G4DNAGillespieDirectMethod.hh

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#ifndef G4DNAGillespieDirectMethod_hh
#define G4DNAGillespieDirectMethod_hh 1
#include "globals.hh"
#include "G4DNAMesh.hh"
#include "G4Track.hh"
#include "G4Molecule.hh"
#include "G4MolecularConfiguration.hh"
#include "G4MoleculeTable.hh"
#include "G4ITTrackHolder.hh"
#include "G4DNAEventSet.hh"
class G4DNAMolecularReactionData;
class G4DNAScavengerMaterial;
class G4MolecularConfiguration;
class G4ChemEquilibrium;
class G4DNAGillespieDirectMethod
{
 public:
  G4DNAGillespieDirectMethod();
  ~G4DNAGillespieDirectMethod();
  using MolType      = const G4MolecularConfiguration*;
  using Index        = G4VDNAMesh::Index;
  using Voxel        = G4DNAMesh::Voxel;
  using JumpingData  = std::pair<MolType, Index>;
  using ReactionData = const G4DNAMolecularReactionData;
  using EventIt      = G4DNAEventSet::EventSet::iterator;
 
  G4double PropensityFunction(const Voxel& voxel, ReactionData* data);
  G4double PropensityFunction(const Voxel& voxel, MolType moleType);
  inline void SetVoxelMesh(G4DNAMesh& mesh) { fpMesh = &mesh; }
  void SetTimeStep(const G4double& stepTime);
  void Initialize();
  void CreateEvent(const Index& index);
  void CreateEvents();
  void SetEventSet(G4DNAEventSet*);
  inline void SetVerbose(const G4int& verbose)
  {
      fVerbose = verbose;
  }
  G4bool SetEquilibrium(const G4DNAMolecularReactionData* pReaction);
  void ResetEquilibrium();
 
 
 private:
  G4double Reaction(const Voxel& voxel);
  G4double DiffusiveJumping(const Voxel& voxel);
  G4double ComputeNumberInNode(const Voxel& voxel, MolType type);
  G4double VolumeOfNode(const Voxel& voxel);
  G4DNAMolecularReactionTable* fMolecularReactions;
  G4DNAMesh* fpMesh = nullptr;
  G4double fTimeStep = DBL_MAX;
  G4DNAEventSet* fpEventSet = nullptr;
  G4double fVerbose         = 0;
  std::map<G4double /*Propensity*/, ReactionData*> fReactionDataMap;
  std::map<G4double /*Propensity*/, JumpingData> fJumpingDataMap;
  G4bool FindScavenging(const Voxel& voxel, MolType, G4double&);
  G4DNAScavengerMaterial* fpScavengerMaterial = nullptr;
  std::map<G4int,std::unique_ptr<G4ChemEquilibrium>> fEquilibriumProcesses;
  G4bool IsEquilibrium(const G4int& reactionType) const;
 
};
#endif