Gabriele Cosmo
88 lines
3.8 KiB
C++
88 lines
3.8 KiB
C++
//
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// ********************************************************************
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// * License and Disclaimer *
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// * *
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// * The Geant4 software is copyright of the Copyright Holders of *
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// * the Geant4 Collaboration. It is provided under the terms and *
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// * conditions of the Geant4 Software License, included in the file *
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// * LICENSE and available at http://cern.ch/geant4/license . These *
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// * include a list of copyright holders. *
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// * *
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// * Neither the authors of this software system, nor their employing *
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// * institutes,nor the agencies providing financial support for this *
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// * work make any representation or warranty, express or implied, *
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// * regarding this software system or assume any liability for its *
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// * use. Please see the license in the file LICENSE and URL above *
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// * for the full disclaimer and the limitation of liability. *
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// * *
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// * This code implementation is the result of the scientific and *
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// * technical work of the GEANT4 collaboration. *
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// * By using, copying, modifying or distributing the software (or *
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// * any work based on the software) you agree to acknowledge its *
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// * use in resulting scientific publications, and indicate your *
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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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//
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#ifndef G4DNAGillespieDirectMethod_hh
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#define G4DNAGillespieDirectMethod_hh 1
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#include "globals.hh"
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#include "G4DNAMesh.hh"
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#include "G4Track.hh"
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#include "G4Molecule.hh"
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#include "G4MolecularConfiguration.hh"
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#include "G4MoleculeTable.hh"
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#include "G4ITTrackHolder.hh"
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#include "G4DNAEventSet.hh"
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class G4DNAMolecularReactionData;
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class G4DNAScavengerMaterial;
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class G4MolecularConfiguration;
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class G4ChemEquilibrium;
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class G4DNAGillespieDirectMethod
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{
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public:
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G4DNAGillespieDirectMethod();
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~G4DNAGillespieDirectMethod();
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using MolType = const G4MolecularConfiguration*;
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using Index = G4VDNAMesh::Index;
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using Voxel = G4DNAMesh::Voxel;
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using JumpingData = std::pair<MolType, Index>;
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using ReactionData = const G4DNAMolecularReactionData;
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using EventIt = G4DNAEventSet::EventSet::iterator;
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G4double PropensityFunction(const Voxel& voxel, ReactionData* data);
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G4double PropensityFunction(const Voxel& voxel, MolType moleType);
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inline void SetVoxelMesh(G4DNAMesh& mesh) { fpMesh = &mesh; }
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void SetTimeStep(const G4double& stepTime);
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void Initialize();
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void CreateEvent(const Index& index);
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void CreateEvents();
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void SetEventSet(G4DNAEventSet*);
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inline void SetVerbose(const G4int& verbose)
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{
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fVerbose = verbose;
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}
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G4bool SetEquilibrium(const G4DNAMolecularReactionData* pReaction);
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void ResetEquilibrium();
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private:
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G4double Reaction(const Voxel& voxel);
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G4double DiffusiveJumping(const Voxel& voxel);
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G4double ComputeNumberInNode(const Voxel& voxel, MolType type);
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G4double VolumeOfNode(const Voxel& voxel);
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G4DNAMolecularReactionTable* fMolecularReactions;
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G4DNAMesh* fpMesh = nullptr;
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G4double fTimeStep = DBL_MAX;
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G4DNAEventSet* fpEventSet = nullptr;
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G4double fVerbose = 0;
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std::map<G4double /*Propensity*/, ReactionData*> fReactionDataMap;
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std::map<G4double /*Propensity*/, JumpingData> fJumpingDataMap;
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G4bool FindScavenging(const Voxel& voxel, MolType, G4double&);
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G4DNAScavengerMaterial* fpScavengerMaterial = nullptr;
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std::map<G4int,std::unique_ptr<G4ChemEquilibrium>> fEquilibriumProcesses;
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G4bool IsEquilibrium(const G4int& reactionType) const;
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};
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#endif
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