Import Geant4 9.6.0 source tree

source/processes/electromagnetic/dna/utils/include/G4DNAChemistryManager.hh

@@ -23,6 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+// $Id: G4DNAChemistryManager.hh 64057 2012-10-30 15:04:49Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara@cenbg.in2p3.fr)
 //
@@ -44,13 +45,15 @@
 #include <memory>
 
 class G4Track;
-class G4WaterExcitationStructure;
-class G4WaterIonisationStructure;
+class G4DNAWaterExcitationStructure;
+class G4DNAWaterIonisationStructure;
+class G4Molecule;
 
 enum ElectronicModification
 {
-    fIonizedMolecule,
-    fExcitedMolecule
+    eIonizedMolecule,
+    eExcitedMolecule,
+    eDissociativeAttachment
 };
 
 /**
@@ -58,12 +61,18 @@ enum ElectronicModification
   * It creates the water molecules and the solvated electrons and
   * and send them to G4ITStepManager to be treated in the chemistry stage.
   * For this, the fActiveChemistry flag needs to be on.
+  * It is also possible to give already molecule's pointers already built.
+  * G4DNAChemistryManager will then be in charge of creating the track and loading
+  * it to the IT system.
   * The user can also ask to create a file containing a information about the
   * creation of water molecules and solvated electrons.
   */
 
 class G4DNAChemistryManager
 {
+    friend class std::auto_ptr<G4DNAChemistryManager>;
+    ~G4DNAChemistryManager();
+
 public:
     static G4DNAChemistryManager* Instance();
 
@@ -72,8 +81,6 @@ public:
       */
     static void DeleteInstance();
 
-    ~G4DNAChemistryManager();
-
     /**
       * Tells the chemMan to write into a file
       * the position and electronic state of the water molecule
@@ -106,9 +113,31 @@ public:
     void CreateSolvatedElectron(const G4Track* /*theIncomingTrack*/,
                                 G4ThreeVector* finalPosition = 0);
 
+    /**
+      * WARNING : In case chemistry is not activated, PushMolecule will take care
+      * of deleting the transfered molecule.
+      * Before calling this method, it is also possible to check if the chemistry is activated
+      * through IsChemistryActived().
+      * This method will create the track corresponding to the transfered molecule and will be in charge
+      * of loading the new track to the system.
+      */
+
+    void PushMolecule(G4Molecule*& molecule,
+                      double time, const G4ThreeVector& position, int parentID);
+
+    /**
+      * WARNING : In case chemistry is not activated, PushMoleculeAtParentTimeAndPlace
+      * will take care of deleting the transfered molecule.
+      * Before calling this method, it is also possible to check if the chemistry is activated
+      * through IsChemistryActived().
+      * This method will create the track corresponding to the transfered molecule and will be in charge
+      * of loading the new track to the system.
+      */
+    void PushMoleculeAtParentTimeAndPlace(G4Molecule*& molecule,
+                                          const G4Track* /*theIncomingTrack*/);
 protected :
-    G4WaterExcitationStructure* GetExcitationLevel();
-    G4WaterIonisationStructure* GetIonisationLevel();
+    G4DNAWaterExcitationStructure* GetExcitationLevel();
+    G4DNAWaterIonisationStructure* GetIonisationLevel();
 
 private:
     G4DNAChemistryManager();
@@ -118,8 +147,8 @@ private:
     std::ofstream  fOutput;
     G4bool fWriteFile;
 
-    G4WaterExcitationStructure* fExcitationLevel;
-    G4WaterIonisationStructure* fIonisationLevel;
+    G4DNAWaterExcitationStructure* fExcitationLevel;
+    G4DNAWaterIonisationStructure* fIonisationLevel;
 };
 
 inline G4bool G4DNAChemistryManager::IsChemistryActived()

source/processes/electromagnetic/dna/utils/include/G4DNACrossSectionDataSet.hh

@@ -24,8 +24,7 @@
 // ********************************************************************
 //
 //
-// $Id: G4DNACrossSectionDataSet.hh,v 1.7 2009-09-25 07:41:34 sincerti Exp $
-// GEANT4 tag $Name: not supported by cvs2svn $
+// $Id$
 //
 // Author: Riccardo Capra <capra@ge.infn.it>
 //
@@ -49,6 +48,8 @@
 #ifndef  G4DNACROSSSECTIONDATASET_HH
 #define  G4DNACROSSSECTIONDATASET_HH 1
 
+#include <CLHEP/Units/SystemOfUnits.h>
+
 #include "G4ShellEMDataSet.hh"
 
 class G4DNACrossSectionDataSet : public G4VEMDataSet
@@ -56,8 +57,8 @@ class G4DNACrossSectionDataSet : public G4VEMDataSet
 
 public:
   G4DNACrossSectionDataSet(G4VDataSetAlgorithm* algo, 
-			   G4double xUnit=MeV, 
-			   G4double dataUnit=barn);
+			   G4double xUnit=CLHEP::MeV, 
+			   G4double dataUnit=CLHEP::barn);
 
   virtual ~G4DNACrossSectionDataSet();
 

source/processes/electromagnetic/dna/utils/include/G4DNADamages.hh

@@ -0,0 +1,108 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// $Id: G4DNADamages.hh 65022 2012-11-12 16:43:12Z gcosmo $
+//
+#ifndef G4DNADAMAGES_HH
+#define G4DNADAMAGES_HH 1
+
+#include "G4Molecule.hh"
+
+class G4VDNAHit
+{
+public :
+    G4VDNAHit(){;}
+    virtual ~G4VDNAHit(){;}
+};
+
+class G4DNAIndirectHit : public G4VDNAHit
+{
+public :
+    G4DNAIndirectHit(const G4String& baseName, const G4Molecule* molecule,
+                     const G4ThreeVector& position, G4double time);
+    virtual ~G4DNAIndirectHit();
+
+    inline const G4Molecule* GetMolecule() {return fpMolecule;}
+    inline const G4ThreeVector& GetPosition() {return fPosition;}
+    inline const G4String& GetBaseName() {return fBaseName;}
+    inline double GetTime() {return fTime;}
+
+    void Print();
+
+protected :
+    const G4Molecule* fpMolecule;
+    G4ThreeVector fPosition;
+    G4double fTime;
+    G4String fBaseName;
+};
+
+class G4DNADamages
+{
+public:
+    static G4DNADamages* Instance();
+    static void DeleteInstance();
+
+    virtual void Reset();
+
+    //void AddDirectDamage();
+    virtual void AddIndirectDamage(const G4String& baseName,const G4Molecule* molecule,
+                           const G4ThreeVector& position, double time);
+
+    inline const std::vector<G4DNAIndirectHit*>* GetIndirectHits();
+    inline virtual int GetNIndirectHits() const
+    {
+        if(fJustCountDamage)
+            return fNIndirectDamages;
+
+        return fIndirectHits.size();
+    }
+
+    inline virtual void SetOnlyCountDamages(bool flag = true)
+    {
+        fJustCountDamage = flag;
+    }
+
+    inline virtual bool OnlyCountDamages() const
+    {
+        return fJustCountDamage;
+    }
+
+protected :
+    G4DNADamages();
+    static G4DNADamages* fpInstance;
+    virtual ~G4DNADamages();
+
+    G4bool fJustCountDamage;
+    G4int fNIndirectDamages;
+    std::vector<G4DNAIndirectHit*> fIndirectHits;
+    std::map<G4Molecule, const G4Molecule*> fMolMap;
+};
+
+inline const std::vector<G4DNAIndirectHit*>* G4DNADamages::GetIndirectHits()
+{
+    return &fIndirectHits;
+}
+
+#endif // G4DNADAMAGES_HH

source/processes/electromagnetic/dna/utils/include/G4DNAGenericIonsManager.hh

@@ -24,8 +24,7 @@
 // ********************************************************************
 //
 //
-// $Id: G4DNAGenericIonsManager.hh,v 1.4 2009-06-10 13:32:58 mantero Exp $
-// GEANT4 tag $Name: not supported by cvs2svn $
+// $Id$
 
 #ifndef   G4DNAGENERICIONSMANAGER_HH
  #define  G4DNAGENERICIONSMANAGER_HH 1

source/processes/electromagnetic/dna/utils/include/G4DNAMolecularMaterial.hh

@@ -0,0 +1,102 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// $Id: G4DNAMolecularMaterial.hh 64057 2012-10-30 15:04:49Z gcosmo $
+//
+#ifndef G4DNAMolecularMaterial_HH
+#define G4DNAMolecularMaterial_HH
+
+#include "globals.hh"
+#include "G4ios.hh"
+#include <map>
+#include <vector>
+#include "G4VStateDependent.hh"
+
+class G4Material;
+
+struct CompareMaterial
+{
+    // If the materials derives from a base material,
+    // it should be able to find the derived material using the base material.
+    bool operator() (const G4Material* mat1, const G4Material* mat2) const;
+};
+
+typedef std::map<const G4Material*, double,CompareMaterial> ComponentMap;
+
+// G4DNAMolecularMaterial is initialized when G4ApplicationState == G4State_Idle
+
+class G4DNAMolecularMaterial : public G4VStateDependent
+{
+public:
+    static G4DNAMolecularMaterial* Instance();
+    void DeleteInstance();
+    void Initialize();
+
+    virtual G4bool Notify(G4ApplicationState requestedState) ;
+
+    inline const std::vector<ComponentMap>* GetMassFractionTable() const;
+    inline const std::vector<ComponentMap>* GetDensityTable() const;
+//    const std::vector<double>* GetMassFractionTableFor(const G4Material*) const;
+    const std::vector<double>* GetDensityTableFor(const G4Material*) const;
+    const std::vector<double>* GetNumMolPerVolTableFor(const G4Material*) const;
+
+protected :
+    static G4DNAMolecularMaterial* fInstance;
+    G4DNAMolecularMaterial();
+    G4DNAMolecularMaterial(const G4DNAMolecularMaterial& right);
+    G4DNAMolecularMaterial& operator=(const G4DNAMolecularMaterial&);
+    virtual ~G4DNAMolecularMaterial();
+    void Create();
+    void InitializeNumMolPerVol();
+    void InitializeDensity();
+    void RecordMolecularMaterial(G4Material* parentMaterial, G4Material* molecularMaterial, G4double fraction);
+    void SearchMolecularMaterial(G4Material* parentMaterial, G4Material* material, double currentFraction);
+
+    void AddMaterial(const G4Material*, double fraction);
+
+    void PrintNotAMolecularMaterial(const char* methodName, const G4Material* lookForMaterial) const;
+
+    std::vector<ComponentMap>* fpCompFractionTable;
+    std::vector<ComponentMap>* fpCompDensityTable;
+    std::vector<ComponentMap>* fpCompNumMolPerVolTable;
+
+    mutable std::map<const G4Material*,std::vector<double>*,CompareMaterial> fAskedDensityTable;
+    mutable std::map<const G4Material*,std::vector<double>*,CompareMaterial> fAskedNumPerVolTable;
+    mutable std::map<const G4Material*,bool,CompareMaterial> fWarningPrinted;
+
+    G4bool fIsInitialized;
+};
+
+inline const std::vector<ComponentMap> *G4DNAMolecularMaterial::GetMassFractionTable() const
+{
+    return fpCompFractionTable;
+}
+
+inline const std::vector<ComponentMap>* G4DNAMolecularMaterial::GetDensityTable() const
+{
+    return fpCompDensityTable;
+}
+
+#endif // G4DNAMolecularMaterial_HH

source/processes/electromagnetic/dna/utils/include/G4DNAMolecularReactionTable.hh

@@ -23,6 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+// $Id: G4DNAMolecularReactionTable.hh 64057 2012-10-30 15:04:49Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr) 
 //

source/processes/electromagnetic/dna/utils/include/G4DNAWaterExcitationStructure.hh

@@ -23,20 +23,20 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 
-#ifndef G4WATEREXCITATIONSTRUCTURE_HH
-#define G4WATEREXCITATIONSTRUCTURE_HH 1
+#ifndef G4DNAWATEREXCITATIONSTRUCTURE_HH
+#define G4DNAWATEREXCITATIONSTRUCTURE_HH 1
  
 #include "globals.hh"
 #include <vector>
 
  
-class G4WaterExcitationStructure
+class G4DNAWaterExcitationStructure
 {
 public:
   
-  G4WaterExcitationStructure();
+  G4DNAWaterExcitationStructure();
   
-  virtual ~G4WaterExcitationStructure();
+  virtual ~G4DNAWaterExcitationStructure();
   
   G4double ExcitationEnergy(G4int level);
 

source/processes/electromagnetic/dna/utils/include/G4DNAWaterIonisationStructure.hh

@@ -23,20 +23,20 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 
-#ifndef G4WATERIONISATIONSTRUCTURE_HH
-#define G4WATERIONISATIONSTRUCTURE_HH 1
+#ifndef G4DNAWATERIONISATIONSTRUCTURE_HH
+#define G4DNAWATERIONISATIONSTRUCTURE_HH 1
  
 #include "globals.hh"
 #include <vector>
 
  
-class G4WaterIonisationStructure
+class G4DNAWaterIonisationStructure
 {
 public:
   
-  G4WaterIonisationStructure();
+  G4DNAWaterIonisationStructure();
   
-  virtual ~G4WaterIonisationStructure();
+  virtual ~G4DNAWaterIonisationStructure();
   
   G4double IonisationEnergy(G4int level);
 

source/processes/electromagnetic/dna/utils/include/G4VDNAReactionModel.hh

@@ -23,6 +23,8 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+// $Id: G4VDNAReactionModel.hh 64057 2012-10-30 15:04:49Z gcosmo $
+//
 #ifndef G4VReactionModel_
 #define G4VReactionModel_