Geant4 Cross Reference

Cross-Referencing   Geant4
Geant4/processes/electromagnetic/dna/models/include/G4DNAGillespieDirectMethod.hh

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 26 //
 27 #ifndef G4DNAGillespieDirectMethod_hh
 28 #define G4DNAGillespieDirectMethod_hh 1
 29 #include "globals.hh"
 30 #include "G4DNAMesh.hh"
 31 #include "G4Track.hh"
 32 #include "G4Molecule.hh"
 33 #include "G4MolecularConfiguration.hh"
 34 #include "G4MoleculeTable.hh"
 35 #include "G4ITTrackHolder.hh"
 36 #include "G4DNAEventSet.hh"
 37 class G4DNAMolecularReactionData;
 38 class G4DNAScavengerMaterial;
 39 class G4MolecularConfiguration;
 40 class G4ChemEquilibrium;
 41 class G4DNAGillespieDirectMethod
 42 {
 43  public:
 44   G4DNAGillespieDirectMethod();
 45   ~G4DNAGillespieDirectMethod();
 46   using MolType      = const G4MolecularConfiguration*;
 47   using Index        = G4VDNAMesh::Index;
 48   using Voxel        = G4DNAMesh::Voxel;
 49   using JumpingData  = std::pair<MolType, Index>;
 50   using ReactionData = const G4DNAMolecularReactionData;
 51   using EventIt      = G4DNAEventSet::EventSet::iterator;
 52 
 53   G4double PropensityFunction(const Voxel& voxel, ReactionData* data);
 54   G4double PropensityFunction(const Voxel& voxel, MolType moleType);
 55   inline void SetVoxelMesh(G4DNAMesh& mesh) { fpMesh = &mesh; }
 56   void SetTimeStep(const G4double& stepTime);
 57   void Initialize();
 58   void CreateEvent(const Index& index);
 59   void CreateEvents();
 60   void SetEventSet(G4DNAEventSet*);
 61   inline void SetVerbose(const G4int& verbose)
 62   {
 63       fVerbose = verbose;
 64   }
 65   G4bool SetEquilibrium(const G4DNAMolecularReactionData* pReaction);
 66   void ResetEquilibrium();
 67 
 68 
 69  private:
 70   G4double Reaction(const Voxel& voxel);
 71   G4double DiffusiveJumping(const Voxel& voxel);
 72   G4double ComputeNumberInNode(const Voxel& voxel, MolType type);
 73   G4double VolumeOfNode(const Voxel& voxel);
 74   G4DNAMolecularReactionTable* fMolecularReactions;
 75   G4DNAMesh* fpMesh = nullptr;
 76   G4double fTimeStep = DBL_MAX;
 77   G4DNAEventSet* fpEventSet = nullptr;
 78   G4double fVerbose         = 0;
 79   std::map<G4double /*Propensity*/, ReactionData*> fReactionDataMap;
 80   std::map<G4double /*Propensity*/, JumpingData> fJumpingDataMap;
 81   G4bool FindScavenging(const Voxel& voxel, MolType, G4double&);
 82   G4DNAScavengerMaterial* fpScavengerMaterial = nullptr;
 83   std::map<G4int,std::unique_ptr<G4ChemEquilibrium>> fEquilibriumProcesses;
 84   G4bool IsEquilibrium(const G4int& reactionType) const;
 85 
 86 };
 87 #endif
 88