Gabriele Cosmo
253 lines
8.6 KiB
C++
253 lines
8.6 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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// Author: Mathieu Karamitros
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// The code is developed in the framework of the ESA AO7146
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//
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// We would be very happy hearing from you, send us your feedback! :)
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//
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// In order for Geant4-DNA to be maintained and still open-source,
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// article citations are crucial.
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// If you use Geant4-DNA chemistry and you publish papers about your software,
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// in addition to the general paper on Geant4-DNA:
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//
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// Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
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//
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// we would be very happy if you could please also cite the following
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// reference papers on chemistry:
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//
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// J. Comput. Phys. 274 (2014) 841-882
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// Prog. Nucl. Sci. Tec. 2 (2011) 503-508
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#pragma once
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#include "G4ITReactionTable.hh"
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#include "G4MolecularConfiguration.hh"
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#include "G4ReferenceCast.hh"
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#include "G4VDNAMolecularGeometry.hh"
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#include <vector>
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#include <map>
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#include <functional>
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#include <memory>
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class G4VDNAReactionModel;
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class G4DNAMolecularReactionTable;
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class G4ReactionTableMessenger;
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/**
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* G4DNAMolecularReactionData contains the information
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* relative to a given reaction (eg : °OH + °OH -> H2O2)
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*/
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class G4DNAMolecularReactionData
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{
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public:
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//----------------------------------------------------------------------------
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G4DNAMolecularReactionData(G4double reactionRate,
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const G4MolecularConfiguration* reactive1,
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const G4MolecularConfiguration* reactive2);
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G4DNAMolecularReactionData(G4double reactionRate,
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const G4String& reactive1,
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const G4String& reactive2);
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~G4DNAMolecularReactionData();
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using Reactant = const G4MolecularConfiguration;
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using ReactantPair = std::pair<Reactant*, Reactant*>;
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using ReactionProducts = std::vector<Reactant*>;
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int GetReactionID() const;
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void SetReactionID(int ID);
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ReactantPair GetReactants();
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Reactant* GetReactant1() const;
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Reactant* GetReactant2() const;
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void SetObservedReactionRateConstant(G4double rate);
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G4double GetObservedReactionRateConstant() const;
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G4double GetActivationRateConstant() const;
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G4double GetDiffusionRateConstant() const;
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void SetReactionRadius(G4double radius);
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G4double GetReactionRadius() const;
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void SetEffectiveReactionRadius(G4double radius);
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G4double GetEffectiveReactionRadius() const;
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G4double GetOnsagerRadius() const;
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void SetProbability(G4double prob);
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G4double GetProbability() const;
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void SetReactionType(G4int type);
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G4int GetReactionType() const;
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void SetReactant1(Reactant* reactive);
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void SetReactant2(Reactant* reactive);
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void SetReactants(Reactant* reactive1,
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Reactant* reactive2);
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void AddProduct(Reactant* molecule);
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void SetReactant1(const G4String& reactive);
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void SetReactant2(const G4String& reactive);
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void SetReactants(const G4String& reactive1, const G4String& reactive2);
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void AddProduct(const G4String& molecule);
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G4int GetNbProducts() const;
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Reactant* GetProduct(G4int i) const;
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const ReactionProducts* GetProducts() const;
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void RemoveProducts();
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//----------------------------------------------------------------------------
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// Temperature scaling
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using RateParam = std::function<double (double)>;
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static double PolynomialParam(double temp_K, std::vector<double> P);
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static double ArrehniusParam(double temp_K, std::vector<double> P);
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static double ScaledParameterization(double temp_K,
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double temp_init,
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double rateCste_init);
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void SetPolynomialParameterization(const std::vector<double>& P);
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void SetArrehniusParameterization(double A0, double E_R);
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void SetScaledParameterization(double temperature_K,
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double rateCste);
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void ScaleForNewTemperature(double temp_K);
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void ComputeEffectiveRadius();
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protected:
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G4DNAMolecularReactionData();
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Reactant* fpReactant1;
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Reactant* fpReactant2;
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G4double fObservedReactionRate;
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G4double fActivationRate;
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G4double fDiffusionRate;
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G4double fOnsagerRadius;
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G4double fReactionRadius;
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G4double fEffectiveReactionRadius;
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G4double fProbability;
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G4int fType;
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ReactionProducts fProducts;
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RateParam fRateParam;
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int fReactionID;
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};
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/**
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* G4DNAMolecularReactionTable sorts out the G4DNAMolecularReactionData
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* for bimolecular reaction
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*/
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class G4DNAMolecularReactionTable : public G4ITReactionTable
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{
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protected:
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G4DNAMolecularReactionTable();
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static G4DNAMolecularReactionTable* fpInstance;
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public:
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static G4DNAMolecularReactionTable* GetReactionTable();
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static G4DNAMolecularReactionTable* Instance();
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static void DeleteInstance();
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~G4DNAMolecularReactionTable() override;
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using Reactant = const G4MolecularConfiguration;
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using Data = const G4DNAMolecularReactionData;
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using ReactantList = std::vector<Reactant*>;
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using DataList = std::vector<Data*>;
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using SpecificDataList = std::map<Reactant*, Data*>;
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using ReactionDataMap = std::map<Reactant*, SpecificDataList>;
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using ReactivesMV = std::map<Reactant*, ReactantList>;
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using ReactionDataMV = std::map<Reactant*, DataList>;
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/**
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* Define a reaction :
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* First argument : reaction rate
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* Second argument : reactant 1
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* Third argument : reactant 2
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* Fourth argument : a std::vector holding the molecular products
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* if this last argument is NULL then it will be interpreted as
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* a reaction giving no products
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*/
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void SetReaction(G4double observedReactionRate,
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Reactant* reactive1,
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Reactant* reactive2);
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void SetReaction(G4DNAMolecularReactionData*);
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void SetGeometry(G4VDNAMolecularGeometry* geometry){fGeometry = geometry;};
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G4VDNAMolecularGeometry* GetGeometry() const;
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Data* GetReactionData(Reactant*, Reactant*) const;
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Data* GetReactionData(const G4String&, const G4String&) const;
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Data* GetReaction(int reactionID) const;
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size_t GetNReactions() const;
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//_________________________________________________________________
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/**
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* Given a molecule's type, it returns with which a reaction is allowed
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*/
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const ReactantList* CanReactWith(Reactant*) const;
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const SpecificDataList* GetReativesNData(const G4MolecularConfiguration*) const;
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const DataList* GetReactionData(const G4MolecularConfiguration*) const;
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const ReactionDataMap& GetAllReactionData();
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DataList GetVectorOfReactionData();
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void ScaleReactionRateForNewTemperature(double temp_K);
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//_________________________________________________________________
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void PrintTable(G4VDNAReactionModel* = nullptr);
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void Reset();
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protected:
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G4bool fVerbose{false};
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G4VDNAMolecularGeometry* fGeometry{nullptr};
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ReactionDataMap fReactionData;
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ReactivesMV fReactantsMV;
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ReactionDataMV fReactionDataMV;
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std::vector<std::unique_ptr<Data>> fVectorOfReactionData;
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std::unique_ptr<G4ReactionTableMessenger> fpMessenger;
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};
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