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 //
 // ********************************************************************
 // * 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.          *
 // ********************************************************************
 //
 //
 
 // Author: Mathieu Karamitros
 //
 // The code is developed in the framework of the ESA AO7146
 //
 // We would be very happy hearing from you, send us your feedback! :)
 //
 // In order for Geant4-DNA to be maintained and still open-source,
 // article citations are crucial. 
 // If you use Geant4-DNA chemistry and you publish papers about your software, 
 // in addition to the general paper on Geant4-DNA:
 //
 // Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
 //
 // we would be very happy if you could please also cite the following
 // reference papers on chemistry:
 //
 // J. Comput. Phys. 274 (2014) 841-882
 // Prog. Nucl. Sci. Tec. 2 (2011) 503-508
 
 #pragma once
 
 #include "globals.hh"
 #include "G4ThreeVector.hh"
 #include <fstream>
 #include <memory>
 #include "G4UImessenger.hh"
 #include "G4VStateDependent.hh"
 
 class G4Track;
 class G4DNAWaterExcitationStructure;
 class G4DNAWaterIonisationStructure;
 class G4Molecule;
 class G4VUserChemistryList;
 class G4UIcmdWithABool;
 class G4UIcmdWithADoubleAndUnit;
 class G4UIcmdWithoutParameter;
 class G4UIcmdWithAnInteger;
 class G4ITGun;
 class G4VPhysChemIO;
 
 enum ElectronicModification
 {
     eIonizedMolecule,
     eExcitedMolecule,
     eDissociativeAttachment
 };
 
 /**
  * WARNING: THIS CLASS IS A PROTOTYPE
  * G4DNAChemistryManager is called from the physics models.
  * It creates the water molecules and the solvated electrons and
  * and send them to G4ITStepManager to be treated in the chemistry stage.
  * For this, the fActiveChemistry flag needs to be on.
  * It is also possible to give already molecule's pointers already built.
  * G4DNAChemistryManager will then be in charge of creating the track and loading
  * it to the IT system.
  * The user can also ask to create a file containing a information about the
  * creation of water molecules and solvated electrons.
  */
 class G4DNAChemistryManager: public G4UImessenger,
                              public G4VStateDependent
 {
 protected:
     ~G4DNAChemistryManager() override;
 
 public:
     //============================================================================
     // STATIC METHODS
     //============================================================================
     static G4DNAChemistryManager* Instance();
     static G4DNAChemistryManager* GetInstanceIfExists();
 
     static void DeleteInstance();
     static G4bool IsActivated();
 
     //============================================================================
     // VIRTUAL METHODS
     //============================================================================
     // G4VStateDependent
     G4bool Notify(G4ApplicationState requestedState) override;
     // G4UImessenger
     void SetNewValue(G4UIcommand*, G4String) override;
     G4String GetCurrentValue(G4UIcommand* pCommand) override;
 
     //============================================================================
     // INITIALIZATION AND FINALIZATION METHODS
     //============================================================================
     G4bool IsChemistryActivated();
     void SetChemistryActivation(G4bool);
 
     /** Chemistry list is managed outside the chemistry manager (eg. constructor). */
     void SetChemistryList(G4VUserChemistryList&);
 
     /** Not a constructor or when used in standalone? Prefer this method. */
     void SetChemistryList(std::unique_ptr<G4VUserChemistryList>);
 
     // [[deprecated]] : chemistry list should never be nullptr
     void SetChemistryList(G4VUserChemistryList*);
 
     void Deregister(G4VUserChemistryList&);
 
     void Initialize();
     void Run();
     void Clear();
 
     /**
      * @brief Inject custom species to the simulation
      * @details This method should be called per thread, possibly from
      * ActionInitialisation::Build.
      * One can decide to set the same gun for all threads.
      * It is the user responsibility to handle the pointer deletion.
      */
     void SetGun(G4ITGun* pChemSpeciesGun);
 
     void SetPhysChemIO(std::unique_ptr<G4VPhysChemIO> pPhysChemIO);
 
     void SetVerbose(G4int verbose);
 
     /**
      * If the chemistry module is used in standalone (ie. without running the physics
      * stage beforehand), the physics table still needs to be built.
      * It is therefore necessary to flag the chemistry module as being run
      * in standalone.
      */
     void UseAsStandalone(G4bool flag);
     G4bool IsCounterResetWhenRunEnds() const;
 
     void ResetCounterWhenRunEnds(G4bool resetCounterWhenRunEnds);
 
     void ForceMasterReinitialization();
     void TagThreadForReinitialization();
     void ForceThreadReinitialization();
     void ForceRebuildingPhysicsTable();
 
     //============================================================================
     // FILE OPERATIONS
     //============================================================================
     /**
      * Tells the chemMan to write into a file
      * the position and electronic state of the water molecule
      * and the position thermalized or not of the solvated electron
      */
     void WriteInto(const G4String&, std::ios_base::openmode mode =
                    std::ios_base::out);
     void AddEmptyLineInOutputFile();
 
     /**
      * Close the file specified with WriteInto
      */
     void CloseFile();
 
     //============================================================================
     // PUSH MOLECULES
     //============================================================================
     /**
      * Method used by DNA physics model to create a water molecule.
      * The ElectronicModification is a flag telling whether the molecule
      * is ionized or excited, the electronic level is calculated by the
      * model and the IncomingTrack is the track responsible for the creation
      * of this molecule (electron, proton...).
      */
     void CreateWaterMolecule(ElectronicModification,
                              G4int /*electronicLevel*/,
                              const G4Track* /*pIncomingTrack*/);
 
     /**
      * This method should be used by the physics model of the ElectronSolvatation
      * process.
      */
     void CreateSolvatedElectron(const G4Track* /*pIncomingTrack*/,
                                 G4ThreeVector* pFinalPosition = nullptr);
 
     void PushMolecule(std::unique_ptr<G4Molecule> pMolecule,
                       G4double time,
                       const G4ThreeVector& position,
                       G4int parentID);
 
 protected:
     void HandleStandaloneInitialization();
     void PushTrack(G4Track*);
     void SetGlobalTemperature(G4double temperatureKelvin);
 
     G4DNAWaterExcitationStructure* GetExcitationLevel();
     G4DNAWaterIonisationStructure* GetIonisationLevel();
     void InitializeFile();
     void InitializeMaster();
     void InitializeThread();
     void InitializeThreadSharedData();
 
     G4DNAChemistryManager();
 
 private:
     std::unique_ptr<G4UIdirectory> fpChemDNADirectory;
     std::unique_ptr<G4UIcmdWithABool> fpActivateChem;
     std::unique_ptr<G4UIcmdWithAnInteger> fpRunChem;
     std::unique_ptr<G4UIcmdWithoutParameter> fpSkipReactionsFromChemList;
     std::unique_ptr<G4UIcmdWithADoubleAndUnit> fpScaleForNewTemperature;
     std::unique_ptr<G4UIcmdWithoutParameter> fpInitChem;
 
     static G4DNAChemistryManager* fgInstance;
     G4bool fActiveChemistry{false};
 
     struct ThreadLocalData{
         ThreadLocalData();
         ~ThreadLocalData();
         std::unique_ptr<G4VPhysChemIO> fpPhysChemIO;
         G4bool fThreadInitialized = false;
     };
 
     static G4ThreadLocal ThreadLocalData* fpThreadData;
 
     G4bool fMasterInitialized{false};
     G4bool fForceThreadReinitialization{false};
 
     std::unique_ptr<G4DNAWaterExcitationStructure> fpExcitationLevel;
     std::unique_ptr<G4DNAWaterIonisationStructure> fpIonisationLevel;
 
     std::unique_ptr<G4VUserChemistryList> fpUserChemistryList;
     G4bool fOwnChemistryList{false};
     G4bool fUseInStandalone{false};
     G4bool fPhysicsTableBuilt{false};
     G4bool fSkipReactions{false};
 
     G4bool fGeometryClosed{false};
 
     G4int fVerbose{0};
     G4bool fResetCounterWhenRunEnds{true};
 };

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