef G4VERBOSE
  if(verboseLevel != 0)
  {
    G4cout << G4endl;
  }
#endif
 
  fReturnedValue = DBL_MAX;
  fParticleChange.Initialize(track);
  fParticleChange.ProposeTrackStatus(fStopAndKill);
  fpScavengerMaterial->ReduceNumberMoleculePerVolumeUnitForMaterialConf(
    fpMaterialConf, reactionTime);
  State(fPreviousTimeAtPreStepPoint) = -1;
  return &fParticleChange;
}

◆ PostStepGetPhysicalInteractionLength()

G4double G4DNAScavengerProcess::PostStepGetPhysicalInteractionLength	(	const G4Track &	track,
		G4double	previousStepSize,
		G4ForceCondition *	condition )

overridevirtual

Implements G4VProcess.

Definition at line 121 of file G4DNAScavengerProcess.cc.

{
  G4Molecule* molecule = GetMolecule(track);
  auto molConf         = molecule->GetMolecularConfiguration();
  // reset
  fpMolecularConfiguration = nullptr;
  fpMaterialConf           = nullptr;
 
  // this because process for moleculeDifinition not for configuration
  // TODO: need change this
  auto it = fConfMap.find(molConf);
  if(it == fConfMap.end())
  {
    return DBL_MAX;
  }
 
  fpMolecularConfiguration = molConf;
  auto MaterialMap         = it->second;
 
  G4double r1 = G4UniformRand();
  std::map<G4double /*Propensity*/, std::pair<MolType, G4double>>
    ReactionDataMap;
  G4double alpha0 = 0;
 
  for(const auto& mat_it : MaterialMap)
  {
    auto matConf = mat_it.first;
    G4double numMol =
      fpScavengerMaterial->GetNumberMoleculePerVolumeUnitForMaterialConf(
        matConf);
    if(numMol == 0.0)  // ie : not found
    {
      continue;
    }
    if(verboseLevel > 1)
    {
      G4cout << " Material of " << matConf->GetName() << " : " << numMol
             << G4endl;
    }
    // auto data = fReactionMap[mat_it];
    auto data         = mat_it.second;
    auto reactionRate = data->GetObservedReactionRateConstant();  //_const
    G4double propensity =
      numMol * reactionRate / (fpBoundingBox->Volume() * Avogadro);
    auto reactionData = std::make_pair(mat_it.first, propensity);
    if(propensity == 0)
    {
      continue;
    }
    alpha0 += propensity;
    ReactionDataMap[alpha0] = reactionData;
  }
  if(alpha0 == 0)
  {
    if(State(fIsInGoodMaterial))
    {
      ResetNumberOfInteractionLengthLeft();
      State(fIsInGoodMaterial) = false;
    }
    return DBL_MAX;
  }
  auto rSelectedIter = ReactionDataMap.upper_bound(r1 * alpha0);
 
  fpMaterialConf = rSelectedIter->second.first;
 
  State(fIsInGoodMaterial) = true;
  G4double previousTimeStep(-1.);
 
  if(State(fPreviousTimeAtPreStepPoint) != -1)
  {
    previousTimeStep =
      track.GetGlobalTime() - State(fPreviousTimeAtPreStepPoint);
  }
 
  State(fPreviousTimeAtPreStepPoint) = track.GetGlobalTime();
 
  // condition is set to "Not Forced"
  *pForceCond = NotForced;
 
  if((previousTimeStep <= 0.0) ||
     (fpState->theNumberOfInteractionLengthLeft <= 0.0))
  {
    ResetNumberOfInteractionLengthLeft();
  }
  else if(previousTimeStep > 0.0)
  {
    SubtractNumberOfInteractionLengthLeft(previousTimeStep);
  }
 
  fpState->currentInteractionLength = 1 / (rSelectedIter->second.second);
  G4double value                    = DBL_MAX;
  if(fpState->currentInteractionLength < DBL_MAX)
  {
    value = fpState->theNumberOfInteractionLengthLeft *
            (fpState->currentInteractionLength);
  }
#ifdef G4VERBOSE
  if(verboseLevel > 2)
  {
    G4cout << "G4DNAScavengerProcess::PostStepGetPhysicalInteractionLength:: "
           << molConf->GetName() << G4endl;
    G4cout << "theNumberOfInteractionLengthLeft : "
           << fpState->theNumberOfInteractionLengthLeft << G4endl;
    G4cout << "currentInteractionLength : " << fpState->currentInteractionLength
           << G4endl;
    G4cout << "Material : " << fpMaterialConf->GetName()
           << " ID: " << track.GetTrackID()
           << " Track Time : " << track.GetGlobalTime()
           << " name : " << molConf->GetName()
           << " Track Position : " << track.GetPosition()
           << " Returned time : " << G4BestUnit(value, "Time") << G4endl;
  }
#endif
 
  if(value < fReturnedValue)
  {
    fReturnedValue = value;
  }
 
  return value * -1;
  // multiple by -1 to indicate to the tracking system that we are returning a
  // time
}

◆ SetReaction()

void G4DNAScavengerProcess::SetReaction	(	MolType	molConf,
		Data *	pData )

Definition at line 99 of file G4DNAScavengerProcess.cc.

{
  if(fIsInitialized)
  {
    G4ExceptionDescription exceptionDescription;
    exceptionDescription
      << "G4DNASecondOrderReaction was already initialised. ";
    exceptionDescription << "You cannot set a reaction after initialisation.";
    G4Exception("G4DNASecondOrderReaction::SetReaction",
                "G4DNASecondOrderReaction001", FatalErrorInArgument,
                exceptionDescription);
  }
  auto materialConf = pData->GetReactant1() == molConf ? pData->GetReactant2()
                                                       : pData->GetReactant1();
  if(verboseLevel > 0)
  {
    G4cout << "G4DNAScavengerProcess::SetReaction : " << molConf->GetName()
           << "   materialConf : " << materialConf->GetName() << G4endl;
  }
  fConfMap[molConf][materialConf] = pData;
}

◆ StartTracking()

void G4DNAScavengerProcess::StartTracking ( G4Track * track )

overridevirtual

Reimplemented from G4VProcess.

Definition at line 92 of file G4DNAScavengerProcess.cc.

{
  G4VProcess::StartTracking(track);
  G4VITProcess::fpState = std::make_shared<G4DNAScavengerProcessState>();
  G4VITProcess::StartTracking(track);
}

Member Data Documentation

◆ fConfMap

std::map<MolType , std::map<MolType , Data*> > G4DNAScavengerProcess::fConfMap

protected

Definition at line 98 of file G4DNAScavengerProcess.hh.

Referenced by PostStepDoIt(), PostStepGetPhysicalInteractionLength(), SetReaction(), and ~G4DNAScavengerProcess().

◆ fIsInitialized

G4bool G4DNAScavengerProcess::fIsInitialized

protected

Definition at line 93 of file G4DNAScavengerProcess.hh.

Referenced by BuildPhysicsTable(), G4DNAScavengerProcess(), and SetReaction().

◆ fParticleChange

G4ParticleChange G4DNAScavengerProcess::fParticleChange

protected

Definition at line 95 of file G4DNAScavengerProcess.hh.

Referenced by G4DNAScavengerProcess(), and PostStepDoIt().

◆ fpBoundingBox

const G4DNABoundingBox* G4DNAScavengerProcess::fpBoundingBox

protected

Definition at line 101 of file G4DNAScavengerProcess.hh.

Referenced by PostStepGetPhysicalInteractionLength().

◆ fpMaterialConf

MolType G4DNAScavengerProcess::fpMaterialConf

protected

Definition at line 100 of file G4DNAScavengerProcess.hh.

Referenced by G4DNAScavengerProcess(), PostStepDoIt(), and PostStepGetPhysicalInteractionLength().

◆ fpMaterialVector

std::vector<MolType> G4DNAScavengerProcess::fpMaterialVector

protected

Definition at line 99 of file G4DNAScavengerProcess.hh.

◆ fpMolecularConfiguration

const G4MolecularConfiguration* G4DNAScavengerProcess::fpMolecularConfiguration

protected

Definition at line 96 of file G4DNAScavengerProcess.hh.

Referenced by G4DNAScavengerProcess(), PostStepDoIt(), and PostStepGetPhysicalInteractionLength().

◆ fpScavengerMaterial

G4DNAScavengerMaterial* G4DNAScavengerProcess::fpScavengerMaterial {nullptr}

protected

Definition at line 102 of file G4DNAScavengerProcess.hh.

102{nullptr};

Referenced by BuildPhysicsTable(), PostStepDoIt(), and PostStepGetPhysicalInteractionLength().

◆ fReturnedValue

G4double G4DNAScavengerProcess::fReturnedValue

protected

Definition at line 94 of file G4DNAScavengerProcess.hh.

Referenced by G4DNAScavengerProcess(), PostStepDoIt(), and PostStepGetPhysicalInteractionLength().

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

Classes

Public Types

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Data

◆ MolType

Constructor & Destructor Documentation

◆ G4DNAScavengerProcess() [1/2]

◆ ~G4DNAScavengerProcess()

◆ G4DNAScavengerProcess() [2/2]

Member Function Documentation

◆ AlongStepDoIt()

◆ AlongStepGetPhysicalInteractionLength()

◆ AtRestDoIt()

◆ AtRestGetPhysicalInteractionLength()

◆ BuildPhysicsTable()

◆ operator=()

◆ PostStepDoIt()

◆ PostStepGetPhysicalInteractionLength()

◆ SetReaction()

◆ StartTracking()

Member Data Documentation

◆ fConfMap

◆ fIsInitialized

◆ fParticleChange

◆ fpBoundingBox

◆ fpMaterialConf

◆ fpMaterialVector

◆ fpMolecularConfiguration

◆ fpScavengerMaterial

◆ fReturnedValue