#include <G4MoleculeCounter.hh>

Inheritance diagram for G4MoleculeCounter:

Collaboration diagram for G4MoleculeCounter:

Classes
struct	Search

Public Types
typedef std::map < G4MolecularConfiguration *, NbMoleculeAgainstTime >	CounterMapType

typedef std::unique_ptr < std::vector < G4MolecularConfiguration * > >	RecordedMolecules

Public Member Functions
void	Initialize () override

void	ResetCounter () override

void	AddAMoleculeAtTime (G4MolecularConfiguration , G4double time, const G4ThreeVector position=nullptr, int number=1) override

void	RemoveAMoleculeAtTime (G4MolecularConfiguration , G4double time, const G4ThreeVector position=nullptr, int number=1) override

void	DontRegister (const G4MoleculeDefinition *) override

bool	IsRegistered (const G4MoleculeDefinition *) override

void	RegisterAll () override

int	GetNMoleculesAtTime (G4MolecularConfiguration *molecule, double time)

const NbMoleculeAgainstTime &	GetNbMoleculeAgainstTime (G4MolecularConfiguration *molecule)

RecordedMolecules	GetRecordedMolecules ()

RecordedTimes	GetRecordedTimes ()

void	SetVerbose (G4int)

G4int	GetVerbose ()

void	SetTimeSlice (double)

void	Dump ()

G4bool	IsTimeCheckedForConsistency () const

void	CheckTimeForConsistency (G4bool flag)

Static Public Member Functions
static G4MoleculeCounter *	Instance ()

Static Public Member Functions inherited from G4VMoleculeCounter
static void	SetInstance (G4VMoleculeCounter *)

static void	DeleteInstance ()

static G4VMoleculeCounter *	Instance ()

static void	InitializeInstance ()

static void	Use (G4bool flag=true)

static G4bool	InUse ()

Protected Member Functions
	G4MoleculeCounter ()

virtual	~G4MoleculeCounter ()

G4bool	SearchTimeMap (G4MolecularConfiguration *molecule)

int	SearchUpperBoundTime (double time, bool sameTypeOfMolecule)

Protected Member Functions inherited from G4VMoleculeCounter
	G4VMoleculeCounter ()

virtual	~G4VMoleculeCounter ()

Protected Attributes
CounterMapType	fCounterMap

std::map< const G4MoleculeDefinition *, G4bool >	fDontRegister

G4int	fVerbose

G4bool	fCheckTimeIsConsistentWithScheduler

std::unique_ptr< Search >	fpLastSearch

Friends
class	G4Molecule

class	G4VMoleculeCounter

Additional Inherited Members
Static Protected Attributes inherited from G4VMoleculeCounter
static G4ThreadLocal G4VMoleculeCounter *	fpInstance = 0

static G4bool	fUse = false

Detailed Description

Definition at line 79 of file G4MoleculeCounter.hh.

Member Typedef Documentation

typedef std::map<G4MolecularConfiguration*, NbMoleculeAgainstTime> G4MoleculeCounter::CounterMapType

Definition at line 84 of file G4MoleculeCounter.hh.

typedef std::unique_ptr<std::vector<G4MolecularConfiguration*> > G4MoleculeCounter::RecordedMolecules

Definition at line 86 of file G4MoleculeCounter.hh.

Constructor & Destructor Documentation

G4MoleculeCounter::G4MoleculeCounter ( )

protected

Definition at line 51 of file G4MoleculeCounter.cc.

 {
   fVerbose = 0;
   fCheckTimeIsConsistentWithScheduler = true;
   if(compDoubleWithPrecision::fPrecision == 0)
   {
     compDoubleWithPrecision::fPrecision = 0.5*picosecond;
   }
 }

G4MoleculeCounter::~G4MoleculeCounter ( )

protectedvirtual

Definition at line 63 of file G4MoleculeCounter.cc.

64 {

65 }

Member Function Documentation

void G4MoleculeCounter::AddAMoleculeAtTime	(	G4MolecularConfiguration *	molecule,
		G4double	time,
		const G4ThreeVector *	position = `nullptr`,
		int	number = `1`
	)

overridevirtual

Implements G4VMoleculeCounter.

Definition at line 217 of file G4MoleculeCounter.cc.

 {
   if (fDontRegister[molecule->GetDefinition()]) return;
 
   if (fVerbose){
     G4cout << "G4MoleculeCounter::AddAMoleculeAtTime : " << molecule->GetName()
            << " at time : " << G4BestUnit(time, "Time") << G4endl;
   }
 
   CounterMapType::iterator counterMap_i =
       fCounterMap.find(molecule);
 
   if (counterMap_i == fCounterMap.end()){
     fCounterMap[molecule][time] = number;
   }
   else if (counterMap_i->second.empty()){
     counterMap_i->second[time] = number;
   }
   else{
     NbMoleculeAgainstTime::reverse_iterator end = counterMap_i->second.rbegin();
 
     if (end->first <= time ||
         fabs(end->first - time) <= compDoubleWithPrecision::fPrecision)
       // Case 1 = new time comes after last recorded data
       // Case 2 = new time is about the same as the last recorded one
     {
       double newValue =  end->second + number;
       counterMap_i->second[time] = newValue;
     }
     else
     {
 //      if(fabs(time - G4Scheduler::Instance()->GetGlobalTime()) >
 //         G4Scheduler::Instance()->GetTimeTolerance())
       {
         G4ExceptionDescription errMsg;
         errMsg << "Time of species "
             << molecule->GetName() << " is "
             << G4BestUnit(time, "Time") << " while "
             << " global time is "
             << G4BestUnit(G4Scheduler::Instance()->GetGlobalTime(), "Time")
             << G4endl;
         G4Exception("G4MoleculeCounter::RemoveAMoleculeAtTime",
                     "TIME_DONT_MATCH",
                     FatalException, errMsg);
       }
     }
   }
 }

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void G4MoleculeCounter::CheckTimeForConsistency ( G4bool flag )

inline

Definition at line 170 of file G4MoleculeCounter.hh.

   {
     fCheckTimeIsConsistentWithScheduler = flag;
   }

void G4MoleculeCounter::DontRegister ( const G4MoleculeDefinition * molDef )

inlineoverridevirtual

Reimplemented from G4VMoleculeCounter.

Definition at line 218 of file G4MoleculeCounter.hh.

 {
   fDontRegister[molDef] = true;
 }

void G4MoleculeCounter::Dump ( )

Definition at line 440 of file G4MoleculeCounter.cc.

 {
   CounterMapType::iterator it = fCounterMap.begin();
   CounterMapType::iterator end = fCounterMap.end();
 
   for(;it!=end;++it)
   {
     G4MolecularConfiguration* molConf = it->first;
 
     G4cout << " --- > For " << molConf->GetName() << G4endl;
     NbMoleculeAgainstTime::iterator it2 = it->second.begin();
     NbMoleculeAgainstTime::iterator end2 = it->second.end();
 
     for(;it2!=end2;++it2)
     {
       G4cout << " " << G4BestUnit(it2->first, "Time")
              << "    " << it2->second << G4endl;
     }
   }
 }

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const NbMoleculeAgainstTime & G4MoleculeCounter::GetNbMoleculeAgainstTime ( G4MolecularConfiguration * molecule )

inline

Definition at line 196 of file G4MoleculeCounter.hh.

 {
   return fCounterMap[molecule];
 }

int G4MoleculeCounter::GetNMoleculesAtTime	(	G4MolecularConfiguration *	molecule,
		double	time
	)

Definition at line 208 of file G4MoleculeCounter.cc.

 {
   G4bool sameTypeOfMolecule = SearchTimeMap(molecule);
   return SearchUpperBoundTime(time, sameTypeOfMolecule);
 }

G4MoleculeCounter::RecordedMolecules G4MoleculeCounter::GetRecordedMolecules ( )

Definition at line 368 of file G4MoleculeCounter.cc.

 {
   if (fVerbose > 1)
   {
     G4cout << "Entering in G4MoleculeCounter::RecordMolecules" << G4endl;
   }
 
   CounterMapType::iterator it;
   RecordedMolecules output (new vector<G4MolecularConfiguration*>);
 
   for(it = fCounterMap.begin(); it != fCounterMap.end(); it++)
   {
     output->push_back(it->first);
   }
   return output;
 }

RecordedTimes G4MoleculeCounter::GetRecordedTimes ( )

Definition at line 387 of file G4MoleculeCounter.cc.

 {
   RecordedTimes output(new std::set<G4double>);
 
   //G4double time;
 
   CounterMapType::iterator it;
   CounterMapType::const_iterator ite;
 
   NbMoleculeAgainstTime::iterator it2;
   NbMoleculeAgainstTime::const_iterator ite2;
 
   // iterate on each molecule
   for (it = fCounterMap.begin(), ite = fCounterMap.end(); it != ite; ++it)
   {
     // iterate on each time
     for (it2 = (it->second).begin(), ite2 = (it->second).end(); it2 != ite2;
         ++it2)
     {
       //time = it2->first;
       output->insert(it2->first);
     }
   }
 
   return output;
 }

G4int G4MoleculeCounter::GetVerbose ( )

inline

Definition at line 210 of file G4MoleculeCounter.hh.

 {
   return fVerbose;
 }

void G4MoleculeCounter::Initialize ( )

overridevirtual

Implements G4VMoleculeCounter.

Definition at line 69 of file G4MoleculeCounter.cc.

 {
 //  G4cout << "G4MoleculeCounter::Initialize" << G4endl;
   
   G4ConfigurationIterator mol_iterator = G4MoleculeTable::Instance()
       ->GetConfigurationIterator();
   while ((mol_iterator)())
   {
     if(IsRegistered(mol_iterator.value()->GetDefinition()) == false)
     {
       continue;
     }
 
     //    G4cout << "G4MoleculeCounter::Initialize" << G4endl;
     //    G4cout << mol_iterator->value()->GetName() << G4endl;
     fCounterMap[mol_iterator.value()]; // initialize the second map
   }
 }

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G4MoleculeCounter * G4MoleculeCounter::Instance ( )

static

Definition at line 44 of file G4MoleculeCounter.cc.

                                               {
   if (!fpInstance) fpInstance = new G4MoleculeCounter();
   return dynamic_cast<G4MoleculeCounter*>(fpInstance);
 }

bool G4MoleculeCounter::IsRegistered ( const G4MoleculeDefinition * molDef )

inlineoverridevirtual

Reimplemented from G4VMoleculeCounter.

Definition at line 226 of file G4MoleculeCounter.hh.

 {
   if(fDontRegister.find(molDef) == fDontRegister.end()) return true;
   return false;
 }

G4bool G4MoleculeCounter::IsTimeCheckedForConsistency ( ) const

inline

Definition at line 165 of file G4MoleculeCounter.hh.

   {
     return fCheckTimeIsConsistentWithScheduler;
   }

void G4MoleculeCounter::RegisterAll ( )

inlineoverridevirtual

Reimplemented from G4VMoleculeCounter.

Definition at line 234 of file G4MoleculeCounter.hh.

 {
   fDontRegister.clear();
 }

void G4MoleculeCounter::RemoveAMoleculeAtTime	(	G4MolecularConfiguration *	molecule,
		G4double	time,
		const G4ThreeVector *	position = `nullptr`,
		int	number = `1`
	)

overridevirtual

Implements G4VMoleculeCounter.

Definition at line 272 of file G4MoleculeCounter.cc.

 {
   if (fDontRegister[molecule->GetDefinition()]) return;
 
   if (fVerbose)
   {
     G4cout << "G4MoleculeCounter::RemoveAMoleculeAtTime : "
            << molecule->GetName() << " at time : " << G4BestUnit(time, "Time")
            << G4endl;
   }
 
   if(fCheckTimeIsConsistentWithScheduler)
   {
     if(fabs(time - G4Scheduler::Instance()->GetGlobalTime()) >
        G4Scheduler::Instance()->GetTimeTolerance())
     {
       G4ExceptionDescription errMsg;
       errMsg << "Time of species "
           << molecule->GetName() << " is "
           << G4BestUnit(time, "Time") << " while "
           << " global time is "
           << G4BestUnit(G4Scheduler::Instance()->GetGlobalTime(), "Time")
           << G4endl;
       G4Exception("G4MoleculeCounter::RemoveAMoleculeAtTime",
                   "TIME_DONT_MATCH",
                   FatalException, errMsg);
     }
   }
 
   NbMoleculeAgainstTime& nbMolPerTime = fCounterMap[molecule];
 
   if (nbMolPerTime.empty())
   {
     molecule->PrintState();
     Dump();
     G4String errMsg =
         "You are trying to remove molecule " + molecule->GetName()
         + " from the counter while this kind of molecules has not been registered yet";
     G4Exception("G4MoleculeCounter::RemoveAMoleculeAtTime", "",
                 FatalErrorInArgument, errMsg);
 
     return;
   }
   else
   {
     NbMoleculeAgainstTime::reverse_iterator it = nbMolPerTime.rbegin();
     
     if (it == nbMolPerTime.rend()){
       it--;
       
       G4String errMsg = "There was no " + molecule->GetName()
       + " recorded at the time or even before the time asked";
       G4Exception("G4MoleculeCounter::RemoveAMoleculeAtTime", "",
                   FatalErrorInArgument, errMsg);
     }
 
     if (time - it->first < -compDoubleWithPrecision::fPrecision){
       Dump();
       G4ExceptionDescription errMsg;
       errMsg << "Is time going back?? " << molecule->GetName()
              << " is being removed at time " << G4BestUnit(time, "Time")
              << " while last recorded time was "
              << G4BestUnit(it->first, "Time") << ".";
       G4Exception("G4MoleculeCounter::RemoveAMoleculeAtTime",
                   "RETURN_TO_THE_FUTUR",
                   FatalErrorInArgument,
                   errMsg);
     }
 
     double finalN = it->second - number;
 
     if(finalN < 0){
       Dump();
       G4ExceptionDescription errMsg;
       errMsg << "After removal of " << number << " species of "
           << molecule->GetName() << " the final number at time "
           << G4BestUnit(time, "Time") << " is less than zero and so not valid."
           << " Global time is "
           << G4BestUnit(G4Scheduler::Instance()->GetGlobalTime(), "Time")
           << ". Previous selected time is "
           << G4BestUnit(it->first, "Time")
           << G4endl;
       G4Exception("G4MoleculeCounter::RemoveAMoleculeAtTime",
                   "N_INF_0",
                   FatalException, errMsg);
     }
 
     nbMolPerTime[time] = finalN;
   }
 }

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void G4MoleculeCounter::ResetCounter ( )

inlineoverridevirtual

Implements G4VMoleculeCounter.

Definition at line 183 of file G4MoleculeCounter.hh.

 {
   if(fVerbose)
   {
       G4cout << " ---> G4MoleculeCounter::ResetCounter" << G4endl;
   }
   fCounterMap.clear();
   fpLastSearch.reset(0);
 }

G4bool G4MoleculeCounter::SearchTimeMap ( G4MolecularConfiguration * molecule )

protected

Definition at line 97 of file G4MoleculeCounter.cc.

 {
   if (fpLastSearch.get() == 0)
   {
     fpLastSearch.reset(new Search());
   }
   else
   {
     if (fpLastSearch->fLowerBoundSet &&
         fpLastSearch->fLastMoleculeSearched->first == molecule)
       return true;
   }
 
   CounterMapType::iterator mol_it = fCounterMap.find(molecule);
   fpLastSearch->fLastMoleculeSearched = mol_it;
 
   if (mol_it != fCounterMap.end()) // TODO
   {
     fpLastSearch->fLowerBoundTime = fpLastSearch->fLastMoleculeSearched->second
         .end();
     fpLastSearch->fLowerBoundSet = true;
   }
   else
   {
     fpLastSearch->fLowerBoundSet = false;
   }
 
   return false;
 }

int G4MoleculeCounter::SearchUpperBoundTime	(	double	time,
		bool	sameTypeOfMolecule
	)

protected

Definition at line 129 of file G4MoleculeCounter.cc.

 {
   CounterMapType::iterator mol_it = fpLastSearch->fLastMoleculeSearched;
   if (mol_it == fCounterMap.end()) return 0; // RETURN
 
   NbMoleculeAgainstTime& timeMap = mol_it->second;
   if (timeMap.empty()) return 0;
 
   NbMoleculeAgainstTime::iterator end_time = timeMap.end();
 
   if (sameTypeOfMolecule == true)
   {
     //G4cout << "SAME MOLECULE" << G4endl;
     if (fpLastSearch->fLowerBoundSet && fpLastSearch->fLowerBoundTime
         != end_time)
     {
       if (fpLastSearch->fLowerBoundTime->first < time)
       {
         NbMoleculeAgainstTime::iterator upperToLast = fpLastSearch
             ->fLowerBoundTime;
         upperToLast++;
 
         if (upperToLast == end_time)
         {
           return fpLastSearch->fLowerBoundTime->second;
         }
 
         if (upperToLast->first > time)
         {
           return fpLastSearch->fLowerBoundTime->second;
         }
       }
     }
   }
   /*
    else
    {
    G4cout << "--> Molecule has changed" << G4endl;
    }
    */
   //G4cout << "Searching" << G4endl;
   // With upper bound
   NbMoleculeAgainstTime::iterator up_time_it = timeMap.upper_bound(time);
 
   if (up_time_it == end_time)
   {
     NbMoleculeAgainstTime::reverse_iterator last_time = timeMap.rbegin();
 
 //    {
       //G4cout << "RETURN LAST : " << G4BestUnit(time, "Time") << G4endl;
       return last_time->second;
 //    }
 
 //    G4cout << "RETURN 0 (1)" << G4endl;
 //    return 0; // RETURN
   }
   if (up_time_it == timeMap.begin())
   {
 //    G4cout << "RETURN 0 (2)" << G4endl;
     return 0; // RETURN
   }
 
   //G4cout << "Going back : " << up_time_it->first << "-->";
 
   up_time_it--;
 
 //  G4cout << up_time_it->first << G4endl;
 
   fpLastSearch->fLowerBoundTime = up_time_it;
   fpLastSearch->fLowerBoundSet = true;
 
 //  G4cout << "returning : " << fpLastSearch->fLowerBoundTime->second << G4endl;
 
   return fpLastSearch->fLowerBoundTime->second;
 }

void G4MoleculeCounter::SetTimeSlice ( double timeSlice )

Definition at line 90 of file G4MoleculeCounter.cc.

 {
   compDoubleWithPrecision::fPrecision = timeSlice;
 }

void G4MoleculeCounter::SetVerbose ( G4int level )

inline

Definition at line 203 of file G4MoleculeCounter.hh.

 {
   fVerbose = level;
 }

Friends And Related Function Documentation

friend class G4Molecule

friend

Definition at line 117 of file G4MoleculeCounter.hh.

friend class G4VMoleculeCounter

friend

Definition at line 118 of file G4MoleculeCounter.hh.

Member Data Documentation

G4bool G4MoleculeCounter::fCheckTimeIsConsistentWithScheduler

protected

Definition at line 97 of file G4MoleculeCounter.hh.

CounterMapType G4MoleculeCounter::fCounterMap

protected

Definition at line 93 of file G4MoleculeCounter.hh.

std::map<const G4MoleculeDefinition*, G4bool> G4MoleculeCounter::fDontRegister

protected

Definition at line 94 of file G4MoleculeCounter.hh.

std::unique_ptr<Search> G4MoleculeCounter::fpLastSearch

protected

Definition at line 109 of file G4MoleculeCounter.hh.

G4int G4MoleculeCounter::fVerbose

protected

Definition at line 96 of file G4MoleculeCounter.hh.

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

geant4.10.03.p01/source/processes/electromagnetic/dna/molecules/management/include/G4MoleculeCounter.hh
geant4.10.03.p01/source/processes/electromagnetic/dna/molecules/management/src/G4MoleculeCounter.cc

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation