Gabriele Cosmo
359 lines
11 KiB
C++
359 lines
11 KiB
C++
//
|
||
// ********************************************************************
|
||
// * License and Disclaimer *
|
||
// * *
|
||
// * The Geant4 software is copyright of the Copyright Holders of *
|
||
// * the Geant4 Collaboration. It is provided under the terms and *
|
||
// * conditions of the Geant4 Software License, included in the file *
|
||
// * LICENSE and available at http://cern.ch/geant4/license . These *
|
||
// * include a list of copyright holders. *
|
||
// * *
|
||
// * Neither the authors of this software system, nor their employing *
|
||
// * institutes,nor the agencies providing financial support for this *
|
||
// * work make any representation or warranty, express or implied, *
|
||
// * regarding this software system or assume any liability for its *
|
||
// * use. Please see the license in the file LICENSE and URL above *
|
||
// * for the full disclaimer and the limitation of liability. *
|
||
// * *
|
||
// * This code implementation is the result of the scientific and *
|
||
// * technical work of the GEANT4 collaboration. *
|
||
// * By using, copying, modifying or distributing the software (or *
|
||
// * any work based on the software) you agree to acknowledge its *
|
||
// * use in resulting scientific publications, and indicate your *
|
||
// * acceptance of all terms of the Geant4 Software license. *
|
||
// ********************************************************************
|
||
//
|
||
//
|
||
// 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 <CLHEP/Utility/memory.h>
|
||
#include "G4Threading.hh"
|
||
|
||
class G4MolecularDissociationChannel;
|
||
class G4MoleculeDefinition;
|
||
|
||
#include "G4ElectronOccupancy.hh"
|
||
|
||
struct comparator
|
||
{
|
||
bool operator()(const G4ElectronOccupancy& occ1,
|
||
const G4ElectronOccupancy& occ2) const
|
||
{
|
||
// Since this method is called a lot of time,
|
||
// we retrieve only once the totOcc
|
||
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 < occ1.GetSizeOfOrbit();)
|
||
{
|
||
// Since this method is called a lot of time,
|
||
// we retrieve only once the Occ
|
||
|
||
occupancy1 = occ1.GetOccupancy(i);
|
||
occupancy2 = occ2.GetOccupancy(i);
|
||
|
||
if (occupancy1 != occupancy2)
|
||
{
|
||
return occupancy1 < occupancy2;
|
||
}
|
||
else
|
||
{
|
||
i++;
|
||
if (i >= sizeOrbit) return false;
|
||
}
|
||
}
|
||
}
|
||
return false;
|
||
}
|
||
};
|
||
|
||
/** The pointer G4MolecularConfiguration will be shared by all the
|
||
* molecules having the same molecule definition and the same
|
||
* electron occupancy
|
||
* BE CAREFUlL !!! : If you change the mass for instance of a OH^-,
|
||
* this will affect all the OH^- molecule diffusing around
|
||
*/
|
||
class G4MolecularConfiguration
|
||
{
|
||
public:
|
||
|
||
/////////////////
|
||
// Static methods
|
||
|
||
// Get ground state electronic configuration
|
||
static G4MolecularConfiguration* GetMolecularConfiguration(const G4MoleculeDefinition*);
|
||
|
||
// Get for a given moleculeDefinition and a given electronic configuration, the mol conf
|
||
static G4MolecularConfiguration* GetMolecularConfiguration(const G4MoleculeDefinition*,
|
||
const G4ElectronOccupancy& electronOccupancy);
|
||
|
||
// Get for a given moleculeDefinition and a given electronic configuration, the mol conf
|
||
static G4MolecularConfiguration* GetMolecularConfiguration(const G4MoleculeDefinition*,
|
||
int charge);
|
||
|
||
// Release memory of the mol conf manager
|
||
static void DeleteManager();
|
||
///////////////
|
||
|
||
// Methods
|
||
const G4MoleculeDefinition* GetDefinition() const;
|
||
|
||
/** Returns the name of the molecule
|
||
*/
|
||
const G4String& GetName() const;
|
||
|
||
/** Returns the formated name of the molecule
|
||
*/
|
||
const G4String& GetFormatedName() const;
|
||
|
||
/** Returns the nomber of atoms compouning the molecule
|
||
*/
|
||
G4int GetAtomsNumber() const;
|
||
|
||
/** Method used in Geant4-DNA to excite water molecules
|
||
*/
|
||
G4MolecularConfiguration* ExciteMolecule(G4int);
|
||
|
||
/** Method used in Geant4-DNA to ionize water molecules
|
||
*/
|
||
G4MolecularConfiguration* 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.
|
||
*/
|
||
G4MolecularConfiguration* AddElectron(G4int orbit, G4int n = 1);
|
||
|
||
/** Remove n electrons to a given orbit.
|
||
*/
|
||
G4MolecularConfiguration* RemoveElectron(G4int, G4int number = 1);
|
||
|
||
/** Move one electron from an orbit to another.
|
||
*/
|
||
G4MolecularConfiguration* MoveOneElectron(G4int /*orbit*/, G4int /*orbit*/);
|
||
|
||
/** Returns the number of electron.
|
||
*/
|
||
G4double GetNbElectrons() const;
|
||
|
||
/** Display the electronic state of the molecule.
|
||
*/
|
||
void PrintState() const;
|
||
|
||
const std::vector<const G4MolecularDissociationChannel*>* GetDecayChannel() const;
|
||
|
||
G4int GetFakeParticleID() const;
|
||
|
||
inline G4int GetMoleculeID() const;
|
||
|
||
/** 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.
|
||
*
|
||
* Note : Diffusion Coefficient in one medium only
|
||
* For the time being, we will consider only one diffusion
|
||
* coefficient for the all simulation => diffusion in one medium only
|
||
* If the user needs to use the diffusion in different materials,
|
||
* she/he should contact the developpers/mainteners of this package
|
||
*/
|
||
inline void SetDiffusionCoefficient(G4double);
|
||
|
||
/** Returns the diffusion coefficient D.
|
||
*/
|
||
inline G4double GetDiffusionCoefficient() const;
|
||
|
||
/** Set the decay time of the molecule.
|
||
*/
|
||
inline void SetDecayTime(G4double);
|
||
|
||
/** Returns the decay time of the molecule.
|
||
*/
|
||
inline G4double GetDecayTime() const;
|
||
|
||
/** The Van Der Valls Radius of the molecule
|
||
*/
|
||
inline void SetVanDerVaalsRadius(G4double);
|
||
inline G4double GetVanDerVaalsRadius() const;
|
||
|
||
/** Returns the object ElectronOccupancy describing the electronic
|
||
* configuration of the molecule.
|
||
*/
|
||
inline const G4ElectronOccupancy* GetElectronOccupancy() const;
|
||
|
||
/** Returns the charge of molecule.
|
||
*/
|
||
inline G4int GetCharge() const;
|
||
|
||
/** Set the total mass of the molecule.
|
||
*/
|
||
inline void SetMass(G4double);
|
||
|
||
/** Returns the total mass of the molecule.
|
||
*/
|
||
inline G4double GetMass() const;
|
||
|
||
protected:
|
||
G4MolecularConfiguration(const G4MoleculeDefinition*,
|
||
const G4ElectronOccupancy&);
|
||
G4MolecularConfiguration(const G4MoleculeDefinition*, int);
|
||
G4MolecularConfiguration(const G4MolecularConfiguration&);
|
||
G4MolecularConfiguration & operator=(G4MolecularConfiguration &right);
|
||
~G4MolecularConfiguration();
|
||
G4MolecularConfiguration* ChangeConfiguration(const G4ElectronOccupancy& newElectronOccupancy);
|
||
G4MolecularConfiguration* ChangeConfiguration(int charge);
|
||
|
||
const G4MoleculeDefinition* fMoleculeDefinition;
|
||
const G4ElectronOccupancy* fElectronOccupancy;
|
||
|
||
void CheckElectronOccupancy(const char* line) const;
|
||
|
||
public:
|
||
class G4MolecularConfigurationManager
|
||
{
|
||
public:
|
||
G4MolecularConfigurationManager() :
|
||
fMoleculeCreationMutex()
|
||
{
|
||
fLastMoleculeID = -1;
|
||
}
|
||
~G4MolecularConfigurationManager();
|
||
|
||
G4int SetMolecularConfiguration(const G4MoleculeDefinition* molDef,
|
||
const G4ElectronOccupancy& eOcc,
|
||
G4MolecularConfiguration* molConf);
|
||
|
||
G4int SetMolecularConfiguration(const G4MoleculeDefinition* molDef,
|
||
int charge,
|
||
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);
|
||
|
||
static G4Mutex fManagerCreationMutex;
|
||
|
||
void RemoveMolecularConfigurationFromTable(G4MolecularConfiguration*);
|
||
|
||
private:
|
||
typedef std::map<const G4MoleculeDefinition*,
|
||
std::map<G4ElectronOccupancy, G4MolecularConfiguration*, comparator> > MolecularConfigurationTable;
|
||
MolecularConfigurationTable fTable;
|
||
typedef std::map<const G4MoleculeDefinition*,
|
||
std::map<int, G4MolecularConfiguration*, comparator> > MolChargeConfigurationTable;
|
||
MolChargeConfigurationTable fChargeTable;
|
||
G4int fLastMoleculeID;
|
||
|
||
G4Mutex fMoleculeCreationMutex;
|
||
};
|
||
|
||
protected:
|
||
static G4MolecularConfigurationManager* fgManager;
|
||
static G4MolecularConfigurationManager* GetManager();
|
||
|
||
G4double fDynDiffusionCoefficient;
|
||
G4double fDynVanDerVaalsRadius;
|
||
G4double fDynDecayTime;
|
||
G4double fDynMass;
|
||
G4int fDynCharge;
|
||
G4int fMoleculeID;
|
||
/*mutable*/ G4String fFormatedName;
|
||
/*mutable*/ G4String fName;
|
||
};
|
||
|
||
inline const G4MoleculeDefinition* G4MolecularConfiguration::GetDefinition() const
|
||
{
|
||
return fMoleculeDefinition;
|
||
}
|
||
|
||
inline const G4ElectronOccupancy* G4MolecularConfiguration::GetElectronOccupancy() const
|
||
{
|
||
return fElectronOccupancy;
|
||
}
|
||
|
||
inline void G4MolecularConfiguration::SetDiffusionCoefficient(G4double dynDiffusionCoefficient)
|
||
{
|
||
fDynDiffusionCoefficient = dynDiffusionCoefficient;
|
||
}
|
||
|
||
inline G4double G4MolecularConfiguration::GetDiffusionCoefficient() const
|
||
{
|
||
return fDynDiffusionCoefficient;
|
||
}
|
||
|
||
inline void G4MolecularConfiguration::SetDecayTime(G4double dynDecayTime)
|
||
{
|
||
fDynDecayTime = dynDecayTime;
|
||
}
|
||
|
||
inline G4double G4MolecularConfiguration::GetDecayTime() const
|
||
{
|
||
return fDynDecayTime;
|
||
}
|
||
|
||
inline void G4MolecularConfiguration::SetVanDerVaalsRadius(G4double dynVanDerVaalsRadius)
|
||
{
|
||
fDynVanDerVaalsRadius = dynVanDerVaalsRadius;
|
||
}
|
||
|
||
inline G4double G4MolecularConfiguration::GetVanDerVaalsRadius() const
|
||
{
|
||
return fDynVanDerVaalsRadius;
|
||
}
|
||
|
||
inline G4int G4MolecularConfiguration::GetCharge() const
|
||
{
|
||
return fDynCharge;
|
||
}
|
||
|
||
inline void G4MolecularConfiguration::SetMass(G4double aMass)
|
||
{
|
||
fDynMass = aMass;
|
||
}
|
||
|
||
inline G4double G4MolecularConfiguration::GetMass() const
|
||
{
|
||
return fDynMass;
|
||
}
|
||
|
||
inline G4int G4MolecularConfiguration::GetMoleculeID() const
|
||
{
|
||
return fMoleculeID;
|
||
}
|
||
#endif
|