Gabriele Cosmo
77 lines
3.3 KiB
C++
77 lines
3.3 KiB
C++
//
|
|
// ********************************************************************
|
|
// * License and Disclaimer *
|
|
// * *
|
|
// * The Geant4 software is copyright of the Copyright Holders of *
|
|
// * the Geant4 Collaboration. It is provided under the terms and *
|
|
// * conditions of the Geant4 Software License, included in the file *
|
|
// * LICENSE and available at http://cern.ch/geant4/license . These *
|
|
// * include a list of copyright holders. *
|
|
// * *
|
|
// * Neither the authors of this software system, nor their employing *
|
|
// * institutes,nor the agencies providing financial support for this *
|
|
// * work make any representation or warranty, express or implied, *
|
|
// * regarding this software system or assume any liability for its *
|
|
// * use. Please see the license in the file LICENSE and URL above *
|
|
// * for the full disclaimer and the limitation of liability. *
|
|
// * *
|
|
// * This code implementation is the result of the scientific and *
|
|
// * technical work of the GEANT4 collaboration. *
|
|
// * By using, copying, modifying or distributing the software (or *
|
|
// * any work based on the software) you agree to acknowledge its *
|
|
// * use in resulting scientific publications, and indicate your *
|
|
// * acceptance of all terms of the Geant4 Software license. *
|
|
// ********************************************************************
|
|
//
|
|
//
|
|
#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 G4DNAMolecularReactionTable;
|
|
class G4DNAMolecularReactionData;
|
|
class G4DNAScavengerMaterial;
|
|
class G4DNAGillespieDirectMethod
|
|
{
|
|
public:
|
|
G4DNAGillespieDirectMethod();
|
|
~G4DNAGillespieDirectMethod();
|
|
using MolType = const G4MolecularConfiguration*;
|
|
using Key = unsigned int;
|
|
using Index = G4Voxel::Index;
|
|
using JumpingData = std::pair<MolType, Index>;
|
|
using ReactionData = const G4DNAMolecularReactionData;
|
|
using EventIt = G4DNAEventSet::EventSet::iterator;
|
|
|
|
G4double PropensityFunction(const Index& index, ReactionData* data);
|
|
G4double PropensityFunction(const Index& index, MolType moleType);
|
|
inline void SetVoxelMesh(G4DNAMesh& mesh) { fpMesh = &mesh; }
|
|
void SetTimeStep(const G4double& stepTime);
|
|
G4double Reaction(const Index& index);
|
|
G4double DiffusiveJumping(const Index& index);
|
|
G4double ComputeNumberInNode(const Index& index, MolType type);
|
|
G4double VolumeOfNode(const Index& index);
|
|
void Initialize();
|
|
void CreateEvent(unsigned int key);
|
|
void SetEventSet(G4DNAEventSet*);
|
|
|
|
private:
|
|
G4DNAMolecularReactionTable* fMolecularReactions;
|
|
G4DNAMesh* fpMesh;
|
|
G4double fTimeStep;
|
|
G4DNAEventSet* fpEventSet;
|
|
G4double fVerbose;
|
|
std::map<G4double /*Propensity*/, ReactionData*> fReactionDataMap;
|
|
std::map<G4double /*Propensity*/, JumpingData> fJumpingDataMap;
|
|
G4bool FindScavenging(const Index& index, MolType, G4double&);
|
|
G4DNAScavengerMaterial* fpScavengerMaterial;
|
|
};
|
|
#endif
|