Import Geant4 10.0.0 source tree

source/processes/electromagnetic/dna/utils/CMakeLists.txt

@@ -7,7 +7,7 @@
 #
 # Generated on : 24/9/2010
 #
-# $Id: CMakeLists.txt,v 1.1 2010-09-29 18:53:09 bmorgan Exp $
+# $Id: CMakeLists.txt 66892 2013-01-17 10:57:59Z gunter $
 #
 #------------------------------------------------------------------------------
 

source/processes/electromagnetic/dna/utils/GNUmakefile

@@ -1,4 +1,4 @@
-# $Id: GNUmakefile,v 1.8 2009-06-18 16:18:41 mantero Exp $
+# $Id: GNUmakefile 66892 2013-01-17 10:57:59Z gunter $
 # --------------------------------------------------------------------
 # GNUmakefile for electromagnetic sub-library.  John Allison, 25/6/98.
 # --------------------------------------------------------------------

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

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4DNAChemistryManager.hh 64057 2012-10-30 15:04:49Z gcosmo $
+// $Id: G4DNAChemistryManager.hh 75583 2013-11-04 12:16:46Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara@cenbg.in2p3.fr)
 //
@@ -59,7 +59,7 @@ enum ElectronicModification
 /**
   * G4DNAChemistryManager is called from the physics models.
   * It creates the water molecules and the solvated electrons and
-  * and send them to G4ITStepManager to be treated in the chemistry stage.
+  * and send them to synchronous step manager 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
@@ -81,6 +81,7 @@ public:
       */
     static void DeleteInstance();
 
+
     /**
       * Tells the chemMan to write into a file
       * the position and electronic state of the water molecule
@@ -135,17 +136,21 @@ public:
       */
     void PushMoleculeAtParentTimeAndPlace(G4Molecule*& molecule,
                                           const G4Track* /*theIncomingTrack*/);
+
+
+    void AddEmptyLineInOuputFile();
+
 protected :
     G4DNAWaterExcitationStructure* GetExcitationLevel();
     G4DNAWaterIonisationStructure* GetIonisationLevel();
+    void InitializeFile();
+    G4DNAChemistryManager();
 
 private:
-    G4DNAChemistryManager();
     static std::auto_ptr<G4DNAChemistryManager> fInstance;
     bool fActiveChemistry;
-
-    std::ofstream  fOutput;
     G4bool fWriteFile;
+    static G4ThreadLocal std::ofstream*  fOutput;
 
     G4DNAWaterExcitationStructure* fExcitationLevel;
     G4DNAWaterIonisationStructure* fIonisationLevel;

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

@@ -24,7 +24,7 @@
 // ********************************************************************
 //
 //
-// $Id$
+// $Id: G4DNACrossSectionDataSet.hh 70171 2013-05-24 13:34:18Z gcosmo $
 //
 // Author: Riccardo Capra <capra@ge.infn.it>
 //

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

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4DNADamages.hh 65022 2012-11-12 16:43:12Z gcosmo $
+// $Id: G4DNADamages.hh 66872 2013-01-15 01:25:57Z japost $
 //
 #ifndef G4DNADAMAGES_HH
 #define G4DNADAMAGES_HH 1
@@ -91,7 +91,7 @@ public:
 
 protected :
     G4DNADamages();
-    static G4DNADamages* fpInstance;
+    static G4ThreadLocal G4DNADamages* fpInstance;
     virtual ~G4DNADamages();
 
     G4bool fJustCountDamage;

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

@@ -24,7 +24,7 @@
 // ********************************************************************
 //
 //
-// $Id$
+// $Id: G4DNAGenericIonsManager.hh 73124 2013-08-19 07:53:33Z gcosmo $
 
 #ifndef   G4DNAGENERICIONSMANAGER_HH
  #define  G4DNAGENERICIONSMANAGER_HH 1
@@ -33,7 +33,7 @@
  
  #include <map>
  
- class G4Ions;
+ class G4DNAIons;
  class G4ParticleDefinition;
  
  class G4DNAGenericIonsManager

source/processes/electromagnetic/dna/utils/include/G4DNAIons.hh

@@ -0,0 +1,126 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// 31.07.2013: Derived from G4Ions for MT migration (SI)
+// Suggested by Makoto et al.
+
+#ifndef G4DNAIons_h
+#define G4DNAIons_h 1
+
+#include "globals.hh"
+#include "G4ios.hh"
+#include "G4ParticleDefinition.hh"
+
+// ######################################################################
+// ###                          G4DNAIons                                 ###
+// ######################################################################
+
+class G4DNAIons : public G4ParticleDefinition
+{
+ // Class Description
+ //  This is the base class for all Geant4-DNA nuclei, including
+ //  charged states 
+
+ protected:
+   G4DNAIons(){};
+
+
+ public:
+   G4DNAIons(
+       const G4String&     aName,        G4double            mass,
+       G4double            width,        G4double            charge,   
+       G4int               iSpin,        G4int               iParity,    
+       G4int               iConjugation, G4int               iIsospin,   
+       G4int               iIsospin3,    G4int               gParity,
+       const G4String&     pType,        G4int               lepton,      
+       G4int               baryon,       G4int               encoding,
+       G4bool              stable,       G4double            lifetime,
+       G4DecayTable        *decaytable,  G4bool              shortlived,
+       const G4String&     subType ="",
+       G4int               anti_encoding =0,
+       G4double            excitation = 0.0, 
+       G4int               isomer = 0
+   );
+
+ public:
+   virtual    			~G4DNAIons();
+   G4DNAIons*    		IonsDefinition();
+   G4DNAIons*    		Ions();
+
+ public:
+  
+  // Get excitation energy of nucleus
+  G4double GetExcitationEnergy() const ; 
+  
+  // Get Isomer level (=0 for ground state)
+  G4int GetIsomerLevel() const; 
+   
+  private:
+  G4double theExcitationEnergy; 
+  G4int    theIsomerLevel;
+
+};
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+inline
+ G4DNAIons* G4DNAIons::IonsDefinition()
+{
+  return this;
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+inline
+ G4DNAIons* G4DNAIons::Ions() 
+{
+  return this;
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+inline
+ G4double G4DNAIons::GetExcitationEnergy() const 
+{
+  return theExcitationEnergy;
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+inline
+ G4int G4DNAIons::GetIsomerLevel() const
+{
+  return theIsomerLevel;
+}
+    
+#endif
+
+
+
+
+
+
+
+

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

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4DNAMolecularMaterial.hh 64057 2012-10-30 15:04:49Z gcosmo $
+// $Id: G4DNAMolecularMaterial.hh 70171 2013-05-24 13:34:18Z gcosmo $
 //
 #ifndef G4DNAMolecularMaterial_HH
 #define G4DNAMolecularMaterial_HH
@@ -64,6 +64,7 @@ public:
 
 protected :
     static G4DNAMolecularMaterial* fInstance;
+//    static G4ThreadLocal G4DNAMolecularMaterial* fInstance;
     G4DNAMolecularMaterial();
     G4DNAMolecularMaterial(const G4DNAMolecularMaterial& right);
     G4DNAMolecularMaterial& operator=(const G4DNAMolecularMaterial&);

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

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4DNAMolecularReactionTable.hh 64057 2012-10-30 15:04:49Z gcosmo $
+// $Id: G4DNAMolecularReactionTable.hh 70171 2013-05-24 13:34:18Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr) 
 //
@@ -113,6 +113,7 @@ class G4DNAMolecularReactionTable : public G4ITReactionTable
 protected:
     G4DNAMolecularReactionTable();
     static G4DNAMolecularReactionTable* fInstance;
+//    static G4ThreadLocal G4DNAMolecularReactionTable* fInstance;
 
 public :
     static G4DNAMolecularReactionTable* GetReactionTable();

source/processes/electromagnetic/dna/utils/sources.cmake

@@ -11,7 +11,7 @@
 #
 # Generated on : 24/9/2010
 #
-# $Id: sources.cmake,v 1.4 2010-11-15 08:24:43 gcosmo Exp $
+# $Id: sources.cmake 73081 2013-08-16 12:58:22Z gcosmo $
 #
 #------------------------------------------------------------------------------
 
@@ -52,6 +52,7 @@ GEANT4_DEFINE_MODULE(NAME G4emdna-utils
         G4DNACrossSectionDataSet.hh
         G4DNADamages.hh
         G4DNAGenericIonsManager.hh
+	G4DNAIons.hh
         G4DNAMolecularReactionTable.hh
         G4DNAWaterExcitationStructure.hh
         G4DNAWaterIonisationStructure.hh
@@ -62,6 +63,7 @@ GEANT4_DEFINE_MODULE(NAME G4emdna-utils
         G4DNACrossSectionDataSet.cc
         G4DNADamages.cc
         G4DNAGenericIonsManager.cc
+	G4DNAIons.cc
         G4DNAMolecularReactionTable.cc
         G4DNAWaterExcitationStructure.cc
         G4DNAWaterIonisationStructure.cc

source/processes/electromagnetic/dna/utils/src/G4DNAChemistryManager.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4DNAChemistryManager.cc 64057 2012-10-30 15:04:49Z gcosmo $
+// $Id: G4DNAChemistryManager.cc 75583 2013-11-04 12:16:46Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara@cenbg.in2p3.fr)
 //
@@ -48,270 +48,294 @@
 #include "G4ITManager.hh"
 #include "G4MolecularConfiguration.hh"
 #include "G4MoleculeCounter.hh"
+#include "G4Tokenizer.hh"
+#include "G4AutoLock.hh"
 
 using namespace std;
 
-auto_ptr<G4DNAChemistryManager> G4DNAChemistryManager::fInstance(0);
+auto_ptr<G4DNAChemistryManager> G4DNAChemistryManager::fInstance ;
+G4ThreadLocal std::ofstream*  G4DNAChemistryManager::fOutput = 0;
+G4Mutex chemManExistence;
 
 G4DNAChemistryManager::G4DNAChemistryManager() :
-    fActiveChemistry(false)
+ 		fActiveChemistry(false)
 {
-    fExcitationLevel = 0;
-    fIonisationLevel = 0;
-    fWriteFile       = false;
+	fExcitationLevel = 0;
+	fIonisationLevel = 0;
+	fWriteFile       = false;
 }
 
 G4DNAChemistryManager* G4DNAChemistryManager::Instance()
 {
-    if(!fInstance.get()) fInstance = auto_ptr<G4DNAChemistryManager>(new G4DNAChemistryManager());
-    return fInstance.get();
+	if (fInstance.get() == 0)
+	{
+		G4AutoLock lock(&chemManExistence);
+		if(fInstance.get() == 0) // MT : double check at initialisation
+		{
+			fInstance = auto_ptr<G4DNAChemistryManager> (new G4DNAChemistryManager()) ;
+		}
+		lock.unlock();
+	}
+	return fInstance.get();
 }
 
 G4DNAChemistryManager::~G4DNAChemistryManager()
 {
-    if (fOutput.is_open())
-    {
-        fOutput.close();
-    }
-    if(fIonisationLevel) delete fIonisationLevel;
-    if(fExcitationLevel) delete fExcitationLevel;
-    G4DNAMolecularReactionTable::DeleteInstance();
-    G4MoleculeHandleManager::DeleteInstance();
-    G4MolecularConfiguration::DeleteManager();
-    fInstance.release();
-    G4MoleculeCounter::DeleteInstance();
+	if(fIonisationLevel) delete fIonisationLevel;
+	if(fExcitationLevel) delete fExcitationLevel;
+	G4DNAMolecularReactionTable::DeleteInstance();
+	G4MoleculeHandleManager::DeleteInstance();
+	G4MolecularConfiguration::DeleteManager();
+	fInstance.release();
+	G4MoleculeCounter::DeleteInstance();
 }
 
 void G4DNAChemistryManager::DeleteInstance()
 {
-    if(fInstance.get())
-        fInstance.reset();
+	G4AutoLock lock(&chemManExistence);
+	if(fInstance.get())
+	{
+		fInstance.reset();
+	}
+}
+
+void G4DNAChemistryManager::InitializeFile()
+{
+	*fOutput << std::setprecision(6) << std::scientific;
+	*fOutput << setw(11) << left << "#Parent ID"
+			<< setw(10) << "Molecule"
+			<< setw(14) << "Elec Modif"
+			<< setw(13) << "Energy (eV)"
+			<< setw(22) << "X pos of parent [nm]"
+			<< setw(22) << "Y pos of parent [nm]"
+			<< setw(22) << "Z pos of parent [nm]"
+			<< setw(14) << "X pos [nm]"
+			<< setw(14) << "Y pos [nm]"
+			<< setw(14) << "Z pos [nm]"
+			<< G4endl
+			<< setw(21) << "#"
+			<< setw(13) << "1)io/ex=0/1"
+			<< G4endl
+			<< setw(21) << "#"
+			<< setw(13) << "2)level=0...5"
+			<< G4endl;
 }
 
 void G4DNAChemistryManager::WriteInto(const G4String& output,
-                                      ios_base::openmode mode)
+		ios_base::openmode mode)
 {
-    fOutput.open(output.data(), mode);
-    fOutput << std::setprecision(6) << std::scientific;
-
-    fOutput << setw(11) << left << "#Parent ID"
-            << setw(10) << "Molecule"
-            << setw(14) << "Elec Modif"
-            << setw(13) << "Energy (eV)"
-            << setw(22) << "X pos of parent [nm]"
-            << setw(22) << "Y pos of parent [nm]"
-            << setw(22) << "Z pos of parent [nm]"
-            << setw(14) << "X pos [nm]"
-            << setw(14) << "Y pos [nm]"
-            << setw(14) << "Z pos [nm]"
-            << G4endl
-            << setw(21) << "#"
-            << setw(13) << "1)io/ex=0/1"
-            << G4endl
-            << setw(21) << "#"
-            << setw(13) << "2)level=0...5"
-            << G4endl;
-    fWriteFile = true;
+	fOutput =  new std::ofstream();
+	fOutput->open(output.data(), mode);
+	fWriteFile = true;
 }
 
 void G4DNAChemistryManager::CloseFile()
 {
-    if (fOutput.is_open())
-    {
-        fOutput.close();
-    }
-    fWriteFile = false;
+	if (fOutput->is_open())
+	{
+		fOutput->close();
+	}
+
+	fWriteFile = false;
 }
 
 G4DNAWaterExcitationStructure* G4DNAChemistryManager::GetExcitationLevel()
 {
-    if(!fExcitationLevel)
-    {
-        fExcitationLevel = new G4DNAWaterExcitationStructure;
-    }
-    return fExcitationLevel;
+	if(!fExcitationLevel)
+	{
+		fExcitationLevel = new G4DNAWaterExcitationStructure;
+	}
+	return fExcitationLevel;
 }
 
 G4DNAWaterIonisationStructure* G4DNAChemistryManager::GetIonisationLevel()
 {
-    if(!fIonisationLevel)
-    {
-        fIonisationLevel = new G4DNAWaterIonisationStructure;
-    }
-    return fIonisationLevel;
+	if(!fIonisationLevel)
+	{
+		fIonisationLevel = new G4DNAWaterIonisationStructure;
+	}
+	return fIonisationLevel;
 }
 
 void G4DNAChemistryManager::CreateWaterMolecule(ElectronicModification modification,
-                                                G4int electronicLevel,
-                                                const G4Track* theIncomingTrack)
+		G4int electronicLevel,
+		const G4Track* theIncomingTrack)
 {
-    if(fWriteFile)
-    {
-        G4double energy = -1.;
+	if(fWriteFile)
+	{
+		G4double energy = -1.;
 
-        switch (modification)
-        {
-        case eDissociativeAttachment:
-            energy = -1;
-            break;
-        case eExcitedMolecule :
-            energy = GetExcitationLevel()->ExcitationEnergy(electronicLevel);
-            break;
-        case eIonizedMolecule :
-            energy = GetIonisationLevel()->IonisationEnergy(electronicLevel);
-            break;
-        }
+		switch (modification)
+		{
+		case eDissociativeAttachment:
+			energy = -1;
+			break;
+		case eExcitedMolecule :
+			energy = GetExcitationLevel()->ExcitationEnergy(electronicLevel);
+			break;
+		case eIonizedMolecule :
+			energy = GetIonisationLevel()->IonisationEnergy(electronicLevel);
+			break;
+		}
 
-        fOutput << setw(11) << left << theIncomingTrack->GetTrackID()
-                << setw(10) << "H2O"
-                << left << modification
-                << internal <<":"
-                << right <<electronicLevel
-                << left
-                << setw(11) << ""
-                << std::setprecision(2) << std::fixed
-                << setw(13) << energy/eV
-                << std::setprecision(6) << std::scientific
-                << setw(22) << (theIncomingTrack->GetPosition().x())/nanometer
-                << setw(22) << (theIncomingTrack->GetPosition().y())/nanometer
-                << setw(22) << (theIncomingTrack->GetPosition().z())/nanometer
-                << G4endl;
-    }
+		*fOutput << setw(11) << left << theIncomingTrack->GetTrackID()
+                								<< setw(10) << "H2O"
+                								<< left << modification
+                								<< internal <<":"
+                								<< right <<electronicLevel
+                								<< left
+                								<< setw(11) << ""
+                								<< std::setprecision(2) << std::fixed
+                								<< setw(13) << energy/eV
+                								<< std::setprecision(6) << std::scientific
+                								<< setw(22) << (theIncomingTrack->GetPosition().x())/nanometer
+                								<< setw(22) << (theIncomingTrack->GetPosition().y())/nanometer
+                								<< setw(22) << (theIncomingTrack->GetPosition().z())/nanometer
+                								<< G4endl;
+	}
 
-    if(fActiveChemistry)
-    {
-        G4Molecule * H2O = new G4Molecule (G4H2O::Definition());
+	if(fActiveChemistry)
+	{
+		G4Molecule * H2O = new G4Molecule (G4H2O::Definition());
 
-        switch (modification)
-        {
-        case eDissociativeAttachment:
-            H2O -> AddElectron(5,1);
-            break;
-        case eExcitedMolecule :
-            H2O -> ExciteMolecule(electronicLevel);
-            break;
-        case eIonizedMolecule :
-            H2O -> IonizeMolecule(electronicLevel);
-            break;
-        }
+		switch (modification)
+		{
+		case eDissociativeAttachment:
+			H2O -> AddElectron(5,1);
+			break;
+		case eExcitedMolecule :
+			H2O -> ExciteMolecule(electronicLevel);
+			break;
+		case eIonizedMolecule :
+			H2O -> IonizeMolecule(electronicLevel);
+			break;
+		}
 
-        G4Track * H2OTrack = H2O->BuildTrack(1*picosecond,
-                                             theIncomingTrack->GetPosition());
+		G4Track * H2OTrack = H2O->BuildTrack(1*picosecond,
+				theIncomingTrack->GetPosition());
 
-        H2OTrack -> SetParentID(theIncomingTrack->GetTrackID());
-        H2OTrack -> SetTrackStatus(fStopButAlive);
-        H2OTrack -> SetKineticEnergy(0.);
+		H2OTrack -> SetParentID(theIncomingTrack->GetTrackID());
+		H2OTrack -> SetTrackStatus(fStopButAlive);
+		H2OTrack -> SetKineticEnergy(0.);
 
-        G4ITTrackHolder::Instance()->PushTrack(H2OTrack);
-    }
+		G4ITTrackHolder::Instance()->PushTrack(H2OTrack);
+	}
 }
 
 void G4DNAChemistryManager::CreateSolvatedElectron(const G4Track* theIncomingTrack,
-                                                   G4ThreeVector* finalPosition)
+		G4ThreeVector* finalPosition)
 // finalPosition is a pointer because this argument is optional
 {
-    if(fWriteFile)
-    {
-        fOutput << setw(11)<< theIncomingTrack->GetTrackID()
-                << setw(10)<< "e_aq"
-                << setw(14)<< -1
-                << std::setprecision(2) << std::fixed
-                << setw(13)<< theIncomingTrack->GetKineticEnergy()/eV
-                << std::setprecision(6) << std::scientific
-                << setw(22)<< (theIncomingTrack->GetPosition().x())/nanometer
-                << setw(22)<< (theIncomingTrack->GetPosition().y())/nanometer
-                << setw(22)<< (theIncomingTrack->GetPosition().z())/nanometer  ;
+	if(fWriteFile)
+	{
+		*fOutput << setw(11)<< theIncomingTrack->GetTrackID()
+                								<< setw(10)<< "e_aq"
+                								<< setw(14)<< -1
+                								<< std::setprecision(2) << std::fixed
+                								<< setw(13)<< theIncomingTrack->GetKineticEnergy()/eV
+                								<< std::setprecision(6) << std::scientific
+                								<< setw(22)<< (theIncomingTrack->GetPosition().x())/nanometer
+                								<< setw(22)<< (theIncomingTrack->GetPosition().y())/nanometer
+                								<< setw(22)<< (theIncomingTrack->GetPosition().z())/nanometer  ;
 
-        if(finalPosition != 0)
-        {
-            fOutput<< setw(14)<< (finalPosition->x())/nanometer
-                   << setw(14)<< (finalPosition->y())/nanometer
-                   << setw(14)<< (finalPosition->z())/nanometer ;
-        }
+		if(finalPosition != 0)
+		{
+			*fOutput<< setw(14)<< (finalPosition->x())/nanometer
+					<< setw(14)<< (finalPosition->y())/nanometer
+					<< setw(14)<< (finalPosition->z())/nanometer ;
+		}
 
-        fOutput << G4endl;
-    }
+		*fOutput << G4endl;
+	}
 
-    if(fActiveChemistry)
-    {
-        G4Molecule* e_aq = new G4Molecule(G4Electron_aq::Definition());
-        G4Track * e_aqTrack(0);
-        if(finalPosition)
-        {
-            e_aqTrack  = e_aq->BuildTrack(picosecond,*finalPosition);
-        }
-        else
-        {
-            e_aqTrack  = e_aq->BuildTrack(picosecond,theIncomingTrack->GetPosition());
-        }
-        e_aqTrack -> SetTrackStatus(fAlive);
-        e_aqTrack -> SetParentID(theIncomingTrack->GetTrackID());
-        G4ITTrackHolder::Instance()->PushTrack(e_aqTrack);
-        G4ITManager<G4Molecule>::Instance()->Push(e_aqTrack);
-    }
+	if(fActiveChemistry)
+	{
+		G4Molecule* e_aq = new G4Molecule(G4Electron_aq::Definition());
+		G4Track * e_aqTrack(0);
+		if(finalPosition)
+		{
+			e_aqTrack  = e_aq->BuildTrack(picosecond,*finalPosition);
+		}
+		else
+		{
+			e_aqTrack  = e_aq->BuildTrack(picosecond,theIncomingTrack->GetPosition());
+		}
+		e_aqTrack -> SetTrackStatus(fAlive);
+		e_aqTrack -> SetParentID(theIncomingTrack->GetTrackID());
+		G4ITTrackHolder::Instance()->PushTrack(e_aqTrack);
+		G4ITManager<G4Molecule>::Instance()->Push(e_aqTrack);
+	}
 }
 
 
 void G4DNAChemistryManager::PushMolecule(G4Molecule*& molecule, double time,
-                                         const G4ThreeVector& position, int parentID)
+		const G4ThreeVector& position, int parentID)
 {
-    if(fWriteFile)
-    {
-        fOutput << setw(11)<< parentID
-                << setw(10)<< molecule->GetName()
-                << setw(14)<< -1
-                << std::setprecision(2) << std::fixed
-                << setw(13)<< -1
-                << std::setprecision(6) << std::scientific
-                << setw(22)<< (position.x())/nanometer
-                << setw(22)<< (position.y())/nanometer
-                << setw(22)<< (position.z())/nanometer;
-        fOutput << G4endl;
-    }
+	if(fWriteFile)
+	{
+		*fOutput << setw(11)<< parentID
+				<< setw(10)<< molecule->GetName()
+				<< setw(14)<< -1
+				<< std::setprecision(2) << std::fixed
+				<< setw(13)<< -1
+				<< std::setprecision(6) << std::scientific
+				<< setw(22)<< (position.x())/nanometer
+				<< setw(22)<< (position.y())/nanometer
+				<< setw(22)<< (position.z())/nanometer;
+		*fOutput << G4endl;
+	}
 
-    if(fActiveChemistry)
-    {
-        G4Track* track = molecule->BuildTrack(time,position);
-        track -> SetTrackStatus(fAlive);
-        track -> SetParentID(parentID);
-        G4ITTrackHolder::Instance()->PushTrack(track);
-        G4ITManager<G4Molecule>::Instance()->Push(track);
-    }
-    else
-    {
-        delete molecule;
-        molecule = 0;
-    }
+	if(fActiveChemistry)
+	{
+		G4Track* track = molecule->BuildTrack(time,position);
+		track -> SetTrackStatus(fAlive);
+		track -> SetParentID(parentID);
+		G4ITTrackHolder::Instance()->PushTrack(track);
+		G4ITManager<G4Molecule>::Instance()->Push(track);
+	}
+	else
+	{
+		delete molecule;
+		molecule = 0;
+	}
 }
 
 void G4DNAChemistryManager::PushMoleculeAtParentTimeAndPlace(G4Molecule*& molecule,
-                                                             const G4Track* theIncomingTrack)
+		const G4Track* theIncomingTrack)
 {
-    if(fWriteFile)
-    {
-        fOutput << setw(11)<< theIncomingTrack->GetTrackID()
-                << setw(10)<< molecule->GetName()
-                << setw(14)<< -1
-                << std::setprecision(2) << std::fixed
-                << setw(13)<< theIncomingTrack->GetKineticEnergy()/eV
-                << std::setprecision(6) << std::scientific
-                << setw(22)<< (theIncomingTrack->GetPosition().x())/nanometer
-                << setw(22)<< (theIncomingTrack->GetPosition().y())/nanometer
-                << setw(22)<< (theIncomingTrack->GetPosition().z())/nanometer  ;
-        fOutput << G4endl;
-    }
+	if(fWriteFile)
+	{
+		*fOutput << setw(11)<< theIncomingTrack->GetTrackID()
+                								<< setw(10)<< molecule->GetName()
+                								<< setw(14)<< -1
+                								<< std::setprecision(2) << std::fixed
+                								<< setw(13)<< theIncomingTrack->GetKineticEnergy()/eV
+                								<< std::setprecision(6) << std::scientific
+                								<< setw(22)<< (theIncomingTrack->GetPosition().x())/nanometer
+                								<< setw(22)<< (theIncomingTrack->GetPosition().y())/nanometer
+                								<< setw(22)<< (theIncomingTrack->GetPosition().z())/nanometer  ;
+		*fOutput << G4endl;
+	}
 
-    if(fActiveChemistry)
-    {
-        G4Track* track = molecule->BuildTrack(theIncomingTrack->GetGlobalTime(),theIncomingTrack->GetPosition());
-        track -> SetTrackStatus(fAlive);
-        track -> SetParentID(theIncomingTrack->GetTrackID());
-        G4ITTrackHolder::Instance()->PushTrack(track);
-        G4ITManager<G4Molecule>::Instance()->Push(track);
-    }
-    else
-    {
-        delete molecule;
-        molecule = 0;
-    }
+	if(fActiveChemistry)
+	{
+		G4Track* track = molecule->BuildTrack(theIncomingTrack->GetGlobalTime(),theIncomingTrack->GetPosition());
+		track -> SetTrackStatus(fAlive);
+		track -> SetParentID(theIncomingTrack->GetTrackID());
+		G4ITTrackHolder::Instance()->PushTrack(track);
+		G4ITManager<G4Molecule>::Instance()->Push(track);
+	}
+	else
+	{
+		delete molecule;
+		molecule = 0;
+	}
+}
+
+void G4DNAChemistryManager::AddEmptyLineInOuputFile()
+{
+	if(fWriteFile)
+	{
+		*fOutput << G4endl;
+	}
 }

source/processes/electromagnetic/dna/utils/src/G4DNACrossSectionDataSet.cc

@@ -25,7 +25,7 @@
 //
 //
 
-// $Id$
+// $Id: G4DNACrossSectionDataSet.cc 70171 2013-05-24 13:34:18Z gcosmo $
 //
 // Author: Riccardo Capra <capra@ge.infn.it>
 // Code review by MGP October 2007: removed inheritance from concrete class

source/processes/electromagnetic/dna/utils/src/G4DNADamages.cc

@@ -23,12 +23,12 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4DNADamages.cc 65022 2012-11-12 16:43:12Z gcosmo $
+// $Id: G4DNADamages.cc 66872 2013-01-15 01:25:57Z japost $
 //
 #include "G4DNADamages.hh"
 #include "G4UnitsTable.hh"
 
-G4DNADamages* G4DNADamages::fpInstance(0);
+G4ThreadLocal G4DNADamages* G4DNADamages::fpInstance(0);
 
 G4DNAIndirectHit::G4DNAIndirectHit(const G4String& baseName,
                                    const G4Molecule* molecule,

source/processes/electromagnetic/dna/utils/src/G4DNAGenericIonsManager.cc

@@ -23,13 +23,13 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id$
+// $Id: G4DNAGenericIonsManager.cc 73124 2013-08-19 07:53:33Z gcosmo $
 
 #include "G4DNAGenericIonsManager.hh"
 #include "G4PhysicalConstants.hh"
 #include "G4SystemOfUnits.hh"
 #include "G4Alpha.hh"
-#include "G4Ions.hh"
+#include "G4DNAIons.hh"
 
 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
 
@@ -65,88 +65,88 @@ G4DNAGenericIonsManager :: G4DNAGenericIonsManager()
   //         shortlived          subType  anti_encoding
   //         excitation   
   
- G4Ions *helium;
- G4Ions *hydrogen;
- G4Ions *alphaPlus;
- G4Ions *positronium1s;
- G4Ions *positronium2s;
+ G4DNAIons *helium;
+ G4DNAIons *hydrogen;
+ G4DNAIons *alphaPlus;
+ G4DNAIons *positronium1s;
+ G4DNAIons *positronium2s;
  
- G4Ions *carbon;
- G4Ions *nitrogen;
- G4Ions *oxygen;
- G4Ions *iron;
+ G4DNAIons *carbon;
+ G4DNAIons *nitrogen;
+ G4DNAIons *oxygen;
+ G4DNAIons *iron;
 
- iron=     new G4Ions(
+ iron=     new G4DNAIons(
 			"iron",    52.5672*GeV,       0.0*MeV,  +26.0*eplus,
 			0,              +1,             0,
 			0,               0,             0,
-			"nucleus",              +26,            +56,           0,
+			"DNAion",              +26,            +56,           0,
 			true,                -1.0,             0,       
 			false,		      "",               0,             
 			0.0);
 
- oxygen=   new G4Ions(
+ oxygen=   new G4DNAIons(
 			"oxygen",    15.0074*GeV,       0.0*MeV,  +8.0*eplus,
 			0,              +1,             0,
 			0,               0,             0,
-			"nucleus",              +8,            +16,           0,
+			"DNAion",              +8,            +16,           0,
 			true,                -1.0,             0,       
 			false,		      "",               0,             
 			0.0);
 
 
- nitrogen= new G4Ions(
+ nitrogen= new G4DNAIons(
 			"nitrogen",    13.132*GeV,       0.0*MeV,  +7.0*eplus,
 			0,              +1,             0,
 			0,               0,             0,
-			"nucleus",              +7,            +14,           0,
+			"DNAion",              +7,            +14,           0,
 			true,                -1.0,             0,       
 			false,		      "",               0,             
 			0.0);
 
- carbon=   new G4Ions(
+ carbon=   new G4DNAIons(
 			"carbon",    11.267025440*GeV,       0.0*MeV,  +6.0*eplus,
 			0,              +1,             0,
 			0,               0,             0,
-			"nucleus",              +6,            +12,           0,
+			"DNAion",              +6,            +12,           0,
 			true,                -1.0,             0,       
 			false,		      "",               0,             
 			0.0);
  
- helium=   new G4Ions(
+ helium=   new G4DNAIons(
 			"helium",    3.727417*GeV,       0.0*MeV,  +0.0*eplus,
 			0,              +1,             0,
 			0,               0,             0,
-			"nucleus",              +2,            +4,           0,
+			"DNAion",		+2,	       +4,	     0,
 			true,                -1.0,             0,       
 			false,		      "",               0,             
 			0.0);
 
- alphaPlus= new G4Ions("alpha+",    3.727417*GeV,       0.0*MeV,  +1.0*eplus,
+ alphaPlus= new G4DNAIons("alpha+",    3.727417*GeV,       0.0*MeV,  +1.0*eplus,
                                1,              +1,             0,
                                0,               0,             0,
-                       "nucleus",              +1,            +4,           0,
+                       "DNAion",              +1,            +4,           0,
 			true,            -1.0,             0, false,
 			      "",               0,             0.0);
 
- hydrogen= new G4Ions("hydrogen",   0.9382723*GeV,       0.0*MeV,  +0.0*eplus,
+ hydrogen= new G4DNAIons("hydrogen",   0.9382723*GeV,       0.0*MeV,  +0.0*eplus,
                                0,              +1,             0,
                                0,               0,             0,
-                       "nucleus",              +1,            +1,           0,
+                       "DNAion",              +1,            +1,           0,
 		        true,            -1.0,             0, false,
 			      "",               0,             0.0);
 
- positronium1s= new G4Ions("Ps-1s",   2*electron_mass_c2,      0.0*MeV,  +0.0*eplus,
+ positronium1s= new G4DNAIons("Ps-1s",   2*electron_mass_c2,      0.0*MeV,  +0.0*eplus,
                                0,               0,             0,
                                0,               0,             0,
-                       "nucleus",               0,             0,           0,
+                       "DNAion",               0,             0,           0,
 		            true,            -1.0,             0, false,
 			      "",               0,             0.0);
 
- positronium2s= new G4Ions("Ps-2s",   2*electron_mass_c2,      0.0*MeV,  +0.0*eplus,
+ positronium2s= new G4DNAIons("Ps-2s",   2*electron_mass_c2,      0.0*MeV,  +0.0*eplus,
                                0,               0,             0,
                                0,               0,             0,
-                       "nucleus",               0,             0,           0,
+                       "DNAion",               0,             0,           0,
 		            true,            -1.0,             0, false,
 			      "",               0,             0.0);
 

source/processes/electromagnetic/dna/utils/src/G4DNAIons.cc

@@ -0,0 +1,82 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// 31.07.2013: Derived from G4Ions for MT migration (SI)
+// Suggested by Makoto et al.
+
+#include <fstream>
+#include <iomanip>
+
+#include "G4DNAIons.hh"
+#include "G4PhysicalConstants.hh"
+#include "G4SystemOfUnits.hh"
+
+// ######################################################################
+// ###                           G4DNAIons                            ###
+// ######################################################################
+
+G4DNAIons::G4DNAIons(
+       const G4String&     aName,        G4double            mass,
+       G4double            width,        G4double            charge,   
+       G4int               iSpin,        G4int               iParity,    
+       G4int               iConjugation, G4int               iIsospin,   
+       G4int               iIsospin3,    G4int               gParity,
+       const G4String&     pType,        G4int               lepton,      
+       G4int               baryon,       G4int               encoding,
+       G4bool              stable,       G4double            lifetime,
+       G4DecayTable        *decaytable , G4bool              shortlived,
+       const G4String&     subType,
+       G4int               anti_encoding,
+       G4double            excitation,
+       G4int               isomer
+)
+  : G4ParticleDefinition( aName,mass,width,charge,iSpin,iParity,
+           iConjugation,iIsospin,iIsospin3,gParity,pType,
+           lepton,baryon,encoding,stable,lifetime,decaytable,
+			  shortlived, subType, anti_encoding),
+    theExcitationEnergy(excitation),
+    theIsomerLevel(isomer)
+{
+  // isomer level isset to 10 
+  // if isomer level is set to 0 for excited state
+  if ((theExcitationEnergy > 0.0) && (isomer==0)) isomer =9; 
+
+   if (GetAtomicNumber() == 0  ) {
+     // AtomicNumber/Mass is positve even for anti_nulceus
+     SetAtomicNumber( std::abs(G4int(GetPDGCharge()/eplus)) );
+     SetAtomicMass( std::abs(GetBaryonNumber()) );
+   }
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+G4DNAIons::~G4DNAIons()
+{
+}
+
+
+
+
+

source/processes/electromagnetic/dna/utils/src/G4DNAMolecularMaterial.cc

@@ -23,15 +23,21 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4DNAMolecularMaterial.cc 65022 2012-11-12 16:43:12Z gcosmo $
+// $Id: G4DNAMolecularMaterial.cc 70171 2013-05-24 13:34:18Z gcosmo $
 //
 #include "G4DNAMolecularMaterial.hh"
 #include "G4Material.hh"
 #include <utility>
 #include "G4StateManager.hh"
+#include "G4Threading.hh"
+#include "G4AutoLock.hh"
 
 using namespace std;
 
+G4DNAMolecularMaterial* G4DNAMolecularMaterial::fInstance(0);
+//G4ThreadLocal G4DNAMolecularMaterial* G4DNAMolecularMaterial::fInstance(0);
+G4Mutex aMutex=G4MUTEX_INITIALIZER;
+
 
 bool CompareMaterial::operator() (const G4Material* mat1, const G4Material* mat2) const
 {
@@ -59,8 +65,6 @@ bool CompareMaterial::operator() (const G4Material* mat1, const G4Material* mat2
     return mat1 < baseMat2;
 }
 
-G4DNAMolecularMaterial* G4DNAMolecularMaterial::fInstance(0);
-
 G4DNAMolecularMaterial* G4DNAMolecularMaterial::Instance()
 {
     if(! fInstance) new G4DNAMolecularMaterial();
@@ -274,7 +278,11 @@ void G4DNAMolecularMaterial::InitializeNumMolPerVol()
 
 void G4DNAMolecularMaterial::Initialize()
 {
-    if(fIsInitialized) return;
+    G4AutoLock l(&aMutex);
+    if(fIsInitialized)
+    {
+        return;
+    }
 
     const G4MaterialTable* materialTable = G4Material::GetMaterialTable();
 
@@ -371,7 +379,7 @@ const std::vector<double>* G4DNAMolecularMaterial::GetNumMolPerVolTableFor(const
         if(fIsInitialized)
         {
             G4ExceptionDescription exceptionDescription;
-            exceptionDescription << "The pointer fpCompNumMolPerVolTable is not initialized will the singleton of G4DNAMolecularMaterial "
+            exceptionDescription << "The pointer fpCompNumMolPerVolTable is not initialized whereas the singleton of G4DNAMolecularMaterial "
                                  << "has already been initialized."<< G4endl;
             G4Exception("G4DNAMolecularMaterial::GetNumMolPerVolTableFor","G4DNAMolecularMaterial005",
                         FatalException,exceptionDescription);

source/processes/electromagnetic/dna/utils/src/G4DNAMolecularReactionTable.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4DNAMolecularReactionTable.cc 65022 2012-11-12 16:43:12Z gcosmo $
+// $Id: G4DNAMolecularReactionTable.cc 74551 2013-10-14 12:59:14Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr) 
 //
@@ -48,6 +48,7 @@
 using namespace std;
 
 G4DNAMolecularReactionTable* G4DNAMolecularReactionTable::fInstance(0);
+//G4ThreadLocal G4DNAMolecularReactionTable* G4DNAMolecularReactionTable::fInstance(0);
 
 G4DNAMolecularReactionData::G4DNAMolecularReactionData():
     fReactive1(),fReactive2(),
@@ -284,7 +285,7 @@ void G4DNAMolecularReactionTable::PrintTable(G4VDNAReactionModel* pReactionModel
     G4cout<<"Number of possible reactions: "<< n << G4endl;
 
     ////////////////////////////////////////////////////////////////////
-    // Tableau dynamique en fonction du nombre de caractère maximal dans
+    // Tableau dynamique en fonction du nombre de caractere maximal dans
     // chaque colonne
     ////////////////////////////////////////////////////////////////////