Import Geant4 10.2.0 source tree
This commit is contained in:
Gabriele Cosmo
+200
-98
@@ -23,7 +23,7 @@
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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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// $Id: G4DNAMolecularReactionTable.hh 85244 2014-10-27 08:24:13Z gcosmo $
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// $Id: G4DNAMolecularReactionTable.hh 94218 2015-11-09 08:24:48Z gcosmo $
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//
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// Author: Mathieu Karamitros, kara@cenbg.in2p3.fr
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@@ -32,8 +32,8 @@
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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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// 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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@@ -42,145 +42,247 @@
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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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// Prog. Nucl. Sci. Tec. 2 (2011) 503-508
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#ifndef G4MolecularReactionTable_h
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#define G4MolecularReactionTable_h 1
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#include "G4ITReactionTable.hh"
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#include "G4Molecule.hh"
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#include "G4MolecularConfiguration.hh"
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#include <vector>
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#include <map>
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#include <functional>
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#include "G4ReferenceCast.hh"
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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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* 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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G4DNAMolecularReactionData(G4double reactionRate,
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const G4Molecule* reactive1,
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const G4Molecule* reactive2);
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public :
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//----------------------------------------------------------------------------
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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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G4DNAMolecularReactionData(G4double reactionRate,
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G4MolecularConfiguration* reactive1,
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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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const G4Molecule* GetReactive1() const { return fReactive1; }
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const G4Molecule* GetReactive2() const { return fReactive2; }
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//----------------------------------------------------------------------------
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inline int GetReactionID() const { return fReactionID; }
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inline void SetReactionID(int ID) { fReactionID = ID; }
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G4double GetReactionRate() const {return fReactionRate;}
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G4double GetReducedReactionRadius() const {return fReducedReactionRadius;}
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//----------------------------------------------------------------------------
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inline std::pair<G4MolecularConfiguration*, G4MolecularConfiguration*>
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GetReactants()
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{
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return std::make_pair(fReactant1, fReactant2);
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}
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//_____________________________________________________
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void SetReactive1(const G4Molecule* reactive) ;
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void SetReactive2(const G4Molecule* reactive) ;
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void SetReactive(const G4Molecule* reactive1, const G4Molecule* reactive2);
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void AddProduct(const G4Molecule* molecule);
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inline G4MolecularConfiguration* GetReactant1() const
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{
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return fReactant1;
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}
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inline G4MolecularConfiguration* GetReactant2() const
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{
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return fReactant2;
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}
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void SetReactive1(const G4String& reactive) ;
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void SetReactive2(const G4String& reactive) ;
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void SetReactive(const G4String& reactive1, const G4String& reactive2);
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void AddProduct(const G4String& molecule);
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inline void SetObservedReactionRateConstant(G4double rate)
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{
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fObservedReactionRate = rate;
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}
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G4int GetNbProducts() const
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inline G4double GetObservedReactionRateConstant() const
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{
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return fObservedReactionRate;
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}
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inline G4double GetEffectiveReactionRadius() const
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{
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return fEffectiveReactionRadius;
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}
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inline void SetEffectiveReactionRadius(G4double radius)
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{
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fEffectiveReactionRadius = radius;
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}
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//_____________________________________________________
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void SetReactant1(G4MolecularConfiguration* reactive) ;
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void SetReactant2(G4MolecularConfiguration* reactive) ;
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void SetReactants(G4MolecularConfiguration* reactive1,
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G4MolecularConfiguration* reactive2);
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void AddProduct(G4MolecularConfiguration* 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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inline G4int GetNbProducts() const
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{
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if(fProducts) return fProducts->size();
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return 0;
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}
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inline G4MolecularConfiguration* GetProduct(G4int i) const
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{
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if(fProducts) return (*fProducts)[i];
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return 0;
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}
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inline const std::vector<G4MolecularConfiguration*>* GetProducts() const
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{
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return fProducts;
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}
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inline void RemoveProducts()
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{
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if(fProducts)
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{
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if(fProducts) return fProducts->size();
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return 0;
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fProducts->clear();
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delete fProducts;
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}
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}
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const G4Molecule* GetProduct(G4int i) const
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{
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if(fProducts) return (*fProducts)[i];
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return 0;
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}
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//----------------------------------------------------------------------------
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// Temperature scaling
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typedef std::function<double(double)> RateParam;
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protected :
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G4DNAMolecularReactionData();
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const G4Molecule* fReactive1;
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const G4Molecule* fReactive2;
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G4double fReactionRate;
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G4double fReducedReactionRadius;
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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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std::vector<const G4Molecule*>* fProducts;
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};
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void SetPolynomialParameterization(const std::vector<double>& P);
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struct compMoleculeP
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{
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bool operator () (const G4Molecule* molecule1, const G4Molecule* molecule2) const
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{
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return *molecule1<*molecule2;
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}
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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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protected :
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G4DNAMolecularReactionData();
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G4MolecularConfiguration* fReactant1;
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G4MolecularConfiguration* fReactant2;
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G4double fObservedReactionRate;
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G4double fEffectiveReactionRadius;
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std::vector<G4MolecularConfiguration*>* fProducts;
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// G4DNAReactionType fReactionType;
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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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* 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* fInstance;
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// static G4ThreadLocal G4DNAMolecularReactionTable* fInstance;
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G4DNAMolecularReactionTable();
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static G4DNAMolecularReactionTable* fInstance;
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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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virtual ~G4DNAMolecularReactionTable();
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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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G4MolecularConfiguration* reactive1,
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G4MolecularConfiguration* reactive2);
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void SetReaction(G4DNAMolecularReactionData*);
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const G4DNAMolecularReactionData* GetReactionData(G4MolecularConfiguration*,
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G4MolecularConfiguration*) const;
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const G4DNAMolecularReactionData* GetReactionData(const G4String&,
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const G4String&) const;
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public :
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static G4DNAMolecularReactionTable* GetReactionTable();
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static void DeleteInstance();
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virtual ~G4DNAMolecularReactionTable();
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const G4DNAMolecularReactionData* GetReaction(int reactionID) const;
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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 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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const G4Molecule* reactive1, const G4Molecule* reactive2);
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size_t GetNReactions() const
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{ return fVectorOfReactionData.size(); }
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void SetReaction(G4DNAMolecularReactionData*);
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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 std::vector<G4MolecularConfiguration*>*
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CanReactWith(G4MolecularConfiguration*) const ;
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const G4DNAMolecularReactionData* GetReactionData(const G4Molecule*, const G4Molecule*) const;
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const std::map<G4MolecularConfiguration*, const G4DNAMolecularReactionData*>*
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GetReativesNData(G4MolecularConfiguration*) 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 std::vector<const G4Molecule*>* CanReactWith(const G4Molecule* aMolecule) const ;
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const std::map<const G4Molecule*, const G4DNAMolecularReactionData*, compMoleculeP>* GetReativesNData(const G4Molecule* aMolecule) const ;
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const std::vector<const G4DNAMolecularReactionData*>* GetReactionData(const G4Molecule*) const ;
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const std::vector<const G4DNAMolecularReactionData*>*
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GetReactionData(G4MolecularConfiguration*) const;
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inline const std::map<G4MolecularConfiguration*,
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std::map<G4MolecularConfiguration*,
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const G4DNAMolecularReactionData*> >&
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GetAllReactionData()
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{
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return fReactionData;
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}
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//_________________________________________________________________
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void PrintTable(G4VDNAReactionModel* = 0);
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inline const std::vector<const G4DNAMolecularReactionData*>&
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GetVectorOfReactionData()
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{
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return fVectorOfReactionData;
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}
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protected :
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const G4MoleculeHandleManager* fMoleculeHandleManager;
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G4bool fVerbose;
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void ScaleReactionRateForNewTemperature(double temp_K);
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//_________________________________________________
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typedef std::map<const G4Molecule*,
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std::map<const G4Molecule*,
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const G4DNAMolecularReactionData*,
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compMoleculeP>,
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compMoleculeP > ReactionDataMap;
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typedef std::map<const G4Molecule*,std::vector<const G4Molecule*>,compMoleculeP> ReactivesMV ;
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typedef std::map<const G4Molecule*,std::vector<const G4DNAMolecularReactionData*>,compMoleculeP> ReactionDataMV ;
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ReactionDataMap fReactionData;
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ReactivesMV fReactivesMV;
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ReactionDataMV fReactionDataMV;
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//_________________________________________________________________
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void PrintTable(G4VDNAReactionModel* = 0);
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protected :
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G4bool fVerbose;
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//_________________________________________________
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typedef std::map<G4MolecularConfiguration*,
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std::map<G4MolecularConfiguration*,
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const G4DNAMolecularReactionData*> > ReactionDataMap;
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typedef std::map<G4MolecularConfiguration*,
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std::vector<G4MolecularConfiguration*> > ReactivesMV;
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typedef std::map<G4MolecularConfiguration*,
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std::vector<const G4DNAMolecularReactionData*> > ReactionDataMV;
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ReactionDataMap fReactionData;
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ReactivesMV fReactantsMV;
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ReactionDataMV fReactionDataMV;
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std::vector<const G4DNAMolecularReactionData*> fVectorOfReactionData;
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G4ReactionTableMessenger* fpMessenger;
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};
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#endif /*G4MolecularReactionTable_HH*/
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