Gabriele Cosmo
264 lines
9.8 KiB
C++
264 lines
9.8 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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// Author: Mathieu Karamitros
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//
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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 "globals.hh"
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#include "G4ThreeVector.hh"
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#include <fstream>
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#include <memory>
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#include "G4UImessenger.hh"
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#include "G4VStateDependent.hh"
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#include "G4MoleculeCounterManager.hh"
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class G4Track;
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class G4Run;
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class G4DNAWaterExcitationStructure;
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class G4DNAWaterIonisationStructure;
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class G4Molecule;
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class G4VUserChemistryList;
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class G4UIcmdWithABool;
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class G4UIcmdWithADoubleAndUnit;
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class G4UIcmdWithoutParameter;
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class G4UIcmdWithAnInteger;
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class G4ITGun;
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class G4VPhysChemIO;
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enum ElectronicModification
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{
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eIonizedMolecule,
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eExcitedMolecule,
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eDissociativeAttachment
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};
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/**
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* WARNING: THIS CLASS IS A PROTOTYPE
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* G4DNAChemistryManager is called from the physics models.
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* It creates the water molecules and the solvated electrons and
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* and send them to G4ITStepManager to be treated in the chemistry stage.
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* For this, the fActiveChemistry flag needs to be on.
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* It is also possible to give already molecule's pointers already built.
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* G4DNAChemistryManager will then be in charge of creating the track and loading
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* it to the IT system.
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* The user can also ask to create a file containing a information about the
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* creation of water molecules and solvated electrons.
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*/
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class G4DNAChemistryManager: public G4UImessenger,
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public G4VStateDependent
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{
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protected:
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~G4DNAChemistryManager() override;
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public:
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//============================================================================
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// STATIC METHODS
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//============================================================================
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static G4DNAChemistryManager* Instance();
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static G4DNAChemistryManager* GetInstanceIfExists();
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static void DeleteInstance();
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static G4bool IsActivated();
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//============================================================================
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// VIRTUAL METHODS
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//============================================================================
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// G4VStateDependent
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G4bool Notify(G4ApplicationState requestedState) override;
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// G4UImessenger
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void SetNewValue(G4UIcommand*, G4String) override;
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G4String GetCurrentValue(G4UIcommand* pCommand) override;
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//============================================================================
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// INITIALIZATION AND FINALIZATION METHODS
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//============================================================================
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G4bool IsChemistryActivated();
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void SetChemistryActivation(G4bool);
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/** Chemistry list is managed outside the chemistry manager (eg. constructor). */
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void SetChemistryList(G4VUserChemistryList&);
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/** Not a constructor or when used in standalone? Prefer this method. */
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void SetChemistryList(std::unique_ptr<G4VUserChemistryList>);
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// [[deprecated]] : chemistry list should never be nullptr
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void SetChemistryList(G4VUserChemistryList*);
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void Deregister(G4VUserChemistryList&);
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void Initialize();
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void Run();
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void Clear();
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/**
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* @brief Inject custom species to the simulation
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* @details This method should be called per thread, possibly from
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* ActionInitialisation::Build.
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* One can decide to set the same gun for all threads.
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* It is the user responsibility to handle the pointer deletion.
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*/
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void SetGun(G4ITGun* pChemSpeciesGun);
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void SetPhysChemIO(std::unique_ptr<G4VPhysChemIO> pPhysChemIO);
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void SetVerbose(G4int verbose);
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/**
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* If the chemistry module is used in standalone (ie. without running the physics
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* stage beforehand), the physics table still needs to be built.
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* It is therefore necessary to flag the chemistry module as being run
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* in standalone.
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*/
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void UseAsStandalone(G4bool flag);
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void ForceMasterReinitialization();
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void TagThreadForReinitialization();
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void ForceThreadReinitialization();
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void ForceRebuildingPhysicsTable();
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//============================================================================
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// FILE OPERATIONS
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//============================================================================
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/**
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* Tells the chemMan to write into a file
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* the position and electronic state of the water molecule
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* and the position thermalized or not of the solvated electron
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*/
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void WriteInto(const G4String&, std::ios_base::openmode mode =
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std::ios_base::out);
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void AddEmptyLineInOutputFile();
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/**
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* Close the file specified with WriteInto
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*/
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void CloseFile();
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//============================================================================
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// PUSH MOLECULES
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//============================================================================
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/**
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* Method used by DNA physics model to create a water molecule.
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* The ElectronicModification is a flag telling whether the molecule
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* is ionized or excited, the electronic level is calculated by the
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* model and the IncomingTrack is the track responsible for the creation
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* of this molecule (electron, proton...).
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*/
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void CreateWaterMolecule(ElectronicModification,
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G4int /*electronicLevel*/,
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const G4Track* /*pIncomingTrack*/);
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/**
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* This method should be used by the physics model of the ElectronSolvatation
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* process.
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*/
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void CreateSolvatedElectron(const G4Track* /*pIncomingTrack*/,
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G4ThreeVector* pFinalPosition = nullptr);
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void PushMolecule(std::unique_ptr<G4Molecule> pMolecule,
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G4double time,
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const G4ThreeVector &position,
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G4int parentID,
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const G4Track *parentTrack = nullptr);
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//============================================================================
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// Methods called by RunManagers to notify of Runs & Events
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//============================================================================
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void BeginOfEventAction(const G4Event*);
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void BeginOfRunAction(const G4Run*);
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void EndOfEventAction(const G4Event*);
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void EndOfRunAction(const G4Run*);
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protected:
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void HandleStandaloneInitialization();
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void PushTrack(G4Track*);
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void SetGlobalTemperature(G4double temperatureKelvin);
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G4DNAWaterExcitationStructure* GetExcitationLevel();
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G4DNAWaterIonisationStructure* GetIonisationLevel();
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void InitializeFile();
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void InitializeMaster();
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void InitializeThread();
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void InitializeThreadSharedData();
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G4DNAChemistryManager();
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private:
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std::unique_ptr<G4UIdirectory> fpChemDNADirectory;
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std::unique_ptr<G4UIcmdWithABool> fpActivateChem;
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std::unique_ptr<G4UIcmdWithAnInteger> fpRunChem;
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std::unique_ptr<G4UIcmdWithoutParameter> fpSkipReactionsFromChemList;
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std::unique_ptr<G4UIcmdWithADoubleAndUnit> fpScaleForNewTemperature;
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std::unique_ptr<G4UIcmdWithoutParameter> fpInitChem;
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static G4DNAChemistryManager* fgInstance;
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G4bool fActiveChemistry{false};
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struct ThreadLocalData{
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ThreadLocalData();
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~ThreadLocalData();
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std::unique_ptr<G4VPhysChemIO> fpPhysChemIO;
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G4bool fThreadInitialized = false;
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};
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static G4ThreadLocal ThreadLocalData* fpThreadData;
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G4bool fMasterInitialized{false};
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G4bool fForceThreadReinitialization{false};
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std::unique_ptr<G4DNAWaterExcitationStructure> fpExcitationLevel;
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std::unique_ptr<G4DNAWaterIonisationStructure> fpIonisationLevel;
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std::unique_ptr<G4VUserChemistryList> fpUserChemistryList;
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G4bool fOwnChemistryList{false};
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G4bool fUseInStandalone{false};
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G4bool fPhysicsTableBuilt{false};
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G4bool fSkipReactions{false};
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G4bool fGeometryClosed{false};
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G4int fVerbose{0};
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};
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