G4MolecularConfiguration.hh

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// Author: Mathieu Karamitros, kara@cenbg.in2p3.fr

// 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 

#ifndef G4MolecularConfiguration_
#define G4MolecularConfiguration_ 1

#include <vector>
#include <map>
#include "G4Threading.hh"
#include "G4ElectronOccupancy.hh"
#include <cassert>
#include <functional>

class G4MolecularDissociationChannel;
class G4MoleculeDefinition;
class G4Material;
class G4MolecularConfiguration;

struct comparator
{
  bool operator()(const G4ElectronOccupancy& occ1,
                  const G4ElectronOccupancy& occ2) const
  {
    G4int totalOcc1 = occ1.GetTotalOccupancy();
    G4int totalOcc2 = occ2.GetTotalOccupancy();
    if (totalOcc1 != totalOcc2)
    {
      return totalOcc1 < totalOcc2;
    }
    else
    {
      G4int occupancy1 = -1;
      G4int occupancy2 = -1;
      const G4int sizeOrbit = occ1.GetSizeOfOrbit();
      for (G4int i = 0; i < sizeOrbit; i++)
      {
        occupancy1 = occ1.GetOccupancy(i);
        occupancy2 = occ2.GetOccupancy(i);

        if (occupancy1 != occupancy2)
        {
          return occupancy1 < occupancy2;
        }
      }
    }
    return false;
  }
};

class G4MolecularConfiguration
{
public:

  typedef std::function<double(const G4Material*,
                         double,
     const G4MolecularConfiguration*)> G4DiffCoeffParam;

  //____________________________________________________________________________
  // Static methods

  // CREATE FINALIZED SPECIES
  // Get ground state electronic configuration
  static G4MolecularConfiguration*
  GetOrCreateMolecularConfiguration(const G4MoleculeDefinition*);

  // Get for a given moleculeDefinition and a given electronic configuration,
  // the molecular configuration
  static G4MolecularConfiguration*
  GetOrCreateMolecularConfiguration(const G4MoleculeDefinition*,
                                    const G4ElectronOccupancy& eOcc);

  // Get for a given moleculeDefinition and a given electronic configuration,
  // the molecular configuration
  static G4MolecularConfiguration*
  GetOrCreateMolecularConfiguration(const G4MoleculeDefinition*, int charge);

  // CREATE UNFINALIZED SPECIES
  // Create ground state electronic configuration - to be finalized
  static G4MolecularConfiguration*
    CreateMolecularConfiguration(const G4String& userIdentifier,
                                 const G4MoleculeDefinition*,
                                 bool& wasAlreadyCreated);

  static G4MolecularConfiguration*
    CreateMolecularConfiguration(const G4String& userIdentifier,
                                 const G4MoleculeDefinition*,
                                 const G4String& label,
                                 const G4ElectronOccupancy& eOcc,
                                 bool& wasAlreadyCreated);

  static G4MolecularConfiguration*
    CreateMolecularConfiguration(const G4String& userIdentifier,
                                 const G4MoleculeDefinition*,
                                 int charge,
                                 const G4String& label,
                                 bool& wasAlreadyCreated);

  static G4MolecularConfiguration*
    CreateMolecularConfiguration(const G4String& userIdentifier,
                                 const G4MoleculeDefinition*,
                                 const G4String& label,
                                 bool& wasAlreadyCreated);

  // GET MOL CONF
  //
  static G4MolecularConfiguration*
    GetMolecularConfiguration(const G4MoleculeDefinition*,
                              const G4String& label);

  static G4MolecularConfiguration*
    GetMolecularConfiguration(int moleculeID);

  static G4MolecularConfiguration*
    GetMolecularConfiguration(const G4String& userID);

  static int GetNumberOfSpecies();

  static std::map<G4String, G4MolecularConfiguration*>& GetUserIDTable()
  {
    return GetManager()->GetUserIDTable();
  }

  // Release memory of the mol conf manager
  static void DeleteManager();

  static double DiffCoeffWater(double temperature_K);

  void AddDiffCoeffParameterization(const G4DiffCoeffParam&);

  //____________________________________________________________________________

  const G4MoleculeDefinition* GetDefinition() const;

  const G4String& GetName() const;

  const G4String& GetFormatedName() const;

  G4int GetAtomsNumber() const;

  G4MolecularConfiguration* ExciteMolecule(G4int);

  G4MolecularConfiguration* IonizeMolecule(G4int);

  G4MolecularConfiguration* AddElectron(G4int orbit, G4int n = 1);

  G4MolecularConfiguration* RemoveElectron(G4int, G4int number = 1);

  G4MolecularConfiguration* MoveOneElectron(G4int /*orbit*/, G4int /*orbit*/);

  G4double GetNbElectrons() const;

  void PrintState() const;

  const std::vector<const G4MolecularDissociationChannel*>*
  GetDecayChannel() const;

  G4int GetFakeParticleID() const;

  inline G4int GetMoleculeID() const;

  inline void SetDiffusionCoefficient(G4double);

  inline G4double GetDiffusionCoefficient() const;

  inline G4double GetDiffusionCoefficient(const G4Material*,
                                          double temperature) const;

  inline void SetDecayTime(G4double);

  inline G4double GetDecayTime() const;

  inline void SetVanDerVaalsRadius(G4double);
  inline G4double GetVanDerVaalsRadius() const;

  inline const G4ElectronOccupancy* GetElectronOccupancy() const;

  inline G4int GetCharge() const;

  inline void SetMass(G4double);

  inline G4double GetMass() const;

  /*
   * Adds a label to the molecular configuration
   * (Can be used for vibrational states for instance)
   */
  inline void SetLabel(const G4String&);

  /*
   * Returns the label assigned by the user
   */
  inline const G4String& GetLabel() const;

  inline void Finalize();
  static void FinalizeAll();

  inline const G4String& GetUserID() const;

  static void SetGlobalTemperature(G4double);
  static G4double GetGlobalTemperature();

  //___________________________________________________________________________
  // EXPERIMENTAL

  static G4MolecularConfiguration* Load(std::istream&);

  void Serialize(std::ostream&);
  void Unserialize(std::istream&);
  //___________________________________________________________________________


protected:
  G4MolecularConfiguration(const G4MoleculeDefinition*,
                           const G4ElectronOccupancy&,
                           const G4String& label = "");

  G4MolecularConfiguration(const G4MoleculeDefinition*,
                           int charge);

  G4MolecularConfiguration(const G4MoleculeDefinition*,
                           const G4String& label,
                           int charge);

  G4MolecularConfiguration(std::istream&);

  G4MolecularConfiguration(const G4MolecularConfiguration&);
  G4MolecularConfiguration & operator=(G4MolecularConfiguration &right);
  ~G4MolecularConfiguration();
  G4MolecularConfiguration* ChangeConfiguration(const G4ElectronOccupancy& newElectronOccupancy);
  G4MolecularConfiguration* ChangeConfiguration(int charge);

  void CheckElectronOccupancy(const char* line) const;
  void MakeExceptionIfFinalized();
  void SetUserID(const G4String& userID);

  void CreateDefaultDiffCoeffParam();
  static void ScaleAllDiffusionCoefficientsOnWater(double temperature_K);

public:
  class G4MolecularConfigurationManager
  {
  public:
    G4MolecularConfigurationManager() :
        fMoleculeCreationMutex()
    {
      fLastMoleculeID = -1;
    }
    ~G4MolecularConfigurationManager();

    int GetNumberOfCreatedSpecies()
    {
      return fLastMoleculeID+1;
    }

    // TODO: TO BE IMPLEMENTED
//    void InsertMolecularConfiguration(G4MolecularConfiguration*);

    //------------------------------------------------------------------------
    // CALLED FROM CONSTRUCTORS
    G4int Insert(const G4MoleculeDefinition* molDef,
                 const G4ElectronOccupancy& eOcc,
                 G4MolecularConfiguration* molConf);

    G4int Insert(const G4MoleculeDefinition* molDef,
                 int charge,
                 G4MolecularConfiguration* molConf);

    G4int Insert(const G4MoleculeDefinition* molDef,
                 const G4String& label,
                 G4MolecularConfiguration* molConf);

    //------------------------------------------------------------------------
    // CALLED WHEN USER ADD SPECIES
    void AddUserID(const G4String& name,
                   G4MolecularConfiguration* molecule);

    void RecordNewlyLabeledConfiguration(G4MolecularConfiguration* molConf);

    const G4ElectronOccupancy*
      FindCommonElectronOccupancy(const G4MoleculeDefinition* molDef,
                                  const G4ElectronOccupancy& eOcc);

    G4MolecularConfiguration*
      GetMolecularConfiguration(const G4MoleculeDefinition* molDef,
                                const G4ElectronOccupancy& eOcc);

    G4MolecularConfiguration*
      GetMolecularConfiguration(const G4MoleculeDefinition* molDef,
                                int charge);

    G4MolecularConfiguration*
      GetMolecularConfiguration(const G4MoleculeDefinition* molDef,
                                const G4String& label);

    G4MolecularConfiguration* GetMolecularConfiguration(int moleculeID);

    G4MolecularConfiguration* GetMolecularConfiguration(const G4String& userID);

    G4MolecularConfiguration*
      GetOrCreateMolecularConfiguration(const G4MoleculeDefinition* molDef,
                                        const G4ElectronOccupancy& eOcc);

    G4MolecularConfiguration*
      GetOrCreateMolecularConfiguration(const G4MoleculeDefinition* molDef,
                                        int charge);

    static G4Mutex fManagerCreationMutex;

    void RemoveMolecularConfigurationFromTable(G4MolecularConfiguration*);

    const std::vector<G4MolecularConfiguration*>& GetAllSpecies()
    {
      return fMolConfPerID;
    }

    std::map<G4String, G4MolecularConfiguration*>& GetUserIDTable()
    {
      return fUserIDTable;
    }

  private:

    //__________________________________________________________________________
    typedef std::map<G4ElectronOccupancy,
                     G4MolecularConfiguration*,
                     comparator> ElectronOccupancyTable;
    typedef std::map<const G4MoleculeDefinition*,
                     ElectronOccupancyTable > MolElectronConfTable;
    MolElectronConfTable fElecOccTable;

    //__________________________________________________________________________
    typedef std::map<int,
                     G4MolecularConfiguration*> ChargeTable;
    typedef std::map<const G4MoleculeDefinition*,
                     ChargeTable> MolChargeConfTable;
    MolChargeConfTable fChargeTable;

    //__________________________________________________________________________
    typedef std::map<const G4String,
                     G4MolecularConfiguration*> LabelTable;
    typedef std::map<const G4MoleculeDefinition*,
           std::map<const G4String, G4MolecularConfiguration*> > MolLabelConfTable;
    MolLabelConfTable fLabelTable;

    //__________________________________________________________________________
    typedef std::map<G4String, G4MolecularConfiguration*> UserIDTable;
    UserIDTable fUserIDTable;

    //__________________________________________________________________________
    std::vector<G4MolecularConfiguration*> fMolConfPerID;
    // Indexed by molecule ID

    //__________________________________________________________________________
    G4int fLastMoleculeID;
    G4Mutex fMoleculeCreationMutex;
  };

protected:
  static G4MolecularConfigurationManager* fgManager;
  static G4MolecularConfigurationManager* GetManager();

  const G4MoleculeDefinition* fMoleculeDefinition;
  const G4ElectronOccupancy* fElectronOccupancy;

  mutable G4String* fLabel;

  G4double fDynDiffusionCoefficient;
  G4double fDynVanDerVaalsRadius;
  G4double fDynDecayTime;
  G4double fDynMass;
  G4int fDynCharge;
  G4int fMoleculeID;
  /*mutable*/ G4String fFormatedName;
  /*mutable*/ G4String fName;
  G4String fUserIdentifier;
  G4bool fIsFinalized;

  G4DiffCoeffParam fDiffParam;
  static /*G4ThreadLocal*/double fgTemperature;

  static double ReturnDefaultDiffCoeff(const G4Material*,
                                       double,
                                       const G4MolecularConfiguration*
                                       molConf);
};

inline const G4MoleculeDefinition* G4MolecularConfiguration::GetDefinition() const
{
  return fMoleculeDefinition;
}

inline const G4ElectronOccupancy* G4MolecularConfiguration::GetElectronOccupancy() const
{
  return fElectronOccupancy;
}

inline void G4MolecularConfiguration::SetDiffusionCoefficient(G4double dynDiffusionCoefficient)
{
  MakeExceptionIfFinalized();
  fDynDiffusionCoefficient = dynDiffusionCoefficient;
}

inline G4double G4MolecularConfiguration::GetDiffusionCoefficient() const
{
  return fDynDiffusionCoefficient;
}

inline void G4MolecularConfiguration::SetDecayTime(G4double dynDecayTime)
{
  MakeExceptionIfFinalized();
  fDynDecayTime = dynDecayTime;
}

inline G4double G4MolecularConfiguration::GetDecayTime() const
{
  return fDynDecayTime;
}

inline void G4MolecularConfiguration::SetVanDerVaalsRadius(G4double dynVanDerVaalsRadius)
{
  MakeExceptionIfFinalized();
  fDynVanDerVaalsRadius = dynVanDerVaalsRadius;
}

inline G4double G4MolecularConfiguration::GetVanDerVaalsRadius() const
{
  return fDynVanDerVaalsRadius;
}

inline G4int G4MolecularConfiguration::GetCharge() const
{
  return fDynCharge;
}

inline void G4MolecularConfiguration::SetMass(G4double aMass)
{
  MakeExceptionIfFinalized();
  fDynMass = aMass;
}

inline G4double G4MolecularConfiguration::GetMass() const
{
  return fDynMass;
}

inline G4int G4MolecularConfiguration::GetMoleculeID() const
{
  return fMoleculeID;
}

inline void G4MolecularConfiguration::SetLabel(const G4String& label)
{
  assert(fLabel == 0 || *fLabel == "");
  if(fLabel == 0)
  {
    fLabel = new G4String(label);
  }
  else
  {
    *fLabel = label;
  }
  fgManager->RecordNewlyLabeledConfiguration(this);
}

inline const G4String& G4MolecularConfiguration::GetLabel() const
{
  if(fLabel == 0)
    fLabel = new G4String();

  return (*fLabel);
}

inline void G4MolecularConfiguration::Finalize()
{
  CreateDefaultDiffCoeffParam();
  fIsFinalized = true;
}

inline const G4String& G4MolecularConfiguration::GetUserID() const
{
  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);
}

#endif