Gabriele Cosmo
302 lines
10 KiB
C++
302 lines
10 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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// $Id: G4DNAChemistryManager.hh 103042 2017-03-10 11:50:07Z gcosmo $
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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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#ifndef G4DNACHEMISTRYMANAGER_HH
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#define G4DNACHEMISTRYMANAGER_HH
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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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class G4Track;
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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 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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virtual ~G4DNAChemistryManager();
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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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/**
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* You should rather use DeleteInstance than the destructor of this class
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*/
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static void DeleteInstance();
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G4bool IsChemistryActivated();
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void SetChemistryActivation(G4bool);
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static G4bool IsActivated();
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static void Activated(G4bool flag = true);
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//============================================================================
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// VIRTUAL METHODS
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//============================================================================
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virtual G4bool Notify(G4ApplicationState requestedState);
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virtual void SetNewValue(G4UIcommand*, G4String);
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virtual G4String GetCurrentValue(G4UIcommand * command);
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//============================================================================
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// INITIALIZATION AND FINALIZATION METHODS
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//============================================================================
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void Initialize();
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inline void SetChemistryList(G4VUserChemistryList*);
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inline void Deregister(G4VUserChemistryList*);
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void SetGlobalTemperature(G4double temp_K);
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inline void ForceMasterReinitialization();
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inline void TagThreadForReinitialization();
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void Run();
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void Clear();
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void Gun(G4ITGun*, bool physicsTableToBuild = true);
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inline void ForceThreadReinitialization();
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inline 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 AddEmptyLineInOuputFile();
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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* /*theIncomingTrack*/);
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/**
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* On the same idea as the previous method but for solvated electron.
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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* /*theIncomingTrack*/,
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G4ThreeVector* finalPosition = 0);
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/**
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* WARNING : In case chemistry is not activated, PushMolecule will take care
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* of deleting the transfered molecule.
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* Before calling this method, it is also possible to check if the chemistry
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* is activated through IsChemistryActived().
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* This method will create the track corresponding to the transfered molecule
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* and will be in charge of loading the new track to the system.
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*/
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void PushMolecule(G4Molecule*& molecule,
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G4double time,
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const G4ThreeVector& position,
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G4int parentID);
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/**
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* WARNING : In case chemistry is not activated, PushMoleculeAtParentTimeAndPlace
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* will take care of deleting the transfered molecule.
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* Before calling this method, it is also possible to check if the chemistry
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* is activated through IsChemistryActived().
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* This method will create the track corresponding to the transfered molecule
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* and will be in charge of loading the new track to the system.
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*/
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void PushMoleculeAtParentTimeAndPlace(G4Molecule*& molecule,
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const G4Track* /*theIncomingTrack*/);
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inline void SetVerbose(G4int verbose)
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{
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fVerbose = verbose;
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}
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inline void SetBuildPhysicsTable(G4bool flag)
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{fBuildPhysicsTable = flag;}
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G4bool IsCounterResetWhenRunEnds() const
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{
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return fResetCounterWhenRunEnds;
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}
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void ResetCounterWhenRunEnds(G4bool resetCounterWhenRunEnds)
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{
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fResetCounterWhenRunEnds = resetCounterWhenRunEnds;
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}
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void SetPhysChemIO(G4VPhysChemIO* physChemIO);
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protected:
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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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G4DNAChemistryManager();
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private:
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G4UIdirectory* fpChemDNADirectory;
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G4UIcmdWithABool* fpActivateChem;
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G4UIcmdWithoutParameter* fpRunChem;
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G4UIcmdWithoutParameter* fpSkipReactionsFromChemList;
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//G4UIcmdWithADoubleAndUnit* fpGridSize; // not used in release
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G4UIcmdWithADoubleAndUnit* fpScaleForNewTemperature;
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G4UIcmdWithoutParameter* fpInitChem;
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static G4DNAChemistryManager* fgInstance;
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G4bool fActiveChemistry;
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struct ThreadLocalData{
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ThreadLocalData();
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~ThreadLocalData();
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G4VPhysChemIO* fpPhysChemIO;
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G4bool fThreadInitialized_tl;
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};
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static G4ThreadLocal ThreadLocalData* fpThreadData;
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G4bool fMasterInitialized;
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G4bool fForceThreadReinitialization;
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G4DNAWaterExcitationStructure* fpExcitationLevel;
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G4DNAWaterIonisationStructure* fpIonisationLevel;
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G4VUserChemistryList* fpUserChemistryList;
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G4bool fBuildPhysicsTable;
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G4bool fPhysicsTableBuilt;
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G4bool fSkipReactions;
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G4bool fGeometryClosed;
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G4int fVerbose;
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G4bool fResetCounterWhenRunEnds;
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};
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//------------------------------------------------------------------------------
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inline void G4DNAChemistryManager::ForceRebuildingPhysicsTable()
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{
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fPhysicsTableBuilt = false;
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}
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inline void G4DNAChemistryManager::SetChemistryList(G4VUserChemistryList* chemistryList)
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{
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fpUserChemistryList = chemistryList;
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Activated();
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}
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inline void G4DNAChemistryManager::Deregister(G4VUserChemistryList* chemistryList)
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{
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if (fpUserChemistryList == chemistryList) fpUserChemistryList = 0;
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}
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inline void G4DNAChemistryManager::ForceMasterReinitialization()
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{
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fMasterInitialized = false;
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InitializeMaster();
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}
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inline void G4DNAChemistryManager::ForceThreadReinitialization()
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{
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fForceThreadReinitialization = true;
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}
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inline void G4DNAChemistryManager::TagThreadForReinitialization()
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{
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fpThreadData->fThreadInitialized_tl = false;
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}
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#endif // G4DNACHEMISTRYMANAGER_HH
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