Import Geant4 10.1.0 source tree
This commit is contained in:
Gabriele Cosmo
@@ -23,7 +23,7 @@
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// * acceptance of all terms of the Geant4 Software license. *
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// ********************************************************************
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//
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// $Id: G4DNAMolecularReaction.cc 64057 2012-10-30 15:04:49Z gcosmo $
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// $Id: G4DNAMolecularReaction.cc 87061 2014-11-24 11:43:34Z gcosmo $
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//
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// Author: Mathieu Karamitros (kara@cenbg.in2p3.fr)
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//
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@@ -39,49 +39,53 @@
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#include "G4DNAMolecularReaction.hh"
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#include "G4DNAMolecularReactionTable.hh"
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#include "G4VDNAReactionModel.hh"
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#include "G4ITManager.hh"
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#include "G4MoleculeFinder.hh"
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#include "G4UnitsTable.hh"
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using namespace std;
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G4DNAMolecularReaction::G4DNAMolecularReaction():G4VITReactionProcess(),
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fMolReactionTable(reference_cast<const G4DNAMolecularReactionTable*>(fpReactionTable))
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G4DNAMolecularReaction::G4DNAMolecularReaction() :
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G4VITReactionProcess(),
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fMolReactionTable(
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reference_cast<const G4DNAMolecularReactionTable*>(fpReactionTable))
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{
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//ctor
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fVerbose = 0;
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fReactionModel = 0;
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fReactionRadius = -1;
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fDistance = -1;
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//ctor
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fVerbose = 0;
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fReactionModel = 0;
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fReactionRadius = -1;
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fDistance = -1;
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}
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G4DNAMolecularReaction::~G4DNAMolecularReaction()
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{
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//dtor
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if(fpChanges) delete fpChanges;
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//dtor
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if (fpChanges) delete fpChanges;
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}
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G4DNAMolecularReaction::G4DNAMolecularReaction(const G4DNAMolecularReaction& other):G4VITReactionProcess(other),
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fMolReactionTable(reference_cast<const G4DNAMolecularReactionTable*>(fpReactionTable))
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G4DNAMolecularReaction::G4DNAMolecularReaction(const G4DNAMolecularReaction& other) :
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G4VITReactionProcess(other),
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fMolReactionTable(
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reference_cast<const G4DNAMolecularReactionTable*>(fpReactionTable))
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{
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//copy ctor
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fVerbose = other.fVerbose ;
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fMolReactionTable = other.fMolReactionTable;
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fReactionModel = 0;
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fReactionRadius = -1;
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fDistance = -1;
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//copy ctor
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fVerbose = other.fVerbose;
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fMolReactionTable = other.fMolReactionTable;
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fReactionModel = 0;
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fReactionRadius = -1;
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fDistance = -1;
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}
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G4DNAMolecularReaction& G4DNAMolecularReaction::operator=(const G4DNAMolecularReaction& rhs)
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{
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if (this == &rhs) return *this; // handle self assignment
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if (this == &rhs) return *this; // handle self assignment
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fVerbose = rhs.fVerbose ;
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fMolReactionTable = rhs.fMolReactionTable;
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fReactionRadius = -1;
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fDistance = -1;
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fVerbose = rhs.fVerbose;
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fMolReactionTable = rhs.fMolReactionTable;
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fReactionRadius = -1;
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fDistance = -1;
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//assignment operator
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return *this;
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//assignment operator
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return *this;
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}
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G4bool G4DNAMolecularReaction::TestReactibility(const G4Track& trackA,
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@@ -90,118 +94,129 @@ G4bool G4DNAMolecularReaction::TestReactibility(const G4Track& trackA,
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const double /*previousStepTime*/,
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bool userStepTimeLimit) /*const*/
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{
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G4Molecule* moleculeA = GetMolecule(trackA);
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G4Molecule* moleculeB = GetMolecule(trackB);
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G4Molecule* moleculeA = GetMolecule(trackA);
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G4Molecule* moleculeB = GetMolecule(trackB);
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if(!fReactionModel)
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{
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G4ExceptionDescription exceptionDescription ("You have to give a reaction model to the molecular reaction process");
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G4Exception("G4DNAMolecularReaction::TestReactibility","MolecularReaction001",
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FatalErrorInArgument,exceptionDescription);
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return false; // makes coverity happy
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}
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if(fMolReactionTable==0)
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{
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G4ExceptionDescription exceptionDescription ("You have to give a reaction table to the molecular reaction process");
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G4Exception("G4DNAMolecularReaction::TestReactibility","MolecularReaction002",
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FatalErrorInArgument,exceptionDescription);
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return false; // makes coverity happy
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}
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if (!fReactionModel)
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{
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G4ExceptionDescription exceptionDescription(
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"You have to give a reaction model to the molecular reaction process");
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G4Exception("G4DNAMolecularReaction::TestReactibility",
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"MolecularReaction001", FatalErrorInArgument,
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exceptionDescription);
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return false; // makes coverity happy
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}
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if (fMolReactionTable == 0)
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{
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G4ExceptionDescription exceptionDescription(
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"You have to give a reaction table to the molecular reaction process");
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G4Exception("G4DNAMolecularReaction::TestReactibility",
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"MolecularReaction002", FatalErrorInArgument,
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exceptionDescription);
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return false; // makes coverity happy
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}
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// Retrieve reaction range
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fReactionRadius = -1 ; // reaction Range
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fReactionRadius = fReactionModel -> GetReactionRadius(moleculeA, moleculeB);
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// Retrieve reaction range
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fReactionRadius = -1; // reaction Range
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fReactionRadius = fReactionModel->GetReactionRadius(moleculeA, moleculeB);
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fDistance = -1 ; // separation distance
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fDistance = -1; // separation distance
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if(currentStepTime == 0.)
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{
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userStepTimeLimit = false;
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}
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if (currentStepTime == 0.)
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{
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userStepTimeLimit = false;
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}
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G4bool output = fReactionModel->FindReaction(trackA, trackB, fReactionRadius,fDistance, userStepTimeLimit);
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G4bool output = fReactionModel->FindReaction(trackA, trackB, fReactionRadius,
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fDistance, userStepTimeLimit);
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#ifdef G4VERBOSE
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// DEBUG
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if(fVerbose > 1)
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{
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G4cout << "\033[1;39;36m" << "G4MolecularReaction "<< G4endl;
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G4cout << "FindReaction returned : " << G4BestUnit(output,"Length") << G4endl;
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G4cout << " reaction radius : " << G4BestUnit(fReactionRadius,"Length")
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<< " real distance : " << G4BestUnit((trackA.GetPosition() - trackB.GetPosition()).mag(), "Length")
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<< " calculated distance by model (= -1 if real distance > reaction radius and the user limitation step is not reached) : "
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<< G4BestUnit(fDistance,"Length")
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<< G4endl;
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// DEBUG
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if (fVerbose > 1)
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{
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G4cout << "\033[1;39;36m" << "G4MolecularReaction " << G4endl;
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G4cout << "FindReaction returned : " << G4BestUnit(output,"Length") << G4endl;
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G4cout << " reaction radius : " << G4BestUnit(fReactionRadius,"Length")
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<< " real distance : " << G4BestUnit((trackA.GetPosition() - trackB.GetPosition()).mag(), "Length")
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<< " calculated distance by model (= -1 if real distance > reaction radius and the user limitation step is not reached) : "
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<< G4BestUnit(fDistance,"Length")
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<< G4endl;
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G4cout << "TrackID A : " << trackA.GetTrackID()
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<< ", TrackID B : " << trackB.GetTrackID()
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<< " | MolA " << moleculeA->GetName()
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<< ", MolB " << moleculeB->GetName()
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<<"\033[0m\n"
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<< G4endl;
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G4cout << "--------------------------------------------" << G4endl;
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}
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G4cout << "TrackID A : " << trackA.GetTrackID()
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<< ", TrackID B : " << trackB.GetTrackID()
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<< " | MolA " << moleculeA->GetName()
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<< ", MolB " << moleculeB->GetName()
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<<"\033[0m\n"
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<< G4endl;
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G4cout << "--------------------------------------------" << G4endl;
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}
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#endif
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return output ;
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return output;
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}
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G4ITReactionChange* G4DNAMolecularReaction::MakeReaction(const G4Track& trackA, const G4Track& trackB)
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G4ITReactionChange* G4DNAMolecularReaction::MakeReaction(const G4Track& trackA,
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const G4Track& trackB)
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{
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fpChanges = new G4ITReactionChange();
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fpChanges->Initialize(trackA, trackB);
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fpChanges = new G4ITReactionChange();
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fpChanges->Initialize(trackA, trackB);
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G4Molecule* moleculeA = GetMolecule(trackA);
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G4Molecule* moleculeB = GetMolecule(trackB);
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G4Molecule* moleculeA = GetMolecule(trackA);
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G4Molecule* moleculeB = GetMolecule(trackB);
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#ifdef G4VERBOSE
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// DEBUG
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if(fVerbose)
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{
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G4cout << "G4DNAMolecularReaction::MakeReaction" << G4endl;
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G4cout<<"TrackA n°" << trackA.GetTrackID()
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<<"\t | Track B n°" << trackB.GetTrackID() << G4endl;
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// DEBUG
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if (fVerbose)
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{
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G4cout << "G4DNAMolecularReaction::MakeReaction" << G4endl;
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G4cout<<"TrackA n°" << trackA.GetTrackID()
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<<"\t | Track B n°" << trackB.GetTrackID() << G4endl;
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G4cout<<"Track A : Position : " << G4BestUnit(trackA.GetPosition(),"Length")
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<<"\t Global Time : " << G4BestUnit(trackA.GetGlobalTime(), "Time")<< G4endl;
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G4cout<<"Track A : Position : " << G4BestUnit(trackA.GetPosition(),"Length")
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<<"\t Global Time : " << G4BestUnit(trackA.GetGlobalTime(), "Time")<< G4endl;
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G4cout<<"Track B : Position : " << G4BestUnit(trackB.GetPosition() ,"Length")
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<<"\t Global Time : " << G4BestUnit(trackB.GetGlobalTime(), "Time")<< G4endl;
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G4cout<<"Track B : Position : " << G4BestUnit(trackB.GetPosition() ,"Length")
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<<"\t Global Time : " << G4BestUnit(trackB.GetGlobalTime(), "Time")<< G4endl;
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G4cout<<"Reaction range : " << G4BestUnit(fReactionRadius,"Length")
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<< " \t Separation distance : " << G4BestUnit(fDistance,"Length")<< G4endl;
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G4cout << "--------------------------------------------" << G4endl;
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}
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G4cout<<"Reaction range : " << G4BestUnit(fReactionRadius,"Length")
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<< " \t Separation distance : " << G4BestUnit(fDistance,"Length")<< G4endl;
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G4cout << "--------------------------------------------" << G4endl;
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}
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#endif
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const G4DNAMolecularReactionData* reactionData = fMolReactionTable->GetReactionData(moleculeA, moleculeB);
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const G4DNAMolecularReactionData* reactionData = fMolReactionTable
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->GetReactionData(moleculeA, moleculeB);
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G4int nbProducts = reactionData->GetNbProducts();
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G4int nbProducts = reactionData->GetNbProducts();
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if (nbProducts)
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if (nbProducts)
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{
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G4double D1 = moleculeA->GetDiffusionCoefficient();
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G4double D2 = moleculeB->GetDiffusionCoefficient();
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G4double sqrD1 = sqrt(D1);
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G4double sqrD2 = sqrt(D2);
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G4double numerator = sqrD1 + sqrD2;
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G4ThreeVector reactionSite = sqrD1 / numerator * trackA.GetPosition()
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+ sqrD2 / numerator * trackB.GetPosition();
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for (G4int j = 0; j < nbProducts; j++)
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{
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G4double D1 = moleculeA->GetDiffusionCoefficient();
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G4double D2 = moleculeB->GetDiffusionCoefficient();
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G4double sqrD1 = sqrt(D1);
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G4double sqrD2 = sqrt(D2);
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G4double numerator = sqrD1 + sqrD2;
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G4ThreeVector reactionSite = sqrD1/numerator * trackA.GetPosition()
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+ sqrD2/numerator * trackB.GetPosition() ;
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G4Molecule* product = new G4Molecule(*reactionData->GetProduct(j));
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G4Track* productTrack = product->BuildTrack(trackA.GetGlobalTime(),
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reactionSite);
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for (G4int j=0 ; j < nbProducts; j++)
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{
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G4Molecule* product = new G4Molecule(*reactionData->GetProduct(j));
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G4Track* productTrack = product->BuildTrack(trackA.GetGlobalTime(),
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reactionSite);
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// G4cout << ">> G4DNAMolecularReaction::MakeReaction " << G4endl
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// << "\t track A ("<< trackA.GetTrackID() <<"): " << trackA.GetGlobalTime() << G4endl
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// << "\t track B ("<< trackB.GetTrackID() <<"): " << trackB.GetGlobalTime() << G4endl;
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productTrack->SetTrackStatus(fAlive);
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productTrack->SetTrackStatus(fAlive);
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fpChanges->AddSecondary(productTrack);
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G4ITManager<G4Molecule>::Instance()->Push(productTrack);
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}
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fpChanges->AddSecondary(productTrack);
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G4MoleculeFinder::Instance()->Push(productTrack);
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// G4ITManager<G4Molecule>::Instance()->Push(productTrack);
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}
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}
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fpChanges->KillParents(true);
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fpChanges->KillParents(true);
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return fpChanges;
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return fpChanges;
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}
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