Gabriele Cosmo
591 lines
19 KiB
C++
591 lines
19 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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#ifndef G4MolecularConfiguration_
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#define G4MolecularConfiguration_ 1
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#include <vector>
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#include <map>
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#include "G4Threading.hh"
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#include "G4ElectronOccupancy.hh"
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#include <cassert>
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#include <functional>
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class G4MolecularDissociationChannel;
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class G4MoleculeDefinition;
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class G4Material;
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class G4MolecularConfiguration;
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struct comparator
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{
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bool operator()(const G4ElectronOccupancy& occ1,
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const G4ElectronOccupancy& occ2) const
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{
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G4int totalOcc1 = occ1.GetTotalOccupancy();
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G4int totalOcc2 = occ2.GetTotalOccupancy();
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if (totalOcc1 != totalOcc2)
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{
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return totalOcc1 < totalOcc2;
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}
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G4int occupancy1 = -1;
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G4int occupancy2 = -1;
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const G4int sizeOrbit = occ1.GetSizeOfOrbit();
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for (G4int i = 0; i < sizeOrbit; i++)
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{
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occupancy1 = occ1.GetOccupancy(i);
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occupancy2 = occ2.GetOccupancy(i);
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if (occupancy1 != occupancy2)
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{
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return occupancy1 < occupancy2;
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}
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}
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return false;
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}
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};
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/** The pointer G4MolecularConfiguration will be shared by all the
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* molecules having the same molecule definition and the same
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* electron occupancy
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* BE CAREFUlL !!! : If you change the mass for instance of a OH^-,
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* this will affect all the OH^- molecule diffusing around
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*/
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class G4MolecularConfiguration
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{
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public:
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using G4DiffCoeffParam = std::function<double (const G4Material *, double, const G4MolecularConfiguration *)>;
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//____________________________________________________________________________
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// Static methods
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/////////////////////////////////////////////////
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// CREATE FINALIZED SPECIES
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// Get ground state electronic configuration
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static G4MolecularConfiguration*
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GetOrCreateMolecularConfiguration(const G4MoleculeDefinition*);
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// Get for a given moleculeDefinition and a given electronic configuration,
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// the molecular configuration
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static G4MolecularConfiguration*
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GetOrCreateMolecularConfiguration(const G4MoleculeDefinition*,
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const G4ElectronOccupancy& eOcc);
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// Get for a given moleculeDefinition and a given electronic configuration,
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// the molecular configuration
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static G4MolecularConfiguration*
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GetOrCreateMolecularConfiguration(const G4MoleculeDefinition*, int charge);
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/////////////////////////////////////////////////
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// CREATE UNFINALIZED SPECIES
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// Create ground state electronic configuration - to be finalized
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static G4MolecularConfiguration*
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CreateMolecularConfiguration(const G4String& userIdentifier,
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const G4MoleculeDefinition*,
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bool& wasAlreadyCreated);
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static G4MolecularConfiguration*
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CreateMolecularConfiguration(const G4String& userIdentifier,
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const G4MoleculeDefinition*,
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const G4String& label,
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const G4ElectronOccupancy& eOcc,
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bool& wasAlreadyCreated);
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static G4MolecularConfiguration*
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CreateMolecularConfiguration(const G4String& userIdentifier,
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const G4MoleculeDefinition*,
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int charge,
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const G4String& label,
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bool& wasAlreadyCreated);
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static G4MolecularConfiguration*
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CreateMolecularConfiguration(const G4String& userIdentifier,
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const G4MoleculeDefinition*,
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const G4String& label,
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bool& wasAlreadyCreated);
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/////////////////////////////////////////////////
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// GET MOL CONF
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//
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static G4MolecularConfiguration*
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GetMolecularConfiguration(const G4MoleculeDefinition*,
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const G4String& label);
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static G4MolecularConfiguration*
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GetMolecularConfiguration(int moleculeID);
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static G4MolecularConfiguration*
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GetMolecularConfiguration(const G4String& userID);
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static int GetNumberOfSpecies();
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static std::map<G4String, G4MolecularConfiguration*>& GetUserIDTable()
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{
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return GetManager()->GetUserIDTable();
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}
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// Release memory of the mol conf manager
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static void DeleteManager();
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static double DiffCoeffWater(double temperature_K);
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void AddDiffCoeffParameterization(const G4DiffCoeffParam&);
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//____________________________________________________________________________
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const G4MoleculeDefinition* GetDefinition() const;
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/** Returns the name of the molecule
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*/
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const G4String& GetName() const;
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/** Returns the formated name of the molecule
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*/
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const G4String& GetFormatedName() const;
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/** Returns the nomber of atoms compouning the molecule
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*/
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G4int GetAtomsNumber() const;
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/** Method used in Geant4-DNA to excite water molecules
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*/
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G4MolecularConfiguration* ExciteMolecule(G4int) const;
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/** Method used in Geant4-DNA to ionize water molecules
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*/
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G4MolecularConfiguration* IonizeMolecule(G4int) const;
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/** Add n electrons to a given orbit.
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* Note : You can add as many electrons to a given orbit, the result
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* may be unrealist.
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*/
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G4MolecularConfiguration* AddElectron(G4int orbit, G4int n = 1) const;
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/** Remove n electrons to a given orbit.
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*/
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G4MolecularConfiguration* RemoveElectron(G4int, G4int number = 1) const;
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/** Move one electron from an orbit to another.
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*/
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G4MolecularConfiguration* MoveOneElectron(G4int /*orbit*/, G4int /*orbit*/) const;
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/** Returns the number of electron.
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*/
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G4double GetNbElectrons() const;
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/** Display the electronic state of the molecule.
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*/
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void PrintState() const;
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const std::vector<const G4MolecularDissociationChannel*>* GetDissociationChannels() const;
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G4int GetFakeParticleID() const;
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inline G4int GetMoleculeID() const;
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/** Sets the diffusion coefficient D of the molecule used in diffusion
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* processes to calculate the mean square jump distance between two
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* changes of direction. In three dimension : <x^2> = 6 D t where t is
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* the mean jump time between two changes of direction.
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*
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* Note : Diffusion Coefficient in one medium only
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* For the time being, we will consider only one diffusion
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* coefficient for the all simulation => diffusion in one medium only
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* If the user needs to use the diffusion in different materials,
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* she/he should contact the developers/maintainers of this package
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*/
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inline void SetDiffusionCoefficient(G4double);
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/** Returns the diffusion coefficient D.
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*/
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inline G4double GetDiffusionCoefficient() const;
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inline G4double GetDiffusionCoefficient(const G4Material*,
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double temperature) const;
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/** Set the decay time of the molecule.
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*/
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inline void SetDecayTime(G4double);
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/** Returns the decay time of the molecule.
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*/
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inline G4double GetDecayTime() const;
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/** The Van Der Valls Radius of the molecule
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*/
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inline void SetVanDerVaalsRadius(G4double);
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inline G4double GetVanDerVaalsRadius() const;
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/** Returns the object ElectronOccupancy describing the electronic
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* configuration of the molecule.
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*/
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inline const G4ElectronOccupancy* GetElectronOccupancy() const;
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/** Returns the charge of molecule.
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*/
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inline G4int GetCharge() const;
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/** Set the total mass of the molecule.
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*/
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inline void SetMass(G4double);
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/** Returns the total mass of the molecule.
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*/
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inline G4double GetMass() const;
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/*
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* Adds a label to the molecular configuration
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* (Can be used for vibrational states for instance)
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*/
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inline void SetLabel(const G4String&);
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/*
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* Returns the label assigned by the user
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*/
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inline const G4String& GetLabel() const;
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inline void Finalize();
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static void FinalizeAll();
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static void PrintAll(); //hoang added
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inline void UnFinalize();
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void SetUserID(const G4String& userID);//hoang moved it to public
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inline const G4String& GetUserID() const;
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static void SetGlobalTemperature(G4double);
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static G4double GetGlobalTemperature();
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//___________________________________________________________________________
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// EXPERIMENTAL
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static G4MolecularConfiguration* Load(std::istream&);
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void Serialize(std::ostream&);
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void Unserialize(std::istream&);
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//___________________________________________________________________________
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protected:
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G4MolecularConfiguration(const G4MoleculeDefinition*,
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const G4ElectronOccupancy&,
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const G4String& label = "");
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G4MolecularConfiguration(const G4MoleculeDefinition*,
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int charge);
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G4MolecularConfiguration(const G4MoleculeDefinition*,
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const G4String& label,
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int charge);
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G4MolecularConfiguration(std::istream&);
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G4MolecularConfiguration(const G4MolecularConfiguration&);
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G4MolecularConfiguration & operator=(G4MolecularConfiguration &right);
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~G4MolecularConfiguration();
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G4MolecularConfiguration* ChangeConfiguration(const G4ElectronOccupancy& newElectronOccupancy) const;
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G4MolecularConfiguration* ChangeConfiguration(int charge) const;
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void CheckElectronOccupancy(const char* line) const;
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void MakeExceptionIfFinalized();
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void CreateDefaultDiffCoeffParam();
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static void ScaleAllDiffusionCoefficientsOnWater(double temperature_K);
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public:
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class G4MolecularConfigurationManager
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{
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public:
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G4MolecularConfigurationManager()
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{
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fLastMoleculeID = -1;
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}
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~G4MolecularConfigurationManager();
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int GetNumberOfCreatedSpecies()
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{
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return fLastMoleculeID+1;
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}
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//------------------------------------------------------------------------
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// CALLED FROM CONSTRUCTORS
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G4int Insert(const G4MoleculeDefinition* molDef,
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const G4ElectronOccupancy& eOcc,
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G4MolecularConfiguration* molConf);
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G4int Insert(const G4MoleculeDefinition* molDef,
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int charge,
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G4MolecularConfiguration* molConf);
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G4int Insert(const G4MoleculeDefinition* molDef,
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const G4String& label,
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G4MolecularConfiguration* molConf);
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//------------------------------------------------------------------------
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// CALLED WHEN USER ADD SPECIES
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void AddUserID(const G4String& name,
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G4MolecularConfiguration* molecule);
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void RecordNewlyLabeledConfiguration(G4MolecularConfiguration* molConf);
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const G4ElectronOccupancy*
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FindCommonElectronOccupancy(const G4MoleculeDefinition* molDef,
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const G4ElectronOccupancy& eOcc);
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G4MolecularConfiguration*
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GetMolecularConfiguration(const G4MoleculeDefinition* molDef,
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const G4ElectronOccupancy& eOcc);
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G4MolecularConfiguration*
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GetMolecularConfiguration(const G4MoleculeDefinition* molDef,
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int charge);
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G4MolecularConfiguration*
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GetMolecularConfiguration(const G4MoleculeDefinition* molDef,
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const G4String& label);
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G4MolecularConfiguration* GetMolecularConfiguration(int moleculeID);
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G4MolecularConfiguration* GetMolecularConfiguration(const G4String& userID);
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G4MolecularConfiguration*
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GetOrCreateMolecularConfiguration(const G4MoleculeDefinition* molDef,
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const G4ElectronOccupancy& eOcc);
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G4MolecularConfiguration*
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GetOrCreateMolecularConfiguration(const G4MoleculeDefinition* molDef,
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int charge);
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static G4Mutex fManagerCreationMutex;
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void RemoveMolecularConfigurationFromTable(G4MolecularConfiguration*);
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const std::vector<G4MolecularConfiguration*>& GetAllSpecies()
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{
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return fMolConfPerID;
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}
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std::map<G4String, G4MolecularConfiguration*>& GetUserIDTable()
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{
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return fUserIDTable;
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}
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private:
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//__________________________________________________________________________
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using ElectronOccupancyTable = std::map<G4ElectronOccupancy, G4MolecularConfiguration *, comparator>;
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using MolElectronConfTable = std::map<const G4MoleculeDefinition *, ElectronOccupancyTable>;
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MolElectronConfTable fElecOccTable;
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//__________________________________________________________________________
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using ChargeTable = std::map<int, G4MolecularConfiguration *>;
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using MolChargeConfTable = std::map<const G4MoleculeDefinition *, ChargeTable>;
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MolChargeConfTable fChargeTable;
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//__________________________________________________________________________
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using LabelTable = std::map<const G4String, G4MolecularConfiguration *>;
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using MolLabelConfTable = std::map<const G4MoleculeDefinition *, std::map<const G4String, G4MolecularConfiguration *>>;
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MolLabelConfTable fLabelTable;
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//__________________________________________________________________________
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using UserIDTable = std::map<G4String, G4MolecularConfiguration *>;
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UserIDTable fUserIDTable;
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//__________________________________________________________________________
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std::vector<G4MolecularConfiguration*> fMolConfPerID;
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// Indexed by molecule ID
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//__________________________________________________________________________
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G4int fLastMoleculeID;
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G4Mutex fMoleculeCreationMutex;
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};
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protected:
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static G4MolecularConfigurationManager* fgManager;
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static G4MolecularConfigurationManager* GetManager();
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const G4MoleculeDefinition* fMoleculeDefinition;
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const G4ElectronOccupancy* fElectronOccupancy;
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mutable G4String* fLabel;
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G4double fDynDiffusionCoefficient;
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G4double fDynVanDerVaalsRadius;
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G4double fDynDecayTime;
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G4double fDynMass;
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G4int fDynCharge;
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G4int fMoleculeID;
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/*mutable*/ G4String fFormatedName;
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/*mutable*/ G4String fName;
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G4String fUserIdentifier;
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G4bool fIsFinalized;
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G4DiffCoeffParam fDiffParam;
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static /*G4ThreadLocal*/double fgTemperature;
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static double ReturnDefaultDiffCoeff(const G4Material*,
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double,
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const G4MolecularConfiguration*
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molConf);
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};
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inline const G4MoleculeDefinition* G4MolecularConfiguration::GetDefinition() const
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{
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return fMoleculeDefinition;
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}
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inline const G4ElectronOccupancy* G4MolecularConfiguration::GetElectronOccupancy() const
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{
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return fElectronOccupancy;
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}
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inline void G4MolecularConfiguration::SetDiffusionCoefficient(G4double dynDiffusionCoefficient)
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{
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MakeExceptionIfFinalized();
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fDynDiffusionCoefficient = dynDiffusionCoefficient;
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}
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inline G4double G4MolecularConfiguration::GetDiffusionCoefficient() const
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{
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return fDynDiffusionCoefficient;
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}
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inline void G4MolecularConfiguration::SetDecayTime(G4double dynDecayTime)
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{
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MakeExceptionIfFinalized();
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fDynDecayTime = dynDecayTime;
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}
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inline G4double G4MolecularConfiguration::GetDecayTime() const
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{
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return fDynDecayTime;
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}
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inline void G4MolecularConfiguration::SetVanDerVaalsRadius(G4double dynVanDerVaalsRadius)
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{
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MakeExceptionIfFinalized();
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fDynVanDerVaalsRadius = dynVanDerVaalsRadius;
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}
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inline G4double G4MolecularConfiguration::GetVanDerVaalsRadius() const
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{
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return fDynVanDerVaalsRadius;
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}
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inline G4int G4MolecularConfiguration::GetCharge() const
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{
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return fDynCharge;
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}
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inline void G4MolecularConfiguration::SetMass(G4double aMass)
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{
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MakeExceptionIfFinalized();
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fDynMass = aMass;
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}
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inline G4double G4MolecularConfiguration::GetMass() const
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{
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return fDynMass;
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}
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inline G4int G4MolecularConfiguration::GetMoleculeID() const
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{
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return fMoleculeID;
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}
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inline void G4MolecularConfiguration::SetLabel(const G4String& label)
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{
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assert(fLabel == 0 || *fLabel == "");
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if(fLabel == nullptr)
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{
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fLabel = new G4String(label);
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}
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else
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{
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*fLabel = label;
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}
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fgManager->RecordNewlyLabeledConfiguration(this);
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}
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inline const G4String& G4MolecularConfiguration::GetLabel() const
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{
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if(fLabel == nullptr)
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fLabel = new G4String();
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return (*fLabel);
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}
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inline void G4MolecularConfiguration::Finalize()
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{
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CreateDefaultDiffCoeffParam();
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fIsFinalized = true;
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}
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inline const G4String& G4MolecularConfiguration::GetUserID() const
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{
|
||
return fUserIdentifier;
|
||
}
|
||
|
||
inline void G4MolecularConfiguration::AddDiffCoeffParameterization
|
||
(const G4DiffCoeffParam& para)
|
||
{
|
||
fDiffParam = para;
|
||
}
|
||
|
||
inline G4double
|
||
G4MolecularConfiguration::GetDiffusionCoefficient(const G4Material* material,
|
||
double temperature) const
|
||
{
|
||
return fDiffParam(material, temperature, this);
|
||
}
|
||
|
||
inline void G4MolecularConfiguration::UnFinalize()
|
||
{
|
||
fIsFinalized = false;
|
||
}
|
||
|
||
#endif
|