Import Geant4 10.0.0 source tree

source/processes/electromagnetic/dna/management/src/G4AllITManager.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4AllITManager.cc 64057 2012-10-30 15:04:49Z gcosmo $
+// $Id: G4AllITManager.cc 71827 2013-06-25 15:58:24Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr) 
 //
@@ -37,7 +37,7 @@
 
 using namespace std;
 
-auto_ptr<G4AllITManager> G4AllITManager::fInstance(0);
+G4ThreadLocal G4AllITManager* G4AllITManager::fpInstance = 0;
 
 G4AllITManager::G4AllITManager()
 {
@@ -45,14 +45,14 @@ G4AllITManager::G4AllITManager()
 }
 
 G4AllITManager* G4AllITManager::Instance()
-{
-    if(fInstance.get() == 0) fInstance = auto_ptr<G4AllITManager>(new G4AllITManager());
-    return fInstance.get() ;
+{  
+    if (!fpInstance) fpInstance = new G4AllITManager();
+    return fpInstance ;
 }
 
 void G4AllITManager::DeleteInstance()
 {
-    fInstance.reset();
+    if(fpInstance) delete fpInstance;
 }
 
 G4AllITManager::~G4AllITManager()
@@ -67,7 +67,7 @@ G4AllITManager::~G4AllITManager()
         it++;
         fITSubManager.erase(it_tmp);
     }
-    fInstance.release();
+    fpInstance = 0;
 }
 
 void  G4AllITManager::UpdatePositionMap()

source/processes/electromagnetic/dna/management/src/G4IT.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4IT.cc 65022 2012-11-12 16:43:12Z gcosmo $
+// $Id: G4IT.cc 71125 2013-06-11 15:39:09Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr)
 //
@@ -40,7 +40,7 @@
 
 using namespace std;
 
-G4Allocator<G4IT> aITAllocator;
+G4ThreadLocal G4Allocator<G4IT> *aITAllocator = 0;
 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
 ///
 // Static functions
@@ -52,7 +52,7 @@ G4IT* GetIT(const G4Track* track)
 
 G4IT* GetIT(const G4Track& track)
 {
-    return (dynamic_cast<G4IT*>(track.GetUserInformation()));
+   return (dynamic_cast<G4IT*>(track.GetUserInformation()));
 }
 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
 ///
@@ -64,6 +64,7 @@ G4IT::G4IT() : G4VUserTrackInformation("G4IT"),
     fTrackingInformation()
 //    fpTrackingInformation(new G4TrackingInformation())
 {
+    if (!aITAllocator) aITAllocator = new G4Allocator<G4IT>;
     fpITBox=0;
     fpKDNode = 0 ;
     fpTrackNode = 0;
@@ -113,6 +114,7 @@ G4IT::G4IT(G4Track * aTrack) : G4VUserTrackInformation("G4IT"),
     fTrackingInformation()
 //    fpTrackingInformation(new G4TrackingInformation())
 {
+    if (!aITAllocator) aITAllocator = new G4Allocator<G4IT>;
     fpITBox = 0;
     fpTrack = aTrack;
     fpKDNode = 0 ;

source/processes/electromagnetic/dna/management/src/G4ITModelProcessor.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4ITModelProcessor.cc 64057 2012-10-30 15:04:49Z gcosmo $
+// $Id: G4ITModelProcessor.cc 71125 2013-06-11 15:39:09Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr)
 //
@@ -37,11 +37,12 @@
 #include "G4VITTimeStepper.hh"
 #include "G4VITReactionProcess.hh"
 
-std::map<const G4Track*, G4bool> G4ITModelProcessor::fHasReacted ;
+G4ThreadLocal std::map<const G4Track*, G4bool> *G4ITModelProcessor::fHasReacted = 0;
 
 G4ITModelProcessor::G4ITModelProcessor()
 {
     //ctor
+    if (!fHasReacted) fHasReacted = new std::map<const G4Track*, G4bool>;
     fpTrack = 0;
     fpModelHandler = 0;
     fpModel = 0;
@@ -210,8 +211,8 @@ void G4ITModelProcessor::FindReaction(std::map<G4Track*, G4TrackVectorHandle>* t
 
         if(trackA == 0)         continue;
 
-        std::map<const G4Track*, G4bool>::iterator it_hasReacted = fHasReacted.find(trackA);
-        if(it_hasReacted != fHasReacted.end()) continue;
+        std::map<const G4Track*, G4bool>::iterator it_hasReacted = fHasReacted->find(trackA);
+        if(it_hasReacted != fHasReacted->end()) continue;
         if(trackA->GetTrackStatus() == fStopAndKill) continue;
 
         G4IT* ITA = GetIT(trackA);
@@ -232,8 +233,8 @@ void G4ITModelProcessor::FindReaction(std::map<G4Track*, G4TrackVectorHandle>* t
             trackB = *trackB_i;
 
             if(trackB == 0)         continue;
-            it_hasReacted = fHasReacted.find(trackB);
-            if(it_hasReacted != fHasReacted.end()) continue;
+            it_hasReacted = fHasReacted->find(trackB);
+            if(it_hasReacted != fHasReacted->end()) continue;
             if(trackB->GetTrackStatus() == fStopAndKill) continue;
 
             // DEBUG
@@ -272,8 +273,8 @@ void G4ITModelProcessor::FindReaction(std::map<G4Track*, G4TrackVectorHandle>* t
 
             if(changes)
             {
-                fHasReacted[trackA] = true;
-                fHasReacted[trackB] = true;
+                (*fHasReacted)[trackA] = true;
+                (*fHasReacted)[trackB] = true;
                 changes -> GetTrackA();
                 changes -> GetTrackB();
 
@@ -287,5 +288,5 @@ void G4ITModelProcessor::FindReaction(std::map<G4Track*, G4TrackVectorHandle>* t
         }
     }
 
-    fHasReacted.clear();
+    fHasReacted->clear();
 }

source/processes/electromagnetic/dna/management/src/G4ITNavigator.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4ITNavigator.cc 64376 2012-10-31 16:39:40Z gcosmo $
+// $Id: G4ITNavigator.cc 66872 2013-01-15 01:25:57Z japost $
 // 
 // class G4ITNavigator Implementation
 //
@@ -732,7 +732,7 @@ G4double G4ITNavigator::ComputeStep( const G4ThreeVector &pGlobalpoint,
   G4VPhysicalVolume  *motherPhysical = fHistory.GetTopVolume();
   G4LogicalVolume *motherLogical = motherPhysical->GetLogicalVolume();
 
-  static G4int sNavCScalls=0;
+  static G4ThreadLocal G4int sNavCScalls=0;
   sNavCScalls++;
 
   fLastTriedStepComputation= true; 
@@ -1684,7 +1684,7 @@ void G4ITNavigator::ComputeStepLog(const G4ThreeVector& pGlobalpoint,
               << fAccuracyForException/mm << " mm.";
 
       suggestion << " ";
-      static G4int warnNow = 0;
+      static G4ThreadLocal G4int warnNow = 0;
       if( ((++warnNow % 100) == 1) )
       {
         message << G4endl

source/processes/electromagnetic/dna/management/src/G4ITNavigator.cc2

@@ -658,7 +658,6 @@ void G4ITNavigator::CheckNavigatorState() const
 
         G4Exception("G4ITNavigator::CheckNavigatorStateIsValid",
                     "NavigatorStateNotValid",FatalException,exceptionDescription);
-        exit(-1);
         return;
     }
 }
@@ -684,7 +683,6 @@ void G4ITNavigator::NewNavigatorState()
 
         G4Exception("G4ITNavigator::NewNavigatorState",
                     "NoWorldVolume",FatalException,exceptionDescription);
-        exit(-1);
         return;
     }
 
@@ -704,7 +702,6 @@ G4VPhysicalVolume* G4ITNavigator::NewNavigatorStateAndLocate(const G4ThreeVector
 
         G4Exception("G4ITNavigator::NewNavigatorStateAndLocate",
                     "NoWorldVolume",FatalException,exceptionDescription);
-        exit(-1);
         return 0;
     }
 

source/processes/electromagnetic/dna/management/src/G4ITStepProcessor.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4ITStepProcessor.cc 65022 2012-11-12 16:43:12Z gcosmo $
+// $Id: G4ITStepProcessor.cc 74551 2013-10-14 12:59:14Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr) 
 //
@@ -56,7 +56,7 @@
 using namespace std;
 
 static const size_t SizeOfSelectedDoItVector=100;
-static const size_t& gMaxNProcesses(G4VITProcess::GetMaxProcessIndex());
+//static const size_t& gMaxNProcesses(G4VITProcess::GetMaxProcessIndex());
 
 //____________________________________________________________________________________
 
@@ -76,8 +76,10 @@ G4ITStepProcessor::G4ITStepProcessor()
 
 G4ITStepProcessor::G4ITStepProcessorState::G4ITStepProcessorState() :
     G4ITStepProcessorState_Lock(),
-    fSelectedAtRestDoItVector (gMaxNProcesses,0),
-    fSelectedPostStepDoItVector (gMaxNProcesses,0)
+//    fSelectedAtRestDoItVector (gMaxNProcesses,0),
+//    fSelectedPostStepDoItVector (gMaxNProcesses,0)
+    fSelectedAtRestDoItVector (G4VITProcess::GetMaxProcessIndex(),0),
+    fSelectedPostStepDoItVector (G4VITProcess::GetMaxProcessIndex(),0)
 {
     fPhysicalStep = -1.;
     fPreviousStepSize = -1.;
@@ -94,8 +96,10 @@ G4ITStepProcessor::G4ITStepProcessorState::G4ITStepProcessorState() :
 // should not be used
 G4ITStepProcessor::G4ITStepProcessorState::G4ITStepProcessorState(const G4ITStepProcessorState& ) :
     G4ITStepProcessorState_Lock(),
-    fSelectedAtRestDoItVector (gMaxNProcesses,0),
-    fSelectedPostStepDoItVector (gMaxNProcesses,0)
+//    fSelectedAtRestDoItVector (gMaxNProcesses,0),
+//    fSelectedPostStepDoItVector (gMaxNProcesses,0)
+    fSelectedAtRestDoItVector (G4VITProcess::GetMaxProcessIndex(),0),
+    fSelectedPostStepDoItVector (G4VITProcess::GetMaxProcessIndex(),0)
 {
     fPhysicalStep = -1.;
     fPreviousStepSize = -1.;
@@ -115,9 +119,11 @@ G4ITStepProcessor::G4ITStepProcessorState&  G4ITStepProcessor::G4ITStepProcessor
     if(this == &rhs) return *this;
 
     fSelectedAtRestDoItVector.clear();
-    fSelectedAtRestDoItVector.resize(gMaxNProcesses,0);
+//    fSelectedAtRestDoItVector.resize(gMaxNProcesses,0);
+    fSelectedAtRestDoItVector.resize(G4VITProcess::GetMaxProcessIndex(),0);
     fSelectedPostStepDoItVector.clear();
-    fSelectedPostStepDoItVector.resize(gMaxNProcesses,0);
+//    fSelectedPostStepDoItVector.resize(gMaxNProcesses,0);
+    fSelectedPostStepDoItVector.resize(G4VITProcess::GetMaxProcessIndex(),0);
 
     fPhysicalStep = -1.;
     fPreviousStepSize = -1.;

source/processes/electromagnetic/dna/management/src/G4ITStepProcessor2.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4ITStepProcessor2.cc 64057 2012-10-30 15:04:49Z gcosmo $
+// $Id: G4ITStepProcessor2.cc 77292 2013-11-22 10:58:39Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr) 
 //
@@ -35,7 +35,6 @@
 
 #include "G4ITStepProcessor.hh"
 #include "G4LossTableManager.hh"
-#include "G4EnergyLossTables.hh"
 #include "G4ProductionCuts.hh"
 #include "G4ProductionCutsTable.hh"
 #include "G4VITProcess.hh"

source/processes/electromagnetic/dna/management/src/G4ITTrackHolder.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4ITTrackHolder.cc 64374 2012-10-31 16:37:23Z gcosmo $
+// $Id: G4ITTrackHolder.cc 66881 2013-01-16 02:55:54Z adotti $
 //
 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr)
 //
@@ -37,8 +37,9 @@
 
 #include "G4ITTrackHolder.hh"
 #include "G4Track.hh"
+#include "G4Types.hh"
 
-G4ITTrackHolder* G4ITTrackHolder::fInstance(0);
+G4ThreadLocal G4ITTrackHolder* G4ITTrackHolder::fInstance(0);
 
 G4ITTrackHolder::G4ITTrackHolder()
 {

source/processes/electromagnetic/dna/management/src/G4ITTransportation.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4ITTransportation.cc 64374 2012-10-31 16:37:23Z gcosmo $
+// $Id: G4ITTransportation.cc 71125 2013-06-11 15:39:09Z gcosmo $
 //
 /// \brief This class is a slightly modified version of G4Transportation
 ///        initially written by John Apostolakis and colleagues
@@ -172,8 +172,9 @@ G4ITTransportation::G4ITTransportationState::G4ITTransportationState() : G4Proce
     fEndGlobalTimeComputed = false;
     fCandidateEndGlobalTime = -1;
     fParticleIsLooping = false;
-    static G4TouchableHandle nullTouchableHandle; // Points to (G4VTouchable*) 0
-    fCurrentTouchableHandle = nullTouchableHandle;
+    static G4ThreadLocal G4TouchableHandle *nullTouchableHandle = 0;
+    if (!nullTouchableHandle) nullTouchableHandle = new  G4TouchableHandle; // Points to (G4VTouchable*) 0
+    fCurrentTouchableHandle = *nullTouchableHandle;
     fGeometryLimitedStep = false;
     fPreviousSftOrigin = G4ThreeVector(0,0,0);
     fPreviousSafety = 0.0;
@@ -613,10 +614,12 @@ G4VParticleChange* G4ITTransportation::AlongStepDoIt( const G4Track& track,
 
     //    G4cout << "G4ITTransportation::AlongStepDoIt" << G4endl;
     // set  pdefOpticalPhoton
-    static  G4ParticleDefinition* pdefOpticalPhoton =
-            G4ParticleTable::GetParticleTable()->FindParticle("opticalphoton");
+    //Andrea Dotti: the following statement should be in a single line:
+    // G4-MT transformation tools get confused if statement spans two lines
+    // If needed contact: adotti@slac.stanford.edu
+    static G4ThreadLocal  G4ParticleDefinition* pdefOpticalPhoton  = 0 ; if (!pdefOpticalPhoton) pdefOpticalPhoton= G4ParticleTable::GetParticleTable()->FindParticle("opticalphoton");
 
-    static G4int noCalls=0;
+    static G4ThreadLocal G4int noCalls=0;
     noCalls++;
 
     fParticleChange.Initialize(track) ;
@@ -964,7 +967,7 @@ G4ITTransportation::StartTracking(G4Track* track)
     }
 
     // Make sure to clear the chord finders of all fields (ie managers)
-    static G4FieldManagerStore* fieldMgrStore= G4FieldManagerStore::GetInstance();
+    static G4ThreadLocal G4FieldManagerStore* fieldMgrStore = 0 ; if (!fieldMgrStore) fieldMgrStore= G4FieldManagerStore::GetInstance();
     fieldMgrStore->ClearAllChordFindersState();
 
     // Update the current touchable handle  (from the track's)

source/processes/electromagnetic/dna/management/src/G4ITTransportationManager.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4ITTransportationManager.cc 64374 2012-10-31 16:37:23Z gcosmo $
+// $Id: G4ITTransportationManager.cc 66872 2013-01-15 01:25:57Z japost $
 //
 /// \brief {Duplicated version of G4TransportationManager.
 ///         This class just contains the pointer to the navigator object of the
@@ -38,7 +38,7 @@
 #include "G4TransportationManager.hh"
 #include "G4ITNavigator.hh"
 
-G4ITTransportationManager* G4ITTransportationManager::fpInstance (0);
+G4ThreadLocal G4ITTransportationManager* G4ITTransportationManager::fpInstance (0);
 
 G4ITTransportationManager::G4ITTransportationManager()
 {

source/processes/electromagnetic/dna/management/src/G4ITType.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4ITType.cc 64057 2012-10-30 15:04:49Z gcosmo $
+// $Id: G4ITType.cc 74551 2013-10-14 12:59:14Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr) 
 //
@@ -34,8 +34,13 @@
 // -------------------------------------------------------------------
 
 #include "G4ITType.hh"
+#include "G4AutoLock.hh"
 
-G4ITTypeManager* G4ITTypeManager::fgInstance = 0;
+/*G4ThreadLocal*/ G4ITTypeManager* G4ITTypeManager::fgInstance = 0;
+G4ThreadLocal G4ITTypeManager* G4ITTypeManager::fgInstance_local = 0;
+
+G4Mutex deleteMutex=G4MUTEX_INITIALIZER;
+G4Mutex ressourceMutex=G4MUTEX_INITIALIZER;
 
 // static method
 size_t G4ITType::size()
@@ -61,7 +66,26 @@ G4ITTypeManager*  G4ITTypeManager::Instance()
 
 void G4ITTypeManager::DeleteInstance()
 {
-    delete fgInstance ;
+	G4AutoLock lock(&deleteMutex);
+	if(fgInstance)
+	{
+		delete fgInstance ;
+		fgInstance = 0;
+	}
+}
+
+void G4ITTypeManager::ReserveRessource()
+{
+	G4AutoLock lock(&ressourceMutex);
+	fRessource++;
+}
+
+void G4ITTypeManager::ReleaseRessource()
+{
+	G4AutoLock lock(&ressourceMutex);
+	fRessource--;
+
+	if(fRessource <= 0) DeleteInstance();
 }
 
 G4ITTypeManager::G4ITTypeManager()

source/processes/electromagnetic/dna/management/src/G4KDMap.cc

@@ -0,0 +1,120 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+#include "G4KDMap.hh"
+#include <algorithm>
+
+using namespace std;
+
+//typedef std::_Deque_iterator<G4KDNode*,G4KDNode*&,G4KDNode**> _deq_iterator ;
+typedef std::deque<G4KDNode*>::iterator _deq_iterator ;
+
+__1DSortOut::__1DSortOut(int dimension) : fSortOutNDim(dimension)
+{}
+
+int __1DSortOut::GetDimension()
+{
+    return fSortOutNDim.fDimension;
+}
+
+G4KDNode* __1DSortOut::GetMidle(int& main_middle)
+{
+    int contSize = fContainer.size();
+    main_middle = (int) ceil(contSize/2.); // ceil = round up
+    return fContainer[main_middle];
+}
+
+_deq_iterator __1DSortOut::Insert(G4KDNode* pos)
+{
+    return fContainer.insert(fContainer.end(),pos);
+}
+
+G4KDNode* __1DSortOut::PopOutMiddle()
+{
+    int middle;
+    G4KDNode* pos = GetMidle(middle);
+    _deq_iterator deq_pos = fContainer.begin()+middle;
+    fContainer.erase(deq_pos);
+    return pos;
+}
+
+void __1DSortOut::Sort()
+{
+    sort(fContainer.begin(),fContainer.end(),fSortOutNDim);
+}
+
+void __1DSortOut::Erase(_deq_iterator& deq_pos)
+{
+	fContainer.erase(deq_pos);
+}
+
+void G4KDMap::Insert(G4KDNode* pos)
+{
+    vector<_deq_iterator>& vit = fMap[pos];
+
+    size_t maxSize = fSortOut.size();
+
+    cout <<  maxSize << endl;
+    cout <<  fSortOut.capacity() << endl;
+
+    vit.reserve(maxSize);
+
+    for (size_t i = 0; i < fSortOut.size(); ++i)
+    {
+        vit[i]=fSortOut[i]->Insert(pos);
+    }
+
+    fIsSorted = false;
+}
+
+G4KDNode* G4KDMap::PopOutMiddle(int dimension)
+{
+    if(fIsSorted == false) Sort();
+    G4KDNode* output_node = fSortOut[dimension]->PopOutMiddle();
+
+    std::map<G4KDNode*, std::vector<_deq_iterator> >::iterator fMap_it
+    = fMap.find(output_node);
+
+    std::vector<_deq_iterator>&  vit = fMap_it->second;
+
+    for(int i = 0 ; i < (int) fSortOut.size() ; i++)
+    {
+    	if(i != dimension) fSortOut[i]->Erase(vit[i]);
+    }
+
+    fMap.erase(fMap_it);
+
+    return output_node;
+}
+
+void G4KDMap::Sort()
+{
+    for (size_t i = 0; i < fSortOut.size(); ++i)
+    {
+        fSortOut[i]->Sort();
+    }
+
+    fIsSorted = true;
+}

source/processes/electromagnetic/dna/management/src/G4KDTree.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4KDTree.cc 64057 2012-10-30 15:04:49Z gcosmo $
+// $Id: G4KDTree.cc 70171 2013-05-24 13:34:18Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr) 
 //
@@ -71,6 +71,7 @@
 #include <stdlib.h>
 #include <cmath>
 #include "G4KDTree.hh"
+#include "G4KDMap.hh"
 #include "G4KDNode.hh"
 #include "G4KDTreeResult.hh"
 #include <list>
@@ -90,7 +91,7 @@ public:
         size_t size = fDim * sizeof(double);
         memcpy(fMin, min, size);
         memcpy(fMax, max, size);
-   }
+    }
 
 
     ~HyperRect()
@@ -166,7 +167,7 @@ private:
 
 //______________________________________________________________________
 // KDTree methods
-G4KDTree::G4KDTree (int k)
+G4KDTree::G4KDTree (int k) : fKDMap(new G4KDMap(k))
 {
     fDim = k;
     fRoot = 0;
@@ -185,6 +186,8 @@ G4KDTree::~G4KDTree ()
         delete fRect;
         fRect = 0;
     }
+
+    if(fKDMap) delete fKDMap;
 }
 
 void G4KDTree::Clear()
@@ -218,6 +221,45 @@ void G4KDTree::__Clear_Rec(G4KDNode *node)
     delete node;
 }
 
+G4KDNode* G4KDTree::InsertMap(const double& x, const double& y, const double& z, void *data)
+{
+    double buf[3];
+    buf[0] = x;
+    buf[1] = y;
+    buf[2] = z;
+    return InsertMap(buf, data);
+}
+
+G4KDNode* G4KDTree::InsertMap(const double *pos, void *data)
+{
+    G4KDNode* node = new G4KDNode(this,pos,data,0,-2) ;
+    // -2 = valeur intentionnellement absurde
+    fKDMap->Insert(node);
+    return node;
+}
+
+void G4KDTree::Build()
+{
+    int Nnodes = fKDMap->GetSize();
+
+    G4KDNode* root = fKDMap->PopOutMiddle(0);
+
+    fRoot = root;
+    fRect = new HyperRect(fDim,fRoot->GetPosition(),fRoot->GetPosition());
+
+    Nnodes--;
+
+    for(int n = 0 ; n < Nnodes ; n = n+fDim)
+    {
+        for(int dim = 0 ; dim < fDim ; dim ++)
+        {
+            G4KDNode* node = fKDMap->PopOutMiddle(dim);
+            fRoot->Insert(node);
+            fRect->Extend(node->GetPosition());
+        }
+    }
+}
+
 G4KDNode* G4KDTree::Insert(const double *pos, void *data)
 {
     G4KDNode* node = 0 ;
@@ -259,7 +301,7 @@ G4KDNode* G4KDTree::Insert(const double& x, const double& y, const double& z, vo
 
 //__________________________________________________________________
 int G4KDTree::__NearestInRange(G4KDNode *node, const double *pos, const double& range_sq,
-                          const double& range, G4KDTreeResult& list, int ordered, G4KDNode *source_node)
+                               const double& range, G4KDTreeResult& list, int ordered, G4KDNode *source_node)
 {
     if(!node) return 0;
 
@@ -306,7 +348,7 @@ int G4KDTree::__NearestInRange(G4KDNode *node, const double *pos, const double&
 
 //__________________________________________________________________
 void G4KDTree::__NearestToPosition(G4KDNode *node, const double *pos, G4KDNode *&result,
-                         double *result_dist_sq, HyperRect* rect)
+                                   double *result_dist_sq, HyperRect* rect)
 {
     int dir = node->GetAxis();
     int i;
@@ -385,7 +427,7 @@ void G4KDTree::__NearestToPosition(G4KDNode *node, const double *pos, G4KDNode *
 
 G4KDTreeResultHandle G4KDTree::Nearest(const double *pos)
 {
-//    G4cout << "Nearest(pos)" << G4endl ;
+    //    G4cout << "Nearest(pos)" << G4endl ;
 
     if (!fRect) return 0;
 
@@ -418,8 +460,8 @@ G4KDTreeResultHandle G4KDTree::Nearest(const double *pos)
 
 //__________________________________________________________________
 void G4KDTree::__NearestToNode(G4KDNode *source_node, G4KDNode *node,
-                              const double *pos, std::vector<G4KDNode*>& result, double *result_dist_sq,
-                              HyperRect* rect, int& nbresult)
+                               const double *pos, std::vector<G4KDNode*>& result, double *result_dist_sq,
+                               HyperRect* rect, int& nbresult)
 {
     int dir = node->GetAxis();
     double dummy, dist_sq;
@@ -507,7 +549,7 @@ void G4KDTree::__NearestToNode(G4KDNode *source_node, G4KDNode *node,
 
 G4KDTreeResultHandle G4KDTree::Nearest(G4KDNode* node)
 {
-//    G4cout << "Nearest(node)" << G4endl ;
+    //    G4cout << "Nearest(node)" << G4endl ;
     if (!fRect)
     {
         G4cout << "Tree empty" << G4endl ;
@@ -576,9 +618,9 @@ G4KDTreeResultHandle G4KDTree::NearestInRange(const double *pos, const double& r
 }
 
 G4KDTreeResultHandle G4KDTree::NearestInRange(const double& x,
-                                                const double& y,
-                                                const double& z,
-                                                const double& range)
+                                              const double& y,
+                                              const double& z,
+                                              const double& range)
 {
     double buf[3];
     buf[0] = x;

source/processes/electromagnetic/dna/management/src/G4UserTimeStepAction.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4UserReactionAction.cc 64057 2012-10-30 15:04:49Z gcosmo $
+// $Id: G4UserTimeStepAction.cc 74551 2013-10-14 12:59:14Z gcosmo $
 //
 // Author: Mathieu Karamitros (kara@cenbg.in2p3.fr)
 //
@@ -33,17 +33,17 @@
 //
 // -------------------------------------------------------------------
 
-#include "G4UserReactionAction.hh"
+#include "G4UserTimeStepAction.hh"
 
-G4UserReactionAction::G4UserReactionAction()
+G4UserTimeStepAction::G4UserTimeStepAction()
 {;}
 
-G4UserReactionAction::~G4UserReactionAction()
+G4UserTimeStepAction::~G4UserTimeStepAction()
 {;}
 
-G4UserReactionAction::G4UserReactionAction(const G4UserReactionAction& /*other*/){;}
+G4UserTimeStepAction::G4UserTimeStepAction(const G4UserTimeStepAction& /*other*/){;}
 
-G4UserReactionAction& G4UserReactionAction::operator=(const G4UserReactionAction& rhs)
+G4UserTimeStepAction& G4UserTimeStepAction::operator=(const G4UserTimeStepAction& rhs)
 {
     if (this == &rhs) return *this;
     return *this;

source/processes/electromagnetic/dna/management/src/G4VITProcess.cc

@@ -23,20 +23,22 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4VITProcess.cc 64057 2012-10-30 15:04:49Z gcosmo $
+// $Id: G4VITProcess.cc 74551 2013-10-14 12:59:14Z gcosmo $
 //
 #include "G4VITProcess.hh"
 #include "G4SystemOfUnits.hh"
 #include "G4IT.hh"
 
-size_t G4VITProcess::fNbProcess = 0;
+/*G4ThreadLocal*/ size_t *G4VITProcess::fNbProcess = 0;
 
 G4VITProcess::G4VITProcess(const G4String& name, G4ProcessType type) :
     G4VProcess( name, type ),
-    fpState (0),
-    fProcessID(fNbProcess)
+    fpState (0)//,
+			  //fProcessID(fNbProcess)
 {
-        fNbProcess++;
+        if (!fNbProcess) fNbProcess = new size_t (0);
+        fProcessID = *fNbProcess;
+        (*fNbProcess)++;
         SetInstantiateProcessState(true);
         currentInteractionLength            = 0;
         theInteractionTimeLeft              = 0;
@@ -93,26 +95,3 @@ void G4VITProcess::StartTracking(G4Track* track)
     fpState = 0;
 }
 
-void G4VITProcess::SubtractNumberOfInteractionLengthLeft(
-                                  G4double previousStepSize )
-{
-  if (fpState->currentInteractionLength>0.0) {
-    fpState->theNumberOfInteractionLengthLeft -= previousStepSize/(fpState->currentInteractionLength);
-    if(fpState->theNumberOfInteractionLengthLeft<0.) {
-       fpState->theNumberOfInteractionLengthLeft=perMillion;
-    }
-
-  } else {
-#ifdef G4VERBOSE
-    if (verboseLevel>0) {
-      G4cerr << "G4VProcess::SubtractNumberOfInteractionLengthLeft()";
-      G4cerr << " [" << theProcessName << "]" <<G4endl;
-      G4cerr << " currentInteractionLength = " << *currentInteractionLength/cm << " [cm]";
-      G4cerr << " previousStepSize = " << previousStepSize/cm << " [cm]";
-      G4cerr << G4endl;
-    }
-#endif
-    G4Exception("G4VProcess::SubtractNumberOfInteractionLengthLeft()",
-		"Negative currentInteractionLength",EventMustBeAborted,theProcessName);
-  }
-}

source/processes/electromagnetic/dna/management/src/G4VITTimeStepper.cc

@@ -23,7 +23,7 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
-// $Id: G4VITTimeStepper.cc 64057 2012-10-30 15:04:49Z gcosmo $
+// $Id: G4VITTimeStepper.cc 66872 2013-01-15 01:25:57Z japost $
 //
 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr) 
 //
@@ -35,8 +35,8 @@
 
 #include "G4VITTimeStepper.hh"
 
-G4double G4VITTimeStepper::fCurrentGlobalTime = -1;
-G4double G4VITTimeStepper::fUserMinTimeStep   = -1;
+G4ThreadLocal G4double G4VITTimeStepper::fCurrentGlobalTime = -1;
+G4ThreadLocal G4double G4VITTimeStepper::fUserMinTimeStep   = -1;
 
 G4VITTimeStepper::G4VITTimeStepper()
 {

source/processes/electromagnetic/dna/management/src/G4VTrackState.cc

@@ -0,0 +1,37 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+/*
+ * G4VTrackState.cc
+ *
+ *  Created on: 8 avr. 2013
+ *      Author: kara
+ */
+
+#include "G4VTrackState.hh"
+
+int G4VTrackStateID::fgLastID = 0;
+
+template <class T> CLHEP::shared_ptr<G4TrackStateID<T> > G4TrackStateID<T>::fgTrackStateID (0);