G4Molecule.hh

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//
// Contact: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr)
//
// WARNING : This class is released as a prototype.
// It might strongly evolve or even disapear in the next releases.
//
// 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 
//
// ---------------------------------------------------------------------
//  GEANT 4 class header file
//
//  History: first implementation, based on G4DynamicParticle
//           New dependency : G4VUserTrackInformation
//
//      ---------------- G4Molecule  ----------------
//      first design&implementation by Alfonso Mantero, 7 Apr 2009
//      New developments Alfonso Mantero & Mathieu Karamitros
//      Oct/Nov 2009 Class Name changed to G4Molecule
//                   Removed dependency from G4DynamicParticle
//                   New constructors :
//                    copy constructor
//                    direct ionized/excited molecule
//                   New methods :
//                    Get : name,atoms' number,nb electrons,decayChannel
//                    PrintState //To get the electronic level and the
//                                 corresponding name of the excitation
//                    Kinematic :
//                    BuildTrack,GetKineticEnergy,GetDiffusionVelocity
//                    Change the way dynCharge and eNb is calculated
// ---------------------------------------------------------------------
 
#ifndef G4Molecule_h
#define G4Molecule_h 1
 
#include "G4IT.hh"
#include "G4Allocator.hh"
#include "G4MoleculeDefinition.hh"
 
class G4Molecule;
template<>
G4KDNode<G4Molecule>::~G4KDNode();
 
class G4Molecule;
class G4MolecularConfiguration;
class G4MoleculeDefinition;
class G4MolecularDissociationChannel;
class G4DynamicParticle;
class G4Material;
 
G4Molecule* GetMolecule(const G4Track& track);
G4Molecule* GetMolecule(const G4Track* track);
 
/** Class Description
 *  The dynamic molecule holds all the data that change for a molecule
 *  It has a pointer to G4MoleculeDefinition object, which holds
 *   all the "ground level" information.
 */
 
class G4Molecule : public G4IT
{
 
public:
    // With Description
 
    ITDef(G4Molecule) // NOLINT because it's a macro
 
        //From G4VUserTrackInformation
        void Print() const override;
 
    //  new/delete operators are overloded to use G4Allocator
    inline void *operator new(size_t);
#ifdef __IBMCPP__
    inline void *operator new(size_t sz, void* p)
    {
        return p;
    }
#endif
    inline void operator delete(void*);
 
    G4Molecule(const G4Molecule&);
    G4Molecule & operator=(const G4Molecule &right);
    G4bool operator==(const G4Molecule &right) const;
    G4bool operator!=(const G4Molecule &right) const;
    G4bool operator<(const G4Molecule &right) const;
 
    operator int() const
    {
        return GetMoleculeID();
    }
 
    G4ITType GetITSubType() const override
    {
        return GetMoleculeID();
    }
 
public:
    //------ Constructors --------------------------
    /** To build a molecule at ground state according to a given
     * G4MoleculeDefinition that can be obtained from G4GenericMoleculeManager
     */
    G4Molecule(G4MoleculeDefinition* pMoleculeDefinition);
 
    G4Molecule(G4MoleculeDefinition* pMoleculeDefinition, int charge);
 
    /** To build a molecule at a specific excitation/ionisation state according
     * to a ground state that can be obtained from G4GenericMoleculeManager
     */
    G4Molecule(G4MoleculeDefinition* pMoleculeDefinition, G4int, G4int);
 
    /** Specific builder for water molecules to be used in Geant4-DNA,
     * the last option Excitation is true if the molecule is excited, is
     * false is the molecule is ionized.
     */
    G4Molecule(G4MoleculeDefinition* pMoleculeDefinition, G4int, G4bool);
 
    G4Molecule(const G4MolecularConfiguration*);
 
    ~G4Molecule() override;
 
    //-------- Methods -------------------------------
    //Get from static definition
    /** Returns the name of the molecule
     */
    const G4String& GetName() const override;
 
    /** Returns the formated name of the molecule
     */
    const G4String& GetFormatedName() const;
 
    /** Returns the nomber of atoms compouning the molecule
     */
    G4int GetAtomsNumber() const;
 
    /** Will set up the correct molecularConfiguration given
     * an electron configuration
     */
    void SetElectronOccupancy(const G4ElectronOccupancy*);
 
    /** Method used in Geant4-DNA to excite water molecules
     */
    void ExciteMolecule(G4int);
 
    /** Method used in Geant4-DNA to ionize water molecules
     */
    void IonizeMolecule(G4int);
 
    /** Add n electrons to a given orbit.
     * Note : You can add as many electrons to a given orbit, the result
     * may be unrealist.
     */
    void AddElectron(G4int orbit, G4int n = 1);
 
    /** Remove n electrons to a given orbit.
     */
    void RemoveElectron(G4int, G4int number = 1);
 
    /** Move one electron from an orbit to another.
     */
    void MoveOneElectron(G4int /*orbit*/, G4int /*orbit*/);
 
    /** Returns the number of electron.
     */
    G4double GetNbElectrons() const; //This method can be used to check if the electron s number is physical
 
    /** Show the electronic state of the molecule.
     */
    void PrintState() const;
 
    G4Track * BuildTrack(G4double globalTime, const G4ThreeVector& Position);
 
    G4double GetKineticEnergy() const;
 
    G4double GetDiffusionVelocity() const;
 
    const std::vector<const G4MolecularDissociationChannel*>* GetDissociationChannels() const;
 
    G4int GetFakeParticleID() const;
    G4int GetMoleculeID() const;
 
    //-------------Inline functions ---------------------
    /**  Get molecule definition. This G4MoleculeDefinition has the ground
     * electronic state of the molecule.
     */
    const G4MoleculeDefinition* GetDefinition() const;
 
    //methods to set/get changing parameters
 
  /////////////////////////////////////////////////////////////////////////////
    /** Sets the diffusion coefficient D of the molecule used in diffusion
     * processes to calculate the mean square jump distance between two
     * changes of direction. In three dimension : <x^2> = 6 D t where t is
     * the mean jump time between two changes of direction.
     */
    void SetDiffusionCoefficient(G4double);
 
    /** Returns the diffusion coefficient D.
     */
    G4double GetDiffusionCoefficient() const;
 
    /** Returns the diffusion coefficient D.
     */
    G4double GetDiffusionCoefficient(const G4Material*,
                                     double temperature) const;
 
    /** Set the decay time of the molecule.
     */
    void SetDecayTime(G4double);
 
    /** Returns the decay time of the molecule.
     */
    G4double GetDecayTime() const;
 
    /** The Van Der Valls Radius of the molecule
     */
    void SetVanDerVaalsRadius(G4double);
    G4double GetVanDerVaalsRadius() const;
 
    /** Returns the object ElectronOccupancy describing the electronic
     * configuration of the molecule.
     */
    const G4ElectronOccupancy* GetElectronOccupancy() const;
 
    /** Returns the charge of molecule.
     */
    G4int GetCharge() const;
 
    /** Set the total mass of the molecule.
     */
    void SetMass(G4double);
 
    /** Returns the total mass of the molecule.
     */
    G4double GetMass() const;
 
    /** Returns the label of the molecule configuration
     */
    const G4String& GetLabel() const;
 
    void SetLabel(const G4String& label);
 
    void ChangeConfigurationToLabel(const G4String& label);
 
    ////////////////////////////////////////////////////////////////////////
 
    const G4MolecularConfiguration* GetMolecularConfiguration() const;
 
    static G4Molecule* GetMolecule(const G4Track*);
 
private:
    /** Default molecule builder
     */
    G4Molecule();
    const G4MolecularConfiguration* fpMolecularConfiguration;
};
 
#if defined G4EM_ALLOC_EXPORT
extern G4DLLEXPORT G4Allocator<G4Molecule>*& aMoleculeAllocator();
#else
extern G4DLLIMPORT G4Allocator<G4Molecule>*& aMoleculeAllocator();
#endif
 
//////////////////////////
inline void * G4Molecule::operator new(size_t)
//////////////////////////
{
    if (aMoleculeAllocator() == nullptr)
    {
        aMoleculeAllocator() = new G4Allocator<G4Molecule>;
    }
    return (void *)aMoleculeAllocator()->MallocSingle();
}
 
//////////////////////////
inline void G4Molecule::operator delete(void * aMolecule)
//////////////////////////
{
    aMoleculeAllocator()->FreeSingle((G4Molecule *)aMolecule);
}
 
#endif