]> git.uio.no Git - u/mrichter/AliRoot.git/blobdiff - STEER/AliStack.cxx
For embedding: use AliESDEvent instead of AliESD (obsolete)
[u/mrichter/AliRoot.git] / STEER / AliStack.cxx
index 9ee1ed7723cd3ab3ea6eb7905a1bf1ab426019b6..6bff8223966c4cf35ed584baf53ec3d94c22ae40 100644 (file)
 
 ///////////////////////////////////////////////////////////////////////////////
 //                                                                           //
-//  Particles stack class
+//  Particles stack class                                                    //
+//  Implements the TMCVirtualStack of the Virtual Monte Carlo                //
+//  Holds the particles transported during simulation                        //
+//  Is used to compare results of reconstruction with simulation             //
+//  Author A.Morsch                                                          //
 //                                                                           //
 ///////////////////////////////////////////////////////////////////////////////
 
  
-#include <TFile.h>
-#include <TFolder.h>
+#include <TClonesArray.h>
 #include <TObjArray.h>
+#include <TPDGCode.h>
 #include <TParticle.h>
 #include <TParticlePDG.h>
+#include <TDatabasePDG.h>
 #include <TTree.h>
+#include <TDirectory.h>
 
-#include "AliHit.h"
-#include "AliModule.h"
-#include "AliRun.h"
-#include "AliMC.h"
-#include "AliRunLoader.h"
+#include "AliLog.h"
 #include "AliStack.h"
 
 ClassImp(AliStack)
 
 //_______________________________________________________________________
 AliStack::AliStack():
-  fParticles(0),
-  fParticleMap(0),
+  fParticles("TParticle", 1000),
+  fParticleMap(),
   fParticleFileMap(0),
   fParticleBuffer(0),
+  fCurrentTrack(0),
   fTreeK(0),
   fNtrack(0),
   fNprimary(0),
@@ -51,7 +54,7 @@ AliStack::AliStack():
   fCurrentPrimary(-1),
   fHgwmk(0),
   fLoadPoint(0),
-  fEventFolderName(AliConfig::fgkDefaultEventFolderName)
+  fTrackLabelMap(0)
 {
   //
   // Default constructor
@@ -59,11 +62,12 @@ AliStack::AliStack():
 }
 
 //_______________________________________________________________________
-AliStack::AliStack(Int_t size, const char* evfoldname):
-  fParticles(new TClonesArray("TParticle",1000)),
-  fParticleMap(new TObjArray(size)),
+AliStack::AliStack(Int_t size, const char* /*evfoldname*/):
+  fParticles("TParticle",1000),
+  fParticleMap(size),
   fParticleFileMap(0),
   fParticleBuffer(0),
+  fCurrentTrack(0),
   fTreeK(0),
   fNtrack(0),
   fNprimary(0),
@@ -71,7 +75,7 @@ AliStack::AliStack(Int_t size, const char* evfoldname):
   fCurrentPrimary(-1),
   fHgwmk(0),
   fLoadPoint(0),
-  fEventFolderName(evfoldname)
+  fTrackLabelMap(0)
 {
   //
   //  Constructor
@@ -80,29 +84,29 @@ AliStack::AliStack(Int_t size, const char* evfoldname):
 
 //_______________________________________________________________________
 AliStack::AliStack(const AliStack& st):
-  TVirtualMCStack(st),
-  fParticles(0),
-  fParticleMap(0),
-  fParticleFileMap(0),
-  fParticleBuffer(0),
-  fTreeK(0),
-  fNtrack(0),
-  fNprimary(0),
-  fCurrent(-1),
-  fCurrentPrimary(-1),
-  fHgwmk(0),
-  fLoadPoint(0)
+    TVirtualMCStack(st),
+    fParticles("TParticle",1000),
+    fParticleMap(*(st.Particles())),
+    fParticleFileMap(st.fParticleFileMap),
+    fParticleBuffer(0),
+    fCurrentTrack(0),
+    fTreeK((TTree*)(st.fTreeK->Clone())),
+    fNtrack(st.GetNtrack()),
+    fNprimary(st.GetNprimary()),
+    fCurrent(-1),
+    fCurrentPrimary(-1),
+    fHgwmk(0),
+    fLoadPoint(0),
+    fTrackLabelMap(0)
 {
-  //
-  // Copy constructor
-  //
-  st.Copy(*this);
+    // Copy constructor
 }
 
+
 //_______________________________________________________________________
-void AliStack::Copy(AliStack&) const
+void AliStack::Copy(TObject&) const
 {
-  Fatal("Copy","Not implemented!\n");
+  AliFatal("Not implemented!");
 }
 
 //_______________________________________________________________________
@@ -112,12 +116,7 @@ AliStack::~AliStack()
   // Destructor
   //
   
-  if (fParticles) {
-    fParticles->Delete();
-    delete fParticles;
-  }
-  delete fParticleMap;
-  //PH???  delete fTreeK;
+    fParticles.Clear();
 }
 
 //
@@ -125,15 +124,15 @@ AliStack::~AliStack()
 //
 
 //_____________________________________________________________________________
-void AliStack::PushTrack(Int_t done, Int_t parent, Int_t pdg, Float_t *pmom,
-                        Float_t *vpos, Float_t *polar, Float_t tof,
+void AliStack::PushTrack(Int_t done, Int_t parent, Int_t pdg, const Float_t *pmom,
+                        const Float_t *vpos, const Float_t *polar, Float_t tof,
                         TMCProcess mech, Int_t &ntr, Float_t weight, Int_t is)
 { 
   //
   // Load a track on the stack
   //
-  // done     0 if the track has to be transported
-  //          1 if not
+  // done     1 if the track has to be transported
+  //          0 if not
   // parent   identifier of the parent track. -1 for a primary
   // pdg    particle code
   // pmom     momentum GeV/c
@@ -167,8 +166,8 @@ void AliStack::PushTrack(Int_t done, Int_t parent, Int_t pdg, Float_t *pmom,
                 vpos[0], vpos[1], vpos[2], tof, polar[0], polar[1], polar[2],
                 mech, ntr, weight, is);
     } else {
-       Warning("PushTrack", "Particle type %d not defined in PDG Database !\n", pdg);
-       Warning("PushTrack", "Particle skipped !\n");
+       AliWarning(Form("Particle type %d not defined in PDG Database !", pdg));
+       AliWarning("Particle skipped !");
     }
 }
 
@@ -182,8 +181,8 @@ void AliStack::PushTrack(Int_t done, Int_t parent, Int_t pdg,
   //
   // Load a track on the stack
   //
-  // done        0 if the track has to be transported
-  //             1 if not
+  // done        1 if the track has to be transported
+  //             0 if not
   // parent      identifier of the parent track. -1 for a primary
   // pdg         particle code
   // kS          generation status code
@@ -200,13 +199,12 @@ void AliStack::PushTrack(Int_t done, Int_t parent, Int_t pdg,
   // Note: the energy is not calculated from the static mass but
   // it is passed by argument e.
 
-
   const Int_t kFirstDaughter=-1;
   const Int_t kLastDaughter=-1;
-  
-  TClonesArray &particles = *fParticles;
+
+
   TParticle* particle
-    = new(particles[fLoadPoint++]) 
+    = new(fParticles[fLoadPoint++]) 
       TParticle(pdg, is, parent, -1, kFirstDaughter, kLastDaughter,
                px, py, pz, e, vx, vy, vz, tof);
    
@@ -214,31 +212,40 @@ void AliStack::PushTrack(Int_t done, Int_t parent, Int_t pdg,
   particle->SetWeight(weight);
   particle->SetUniqueID(mech);
 
-  if(!done) particle->SetBit(kDoneBit);
+  
+  
+  if(!done) {
+      particle->SetBit(kDoneBit);
+  } else {
+      particle->SetBit(kTransportBit);
+  }
+  
+  
 
   //  Declare that the daughter information is valid
   particle->SetBit(kDaughtersBit);
   //  Add the particle to the stack
-  fParticleMap->AddAtAndExpand(particle, fNtrack);//CHECK!!
+  
+  
+  fParticleMap.AddAtAndExpand(particle, fNtrack);//CHECK!!
 
   if(parent>=0) {
-    particle = dynamic_cast<TParticle*>(fParticleMap->At(parent));
-    if (particle) {
-      particle->SetLastDaughter(fNtrack);
-      if(particle->GetFirstDaughter()<0) particle->SetFirstDaughter(fNtrack);
-    }
-    else {
-      printf("Error in AliStack::PushTrack: Parent %d does not exist\n",parent);
-    }
-  } 
-  else { 
-    //
-    // This is a primary track. Set high water mark for this event
-    fHgwmk = fNtrack;
-    //
-    // Set also number if primary tracks
-    fNprimary = fHgwmk+1;
-    fCurrentPrimary++;
+      particle = dynamic_cast<TParticle*>(fParticleMap.At(parent));
+      if (particle) {
+         particle->SetLastDaughter(fNtrack);
+         if(particle->GetFirstDaughter()<0) particle->SetFirstDaughter(fNtrack);
+      }
+      else {
+         AliError(Form("Parent %d does not exist",parent));
+      }
+  } else { 
+      //
+      // This is a primary track. Set high water mark for this event
+      fHgwmk = fNtrack;
+      //
+      // Set also number if primary tracks
+      fNprimary = fHgwmk+1;
+      fCurrentPrimary++;
   }
   ntr = fNtrack++;
 }
@@ -281,133 +288,202 @@ TParticle*  AliStack::PopPrimaryForTracking(Int_t i)
 }      
 
 //_____________________________________________________________________________
-void AliStack::PurifyKine()
+Bool_t AliStack::PurifyKine()
 {
   //
   // Compress kinematic tree keeping only flagged particles
   // and renaming the particle id's in all the hits
   //
 
-  TObjArray &particles = *fParticleMap;
-  int nkeep=fHgwmk+1, parent, i;
+  int nkeep = fHgwmk + 1, parent, i;
   TParticle *part, *father;
-  TArrayI map(particles.GetLast()+1);
+  fTrackLabelMap.Set(fParticleMap.GetLast()+1);
 
   // Save in Header total number of tracks before compression
-
   // If no tracks generated return now
-  if(fHgwmk+1 == fNtrack) return;
+  if(fHgwmk+1 == fNtrack) return kFALSE;
 
   // First pass, invalid Daughter information
   for(i=0; i<fNtrack; i++) {
-    // Preset map, to be removed later
-    if(i<=fHgwmk) map[i]=i ; 
-    else {
-      map[i] = -99;
-      if((part=dynamic_cast<TParticle*>(particles.At(i)))) {
+      // Preset map, to be removed later
+      if(i<=fHgwmk) fTrackLabelMap[i]=i ; 
+      else {
+         fTrackLabelMap[i] = -99;
+         if((part=dynamic_cast<TParticle*>(fParticleMap.At(i)))) {
 //
 //        Check of this track should be kept for physics reasons 
-          if (KeepPhysics(part)) KeepTrack(i);
+             if (KeepPhysics(part)) KeepTrack(i);
 //
-          part->ResetBit(kDaughtersBit);
-          part->SetFirstDaughter(-1);
-          part->SetLastDaughter(-1);
+             part->ResetBit(kDaughtersBit);
+             part->SetFirstDaughter(-1);
+             part->SetLastDaughter(-1);
+         }
       }
-    }
   }
   // Invalid daughter information for the parent of the first particle
   // generated. This may or may not be the current primary according to
   // whether decays have been recorded among the primaries
-  part = dynamic_cast<TParticle*>(particles.At(fHgwmk+1));
-  particles.At(part->GetFirstMother())->ResetBit(kDaughtersBit);
+  part = dynamic_cast<TParticle*>(fParticleMap.At(fHgwmk+1));
+  fParticleMap.At(part->GetFirstMother())->ResetBit(kDaughtersBit);
   // Second pass, build map between old and new numbering
   for(i=fHgwmk+1; i<fNtrack; i++) {
-    if(particles.At(i)->TestBit(kKeepBit)) {
-      
-      // This particle has to be kept
-      map[i]=nkeep;
-      // If old and new are different, have to move the pointer
-      if(i!=nkeep) particles[nkeep]=particles.At(i);
-      part = dynamic_cast<TParticle*>(particles.At(nkeep));
-      
-      // as the parent is always *before*, it must be already
-      // in place. This is what we are checking anyway!
-      if((parent=part->GetFirstMother())>fHgwmk) 
-       if(map[parent]==-99) Fatal("PurifyKine","map[%d] = -99!\n",parent);
-       else part->SetFirstMother(map[parent]);
-
-      nkeep++;
-    }
+      if(fParticleMap.At(i)->TestBit(kKeepBit)) {
+         // This particle has to be kept
+         fTrackLabelMap[i]=nkeep;
+         // If old and new are different, have to move the pointer
+         if(i!=nkeep) fParticleMap[nkeep]=fParticleMap.At(i);
+         part = dynamic_cast<TParticle*>(fParticleMap.At(nkeep));
+         // as the parent is always *before*, it must be already
+         // in place. This is what we are checking anyway!
+         if((parent=part->GetFirstMother())>fHgwmk) {
+             if(fTrackLabelMap[parent]==-99) Fatal("PurifyKine","fTrackLabelMap[%d] = -99!\n",parent);
+             else part->SetFirstMother(fTrackLabelMap[parent]);}
+         nkeep++;
+      }
   }
   
   // Fix daughters information
   for (i=fHgwmk+1; i<nkeep; i++) {
-    part = dynamic_cast<TParticle*>(particles.At(i));
-    parent = part->GetFirstMother();
-    if(parent>=0) {
-      father = dynamic_cast<TParticle*>(particles.At(parent));
-      if(father->TestBit(kDaughtersBit)) {
-      
-       if(i<father->GetFirstDaughter()) father->SetFirstDaughter(i);
-       if(i>father->GetLastDaughter())  father->SetLastDaughter(i);
-      } else {
-       // Initialise daughters info for first pass
-       father->SetFirstDaughter(i);
-       father->SetLastDaughter(i);
-       father->SetBit(kDaughtersBit);
+      part = dynamic_cast<TParticle*>(fParticleMap.At(i));
+      parent = part->GetFirstMother();
+      if(parent>=0) {
+         father = dynamic_cast<TParticle*>(fParticleMap.At(parent));
+         if(father->TestBit(kDaughtersBit)) {
+             
+             if(i<father->GetFirstDaughter()) father->SetFirstDaughter(i);
+             if(i>father->GetLastDaughter())  father->SetLastDaughter(i);
+         } else {
+             // Initialise daughters info for first pass
+             father->SetFirstDaughter(i);
+             father->SetLastDaughter(i);
+             father->SetBit(kDaughtersBit);
+         }
       }
-    }
-  }
-  
-  // Now loop on all registered hit lists
-  TList* hitLists = gAlice->GetMCApp()->GetHitLists();
-  TIter next(hitLists);
-  TCollection *hitList;
-  while((hitList = dynamic_cast<TCollection*>(next()))) {
-    TIter nexthit(hitList);
-    AliHit *hit;
-    while((hit = dynamic_cast<AliHit*>(nexthit()))) {
-      hit->SetTrack(map[hit->GetTrack()]);
-    }
   }
-
-  // 
-  // This for detectors which have a special mapping mechanism
-  // for hits, such as TPC and TRD
   //
+  // Now the output bit, from fHgwmk to nkeep we write everything and we erase
+  if(nkeep > fParticleFileMap.GetSize()) fParticleFileMap.Set(Int_t (nkeep*1.5));
+  for (i=fHgwmk+1; i<nkeep; ++i) {
+      fParticleBuffer = dynamic_cast<TParticle*>(fParticleMap.At(i));
+      fParticleFileMap[i]=static_cast<Int_t>(TreeK()->GetEntries());
+      TreeK()->Fill();
+      fParticleMap[i]=fParticleBuffer=0;
+  }
   
-   TObjArray* modules = gAlice->Modules();
-   TIter nextmod(modules);
-   AliModule *detector;
-   while((detector = dynamic_cast<AliModule*>(nextmod()))) {
-     detector->RemapTrackHitIDs(map.GetArray());
-     detector->RemapTrackReferencesIDs(map.GetArray());
-   }
-   //
-   gAlice->GetMCApp()->RemapTrackReferencesIDs(map.GetArray());
-
-   // Now the output bit, from fHgwmk to nkeep we write everything and we erase
-   if(nkeep>fParticleFileMap.GetSize()) fParticleFileMap.Set(Int_t (nkeep*1.5));
-
-   for (i=fHgwmk+1; i<nkeep; ++i) {
-     fParticleBuffer = dynamic_cast<TParticle*>(particles.At(i));
-     fParticleFileMap[i]=static_cast<Int_t>(TreeK()->GetEntries());
-     TreeK()->Fill();
-     particles[i]=fParticleBuffer=0;
-    }
+  for (i = nkeep; i < fNtrack; ++i) fParticleMap[i]=0;
+  
+  Int_t toshrink = fNtrack-fHgwmk-1;
+  fLoadPoint-=toshrink;
+  
+  for(i=fLoadPoint; i<fLoadPoint+toshrink; ++i) fParticles.RemoveAt(i);
+  fNtrack=nkeep;
+  fHgwmk=nkeep-1;
+  return kTRUE;
+}
 
-   for (i=nkeep; i<fNtrack; ++i) particles[i]=0;
 
-   Int_t toshrink = fNtrack-fHgwmk-1;
-   fLoadPoint-=toshrink;
-   for(i=fLoadPoint; i<fLoadPoint+toshrink; ++i) fParticles->RemoveAt(i);
+Bool_t AliStack::ReorderKine()
+{
+//
+// In some transport code children might not come in a continuous sequence.
+// In this case the stack  has  to  be reordered in order to establish the 
+// mother daughter relation using index ranges.
+//    
+  if(fHgwmk+1 == fNtrack) return kFALSE;
 
-   fNtrack=nkeep;
-   fHgwmk=nkeep-1;
-   //   delete [] map;
+  //
+  // Howmany secondaries have been produced ?
+  Int_t nNew = fNtrack - fHgwmk - 1;
+    
+  if (nNew > 0) {
+      Int_t i, j;
+      TArrayI map1(nNew);
+      //
+      // Copy pointers to temporary array
+      TParticle** tmp = new TParticle*[nNew];
+      
+      for (i = 0; i < nNew; i++) {
+         if (fParticleMap.At(fHgwmk + 1 + i)) {
+             tmp[i] = (TParticle*) (fParticleMap.At(fHgwmk + 1 + i));
+         } else {
+             tmp[i] = 0x0;
+         }
+         map1[i] = -99;
+      }
+  
+      
+      //
+      // Reset  LoadPoint 
+      // 
+      Int_t loadPoint = fHgwmk + 1;
+      //
+      // Re-Push particles into stack 
+      // The outer loop is over parents, the inner over children.
+      // -1 refers to the primary particle
+      //
+      for (i = -1; i < nNew-1; i++) {
+         Int_t ipa;
+         TParticle* parP;
+         if (i == -1) {
+             ipa  = tmp[0]->GetFirstMother();
+             parP =dynamic_cast<TParticle*>(fParticleMap.At(ipa));
+         } else {
+             ipa = (fHgwmk + 1 + i);
+              // Skip deleted particles
+             if (!tmp[i])                          continue;
+              // Skip particles without children
+             if (tmp[i]->GetFirstDaughter() == -1) continue;
+             parP = tmp[i];
+         }
+          // Reset daughter information
+
+         Int_t idaumin = parP->GetFirstDaughter() - fHgwmk - 1;
+         Int_t idaumax = parP->GetLastDaughter()  - fHgwmk - 1;
+         parP->SetFirstDaughter(-1);
+         parP->SetLastDaughter(-1);
+         for (j = idaumin; j <= idaumax; j++) {
+              // Skip deleted particles
+             if (!tmp[j])        continue;
+              // Skip particles already handled
+             if (map1[j] != -99) continue;
+             Int_t jpa = tmp[j]->GetFirstMother();
+              // Check if daughter of current parent
+             if (jpa == ipa) {
+                 fParticleMap[loadPoint] = tmp[j];
+                 // Re-establish daughter information
+                 parP->SetLastDaughter(loadPoint);
+                 if (parP->GetFirstDaughter() == -1) parP->SetFirstDaughter(loadPoint);
+                 // Set Mother information
+                 if (i != -1) {
+                     tmp[j]->SetFirstMother(map1[i]);
+                 } 
+                 // Build the map
+                 map1[j] = loadPoint;
+                 // Increase load point
+                 loadPoint++;
+             }
+         } // children
+      } // parents
+
+      delete[] tmp;
+
+      //
+      // Build map for remapping of hits
+      // 
+      fTrackLabelMap.Set(fNtrack);
+      for (i = 0; i < fNtrack; i ++) {
+         if (i <= fHgwmk) {
+             fTrackLabelMap[i] = i;
+         } else{
+             fTrackLabelMap[i] = map1[i - fHgwmk -1];
+         }
+      }
+  } // new particles poduced
+  
+  return kTRUE;
 }
 
-Bool_t AliStack::KeepPhysics(TParticle* part)
+Bool_t AliStack::KeepPhysics(const TParticle* part)
 {
     //
     // Some particles have to kept on the stack for reasons motivated
@@ -444,7 +520,6 @@ void AliStack::FinishEvent()
   
 // Update event header
 
-
   if (!TreeK()) {
 //    Fatal("FinishEvent", "No kinematics tree is defined.");
 //    Don't panic this is a probably a lego run
@@ -452,7 +527,7 @@ void AliStack::FinishEvent()
   }  
   
   CleanParents();
-  if(TreeK()->GetEntries() ==0) {
+   if(TreeK()->GetEntries() ==0) {
     // set the fParticleFileMap size for the first time
     fParticleFileMap.Set(fHgwmk+1);
   }
@@ -460,17 +535,16 @@ void AliStack::FinishEvent()
   Bool_t allFilled = kFALSE;
   TObject *part;
   for(Int_t i=0; i<fHgwmk+1; ++i) 
-    if((part=fParticleMap->At(i))) {
+    if((part=fParticleMap.At(i))) {
       fParticleBuffer = dynamic_cast<TParticle*>(part);
       fParticleFileMap[i]= static_cast<Int_t>(TreeK()->GetEntries());
       TreeK()->Fill();
-      //PH      (*fParticleMap)[i]=fParticleBuffer=0;      
       fParticleBuffer=0;      
-      fParticleMap->AddAt(0,i);      
+      fParticleMap.AddAt(0,i);      
       
       // When all primaries were filled no particle!=0
       // should be left => to be removed later.
-      if (allFilled) printf("Why != 0 part # %d?\n",i);
+      if (allFilled) AliWarning(Form("Why != 0 part # %d?\n",i));
     }
     else 
      {
@@ -494,7 +568,7 @@ void AliStack::FlagTrack(Int_t track)
 
   Int_t curr=track;
   while(1) {
-    particle=dynamic_cast<TParticle*>(fParticleMap->At(curr));
+    particle=dynamic_cast<TParticle*>(fParticleMap.At(curr));
     
     // If the particle is flagged the three from here upward is saved already
     if(particle->TestBit(kKeepBit)) return;
@@ -514,14 +588,14 @@ void AliStack::KeepTrack(Int_t track)
   // Flags a track to be kept
   //
   
-  fParticleMap->At(track)->SetBit(kKeepBit);
+  fParticleMap.At(track)->SetBit(kKeepBit);
 }
 
 //_____________________________________________________________________________
-void  AliStack::Reset(Int_t size) 
+void  AliStack::Clean(Int_t size) 
 {
   //
-  // Resets stack
+  // Reset stack data except for fTreeK
   //
   
   fNtrack=0;
@@ -529,26 +603,30 @@ void  AliStack::Reset(Int_t size)
   fHgwmk=0;
   fLoadPoint=0;
   fCurrent = -1;
-  fTreeK = 0x0;
   ResetArrays(size);
 }
 
+//_____________________________________________________________________________
+void  AliStack::Reset(Int_t size) 
+{
+  //
+  // Reset stack data including fTreeK
+  //
+
+  Clean(size);
+  delete fParticleBuffer; fParticleBuffer = 0;
+  fTreeK = 0x0;
+}
+
 //_____________________________________________________________________________
 void  AliStack::ResetArrays(Int_t size) 
 {
   //
   // Resets stack arrays
   //
-
-  if (fParticles) 
-    fParticles->Clear();
-  else
-    fParticles = new TClonesArray("TParticle",1000);
-  if (fParticleMap) {
-    fParticleMap->Clear();
-    if (size>0) fParticleMap->Expand(size);}
-  else
-    fParticleMap = new TObjArray(size);
+  fParticles.Clear();
+  fParticleMap.Clear();
+  if (size>0) fParticleMap.Expand(size);
 }
 
 //_____________________________________________________________________________
@@ -557,13 +635,11 @@ void AliStack::SetHighWaterMark(Int_t)
   //
   // Set high water mark for last track in event
   //
-  
-  fHgwmk = fNtrack-1;
-  fCurrentPrimary=fHgwmk;
-  
-  // Set also number of primary tracks
-  fNprimary = fHgwmk+1;
-  fNtrack   = fHgwmk+1;      
+    
+    fHgwmk = fNtrack-1;
+    fCurrentPrimary=fHgwmk;
+    // Set also number of primary tracks
+    fNprimary = fHgwmk+1;
 }
 
 //_____________________________________________________________________________
@@ -571,10 +647,9 @@ TParticle* AliStack::Particle(Int_t i)
 {
   //
   // Return particle with specified ID
-  
-  //PH  if(!(*fParticleMap)[i]) {
-  if(!fParticleMap->At(i)) {
-    Int_t nentries = fParticles->GetEntriesFast();
+
+  if(!fParticleMap.At(i)) {
+    Int_t nentries = fParticles.GetEntriesFast();
     // algorithmic way of getting entry index
     // (primary particles are filled after secondaries)
     Int_t entry = TreeKEntry(i);
@@ -582,17 +657,18 @@ TParticle* AliStack::Particle(Int_t i)
     // and the fParticleFileMap[i] give the same;
     // give the fatal error if not
     if (entry != fParticleFileMap[i]) {
-      Fatal("Particle",
+      AliFatal(Form(
         "!! The algorithmic way and map are different: !!\n entry: %d map: %d",
-       entry, fParticleFileMap[i]); 
+       entry, fParticleFileMap[i]))
     } 
-      
+    // Load particle at entry into fParticleBuffer
     TreeK()->GetEntry(entry);
-    new ((*fParticles)[nentries]) TParticle(*fParticleBuffer);
-    fParticleMap->AddAt((*fParticles)[nentries],i);
+    // Add to the TClonesarray
+    new (fParticles[nentries]) TParticle(*fParticleBuffer);
+    // Store a pointer in the TObjArray
+    fParticleMap.AddAt(fParticles[nentries],i);
   }
-  //PH  return dynamic_cast<TParticle *>((*fParticleMap)[i]);
-  return dynamic_cast<TParticle*>(fParticleMap->At(i));
+  return dynamic_cast<TParticle*>(fParticleMap.At(i));
 }
 
 //_____________________________________________________________________________
@@ -611,9 +687,18 @@ TParticle* AliStack::ParticleFromTreeK(Int_t id) const
 Int_t AliStack::TreeKEntry(Int_t id) const 
 {
 //
-// return entry number in the TreeK for particle with label id
-// return negative number if label>fNtrack
+// Return entry number in the TreeK for particle with label id
+// Return negative number if label>fNtrack
 //
+// The order of particles in TreeK reflects the order of the transport of primaries and production of secondaries:
+//
+// Before transport there are fNprimary particles on the stack.
+// They are transported one by one and secondaries (fNtrack - fNprimary) are produced. 
+// After the transport of each particles secondaries are written to the TreeK
+// They occupy the entries 0 ... fNtrack - fNprimary - 1
+// The primaries are written after they have been transported and occupy 
+// fNtrack - fNprimary .. fNtrack - 1
+
   Int_t entry;
   if (id<fNprimary)
     entry = id+fNtrack-fNprimary;
@@ -629,12 +714,12 @@ Int_t AliStack::GetCurrentParentTrackNumber() const
   // Return number of the parent of the current track
   //
   
-  TParticle* current = (TParticle*)fParticleMap->At(fCurrent);
+  TParticle* current = (TParticle*)fParticleMap.At(fCurrent);
 
   if (current) 
     return current->GetFirstMother();
   else {
-    Warning("GetCurrentParentTrackNumber", "Current track not found in the stack");
+    AliWarning("Current track not found in the stack");
     return -1;
   }  
 }
@@ -662,9 +747,7 @@ void AliStack::DumpPart (Int_t i) const
   //
   // Dumps particle i in the stack
   //
-  
-  //PH  dynamic_cast<TParticle*>((*fParticleMap)[i])->Print();
-  dynamic_cast<TParticle*>(fParticleMap->At(i))->Print();
+  dynamic_cast<TParticle*>(fParticleMap.At(i))->Print();
 }
 
 //_____________________________________________________________________________
@@ -691,9 +774,9 @@ void AliStack::DumpPStack ()
   printf("\n=======================================================================\n\n");
   
   // print  particle file map
-  printf("\nParticle file map: \n");
-  for (i=0; i<fNtrack; i++) 
-      printf("   %d th entry: %d \n",i,fParticleFileMap[i]);
+  // printf("\nParticle file map: \n");
+  // for (i=0; i<fNtrack; i++) 
+  //     printf("   %d th entry: %d \n",i,fParticleFileMap[i]);
 }
 
 
@@ -705,12 +788,11 @@ void AliStack::DumpLoadedStack() const
   // that are loaded in memory.
   //
 
-  TObjArray &particles = *fParticleMap;
   printf(
         "\n\n=======================================================================\n");
   for (Int_t i=0;i<fNtrack;i++) 
     {
-      TParticle* particle = dynamic_cast<TParticle*>(particles[i]);
+      TParticle* particle = dynamic_cast<TParticle*>(fParticleMap[i]);
       if (particle) {
         printf("-> %d ",i); particle->Print();
         printf("--------------------------------------------------------------\n");
@@ -736,11 +818,10 @@ void AliStack::CleanParents()
   // Set parent/daughter relations
   //
   
-  TObjArray &particles = *fParticleMap;
   TParticle *part;
   int i;
   for(i=0; i<fHgwmk+1; i++) {
-    part = dynamic_cast<TParticle*>(particles.At(i));
+    part = dynamic_cast<TParticle*>(fParticleMap.At(i));
     if(part) if(!part->TestBit(kDaughtersBit)) {
       part->SetFirstDaughter(-1);
       part->SetLastDaughter(-1);
@@ -760,7 +841,7 @@ TParticle* AliStack::GetNextParticle()
   // search secondaries
   //for(Int_t i=fNtrack-1; i>=0; i--) {
   for(Int_t i=fNtrack-1; i>fHgwmk; i--) {
-      particle = dynamic_cast<TParticle*>(fParticleMap->At(i));
+      particle = dynamic_cast<TParticle*>(fParticleMap.At(i));
       if ((particle) && (!particle->TestBit(kDoneBit))) {
          fCurrent=i;    
          return particle;
@@ -770,7 +851,7 @@ TParticle* AliStack::GetNextParticle()
   // take next primary if all secondaries were done
   while (fCurrentPrimary>=0) {
       fCurrent = fCurrentPrimary;    
-      particle = dynamic_cast<TParticle*>(fParticleMap->At(fCurrentPrimary--));
+      particle = dynamic_cast<TParticle*>(fParticleMap.At(fCurrentPrimary--));
       if ((particle) && (!particle->TestBit(kDoneBit))) {
          return particle;
       } 
@@ -778,50 +859,26 @@ TParticle* AliStack::GetNextParticle()
   
   // nothing to be tracked
   fCurrent = -1;
+  
   return particle;  
 }
 //__________________________________________________________________________________________
 
-TTree* AliStack::TreeK()
-{
-//returns TreeK
-  if (fTreeK)
-   {
-     return fTreeK;
-   }
-  else
-   {
-     AliRunLoader *rl = AliRunLoader::GetRunLoader(fEventFolderName);
-     if (rl == 0x0)
-      {
-        Fatal("TreeK","Can not get RunLoader from event folder named %s",fEventFolderName.Data());
-        return 0x0;//pro forma
-      }
-    fTreeK = rl->TreeK();
-    if ( fTreeK == 0x0)
-     {
-      Error("TreeK","Can not get TreeK from RL. Ev. Folder is %s",fEventFolderName.Data());
-     }
-    else
-     {
-      ConnectTree();
-     }
-   }
-  return fTreeK;//never reached
-}
-//__________________________________________________________________________________________
-
-void AliStack::ConnectTree()
+void AliStack::ConnectTree(TTree* tree)
 {
 //
 //  Creates branch for writing particles
 //
-  if (AliLoader::fgDebug) Info("ConnectTree","Connecting TreeK");
+
+  fTreeK = tree;
+    
+  AliDebug(1, "Connecting TreeK");
   if (fTreeK == 0x0)
    {
     if (TreeK() == 0x0)
      {
-      Fatal("ConnectTree","Parameter is NULL");//we don't like such a jokes
+      AliFatal("Parameter is NULL");//we don't like such a jokes
       return;
      }
     return;//in this case TreeK() calls back this method (ConnectTree) 
@@ -831,50 +888,34 @@ void AliStack::ConnectTree()
 
  //  Create a branch for particles   
   
-  if (AliLoader::fgDebug) 
-   Info("ConnectTree","Tree name is %s",fTreeK->GetName());
+  AliDebug(2, Form("Tree name is %s",fTreeK->GetName()));
    
   if (fTreeK->GetDirectory())
    {
-     if (AliLoader::fgDebug)    
-      Info("ConnectTree","and dir is %s",fTreeK->GetDirectory()->GetName());
+     AliDebug(2, Form("and dir is %s",fTreeK->GetDirectory()->GetName()));
    }    
   else
-    Warning("ConnectTree","DIR IS NOT SET !!!");
+    AliWarning("DIR IS NOT SET !!!");
   
-  TBranch *branch=fTreeK->GetBranch(AliRunLoader::fgkKineBranchName);
+  TBranch *branch=fTreeK->GetBranch("Particles");
   if(branch == 0x0)
    {
-    branch = fTreeK->Branch(AliRunLoader::fgkKineBranchName, "TParticle", &fParticleBuffer, 4000);
-    if (AliLoader::fgDebug) Info("ConnectTree","Creating Branch in Tree");
+    branch = fTreeK->Branch("Particles", "TParticle", &fParticleBuffer, 4000);
+    AliDebug(2, "Creating Branch in Tree");
    }  
   else
    {
-    if (AliLoader::fgDebug) Info("ConnectTree","Branch Found in Tree");
+    AliDebug(2, "Branch Found in Tree");
     branch->SetAddress(&fParticleBuffer);
    }
   if (branch->GetDirectory())
    {
-    if (AliLoader::fgDebug) 
-      Info("ConnectTree","Branch Dir Name is %s",branch->GetDirectory()->GetName());
+    AliDebug(1, Form("Branch Dir Name is %s",branch->GetDirectory()->GetName()));
    } 
   else
-    Warning("ConnectTree","Branch Dir is NOT SET");
+    AliWarning("Branch Dir is NOT SET");
 }
-//__________________________________________________________________________________________
-
 
-void AliStack::BeginEvent()
-{
-// start a new event
- Reset();
-}
-
-//_____________________________________________________________________________
-void AliStack::FinishRun()
-{
-// Clean TreeK information
-}
 //_____________________________________________________________________________
 
 Bool_t AliStack::GetEvent()
@@ -883,22 +924,116 @@ Bool_t AliStack::GetEvent()
 // Get new event from TreeK
 
     // Reset/Create the particle stack
-    fTreeK = 0x0;
-
-    if (TreeK() == 0x0) //forces connecting
-     {
-      Error("GetEvent","cannot find Kine Tree for current event\n");
-      return kFALSE;
-     }
-      
     Int_t size = (Int_t)TreeK()->GetEntries();
     ResetArrays(size);
     return kTRUE;
 }
 //_____________________________________________________________________________
 
-void AliStack::SetEventFolderName(const char* foldname)
+Bool_t AliStack::IsStable(Int_t pdg) const
 {
- //Sets event folder name
- fEventFolderName = foldname;
+  //
+  // Decide whether particle (pdg) is stable
+  //
+  
+  
+  // All ions/nucleons are considered as stable
+  // Nuclear code is 10LZZZAAAI
+  if(pdg>1000000000)return kTRUE;
+
+  const Int_t kNstable = 15;
+  Int_t i;
+  
+  Int_t pdgStable[kNstable] = {
+    kGamma,             // Photon
+    kElectron,          // Electron
+    kMuonPlus,          // Muon 
+    kPiPlus,            // Pion
+    kKPlus,             // Kaon
+    kK0Short,           // K0s
+    kK0Long,            // K0l
+    kProton,            // Proton 
+    kNeutron,           // Neutron
+    kLambda0,           // Lambda_0
+    kSigmaMinus,        // Sigma Minus
+    kSigmaPlus,         // Sigma Plus
+    3312,               // Xsi Minus 
+    3322,               // Xsi 
+    3334,               // Omega
+  };
+    
+  Bool_t isStable = kFALSE;
+  for (i = 0; i < kNstable; i++) {
+    if (pdg == TMath::Abs(pdgStable[i])) {
+      isStable = kTRUE;
+      break;
+    }
+  }
+  
+  return isStable;
 }
+
+Bool_t AliStack::IsPhysicalPrimary(Int_t index)
+{
+    //
+    // Test if a particle is a physical primary according to the following definition:
+    // Particles produced in the collision including products of strong and
+    // electromagnetic decay and excluding feed-down from weak decays of strange
+    // particles.
+    //
+    TParticle* p = Particle(index);
+    Int_t ist = p->GetStatusCode();
+    
+    //
+    // Initial state particle
+    if (ist > 1) return kFALSE;
+    
+    Int_t pdg = TMath::Abs(p->GetPdgCode());
+    
+    if (!IsStable(pdg)) return kFALSE;
+    
+    if (index < GetNprimary()) {
+//
+// Particle produced by generator
+       return kTRUE;
+    } else {
+//
+// Particle produced during transport
+//
+
+       Int_t imo =  p->GetFirstMother();
+       TParticle* pm  = Particle(imo);
+       Int_t mpdg = TMath::Abs(pm->GetPdgCode());
+// Check if it comes from a pi0 decay
+//
+// What about the pi0 Dalitz ??
+//     if ((mpdg == kPi0) && (imo < GetNprimary())) return kTRUE; 
+
+// Check if this is a heavy flavor decay product
+       Int_t mfl  = Int_t (mpdg / TMath::Power(10, Int_t(TMath::Log10(mpdg))));
+       //
+       // Light hadron
+       if (mfl < 4) return kFALSE;
+       
+       //
+       // Heavy flavor hadron produced by generator
+       if (imo <  GetNprimary()) {
+           return kTRUE;
+       }
+       
+       // To be sure that heavy flavor has not been produced in a secondary interaction
+       // Loop back to the generated mother
+       while (imo >=  GetNprimary()) {
+           imo = pm->GetFirstMother();
+           pm  =  Particle(imo);
+       }
+       mpdg = TMath::Abs(pm->GetPdgCode());
+       mfl  = Int_t (mpdg / TMath::Power(10, Int_t(TMath::Log10(mpdg))));
+
+       if (mfl < 4) {
+           return kFALSE;
+       } else {
+           return kTRUE;
+       } 
+    } // produced by generator ?
+}