]> git.uio.no Git - u/mrichter/AliRoot.git/blobdiff - STEER/AliStack.cxx
Modifications for G4 simulation:
[u/mrichter/AliRoot.git] / STEER / AliStack.cxx
index 0edddee709fd1721f83efd6428808949e086f593..c86db151e8f227ba132b89f87a8c55d3b2cdaa22 100644 (file)
  * provided "as is" without express or implied warranty.                  *
  **************************************************************************/
 
-/*
-$Log$
-Revision 1.17  2001/12/05 08:51:56  hristov
-The default constructor now creates no objects (thanks to r.Brun). Some corrections required by the previous changes.
-
-Revision 1.16  2001/11/20 09:27:55  hristov
-Possibility to investigate a primary of not yet loaded particle (I.Hrivnacova)
-
-Revision 1.15  2001/09/04 15:10:37  hristov
-Additional protection is included to avoid some problems using Hijing
-
-Revision 1.14  2001/08/30 09:44:06  hristov
-VertexSource_t added to avoid the warnings
-
-Revision 1.13  2001/08/29 13:31:42  morsch
-Protection against (fTreeK == 0) in destructor.
-
-Revision 1.12  2001/07/27 13:03:13  hristov
-Default Branch split level set to 99
-
-Revision 1.11  2001/07/27 12:34:20  jchudoba
-remove the dummy argument in GetEvent method
-
-Revision 1.10  2001/07/20 10:13:54  morsch
-In Particle(Int_t) use GetEntriesFast to speed up the procedure.
-
-Revision 1.9  2001/07/03 08:10:57  hristov
-J.Chudoba's changes merged correctly with the HEAD
-
-Revision 1.6  2001/05/31 06:59:06  fca
-Clean setting and deleting of fParticleBuffer
-
-Revision 1.5  2001/05/30 12:18:46  hristov
-Loop variables declared once
-
-Revision 1.4  2001/05/25 07:25:20  hristov
-AliStack destructor corrected (I.Hrivnacova)
-
-Revision 1.3  2001/05/22 14:33:16  hristov
-Minor changes
-
-Revision 1.2  2001/05/17 05:49:39  fca
-Reset pointers to daughters
-
-Revision 1.1  2001/05/16 14:57:22  alibrary
-New files for folders and Stack
-
-*/
+/* $Id$ */
 
 ///////////////////////////////////////////////////////////////////////////////
 //                                                                           //
-//  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 <iostream.h>
  
+#include <TClonesArray.h>
 #include <TObjArray.h>
+#include <TPDGCode.h>
 #include <TParticle.h>
+#include <TParticlePDG.h>
+#include <TDatabasePDG.h>
 #include <TTree.h>
-#include <TFile.h>
-#include <TFolder.h>
-#include <TROOT.h>
+#include <TDirectory.h>
 
+#include "AliLog.h"
 #include "AliStack.h"
-#include "AliRun.h"
-#include "AliModule.h"
-#include "AliHit.h"
-//#include "ETrackBits.h"
 
 ClassImp(AliStack)
 
-//_____________________________________________________________________________
-AliStack::AliStack(Int_t size)
+//_______________________________________________________________________
+AliStack::AliStack():
+  fParticles("TParticle", 1000),
+  fParticleMap(),
+  fParticleFileMap(0),
+  fParticleBuffer(0),
+  fCurrentTrack(0),
+  fTreeK(0),
+  fNtrack(0),
+  fNprimary(0),
+  fCurrent(-1),
+  fCurrentPrimary(-1),
+  fHgwmk(0),
+  fLoadPoint(0),
+  fTrackLabelMap(0)
 {
   //
-  //  Constructor
+  // Default constructor
   //
-  
-  // Create the particles arrays 
-  fParticles      = new TClonesArray("TParticle",1000);
-  fParticleMap    = new TObjArray(size);
-  fParticleBuffer = 0;
-  fNtrack         = 0;
-  fNprimary       = 0;
-  fCurrent        = -1;
-  fCurrentPrimary = -1;
-  fTreeK          = 0;
 }
 
-
-//_____________________________________________________________________________
-AliStack::AliStack()
+//_______________________________________________________________________
+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),
+  fCurrent(-1),
+  fCurrentPrimary(-1),
+  fHgwmk(0),
+  fLoadPoint(0),
+  fTrackLabelMap(0)
 {
   //
-  //  Default constructor
+  //  Constructor
   //
-  
-  // Create the particles arrays 
-  fParticles      = 0;
-  fParticleMap    = 0;
-  fParticleBuffer = 0;
-  fNtrack         = 0;
-  fCurrent        = -1;
-  fNprimary       = 0;
-  fCurrentPrimary = -1;
-  fTreeK          = 0;
 }
 
+//_______________________________________________________________________
+AliStack::AliStack(const AliStack& st):
+    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
+}
 
-//_____________________________________________________________________________
+
+//_______________________________________________________________________
+void AliStack::Copy(TObject&) const
+{
+  AliFatal("Not implemented!");
+}
+
+//_______________________________________________________________________
 AliStack::~AliStack()
 {
   //
   // Destructor
   //
   
-  if (fParticles) {
-    fParticles->Delete();
-    delete fParticles;
-  }
-  delete fParticleMap;
-  if (fTreeK) delete fTreeK;
+    fParticles.Clear();
 }
 
 //
@@ -143,15 +124,15 @@ AliStack::~AliStack()
 //
 
 //_____________________________________________________________________________
-void AliStack::SetTrack(Int_t done, Int_t parent, Int_t pdg, Float_t *pmom,
-                     Float_t *vpos, Float_t *polar, Float_t tof,
-                     AliMCProcess mech, Int_t &ntr, Float_t weight)
+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
@@ -162,10 +143,6 @@ void AliStack::SetTrack(Int_t done, Int_t parent, Int_t pdg, Float_t *pmom,
   // ntr      on output the number of the track stored
   //
 
-  Float_t mass;
-  const Int_t kfirstdaughter=-1;
-  const Int_t klastdaughter=-1;
-  const Int_t kS=0;
   //  const Float_t tlife=0;
   
   //
@@ -175,63 +152,37 @@ void AliStack::SetTrack(Int_t done, Int_t parent, Int_t pdg, Float_t *pmom,
   // also, this method is potentially dangerous if the mass
   // used in the MC is not the same of the PDG database
   //
-  mass = TDatabasePDG::Instance()->GetParticle(pdg)->Mass();
-  Float_t e=TMath::Sqrt(mass*mass+pmom[0]*pmom[0]+
-                       pmom[1]*pmom[1]+pmom[2]*pmom[2]);
-  
+    TParticlePDG* pmc =  TDatabasePDG::Instance()->GetParticle(pdg);
+    if (pmc) {
+       Float_t mass = TDatabasePDG::Instance()->GetParticle(pdg)->Mass();
+       Float_t e=TMath::Sqrt(mass*mass+pmom[0]*pmom[0]+
+                             pmom[1]*pmom[1]+pmom[2]*pmom[2]);
+       
 //    printf("Loading  mass %f ene %f No %d ip %d parent %d done %d pos %f %f %f mom %f %f %f kS %d m \n",
 //        mass,e,fNtrack,pdg,parent,done,vpos[0],vpos[1],vpos[2],pmom[0],pmom[1],pmom[2],kS);
   
-  TClonesArray &particles = *fParticles;
-  TParticle* particle
-   = new(particles[fLoadPoint++]) 
-     TParticle(pdg, kS, parent, -1, kfirstdaughter, klastdaughter,
-               pmom[0], pmom[1], pmom[2], e, vpos[0], vpos[1], vpos[2], tof);
-  particle->SetPolarisation(TVector3(polar[0],polar[1],polar[2]));
-  particle->SetWeight(weight);
-  particle->SetUniqueID(mech);
-  if(!done) particle->SetBit(kDoneBit);
-  
-  
-  //  Declare that the daughter information is valid
-  particle->SetBit(kDaughtersBit);
-  //  Add the particle to the stack
-  fParticleMap->AddAtAndExpand(particle, fNtrack);
 
-  if(parent>=0) {
-    particle = (TParticle*) fParticleMap->At(parent);
-    if (particle) {
-      particle->SetLastDaughter(fNtrack);
-      if(particle->GetFirstDaughter()<0) particle->SetFirstDaughter(fNtrack);
-    }
-    else {
-      printf("Error in AliStack::SetTrack: Parent %d does not exist\n",parent);
+       PushTrack(done, parent, pdg, pmom[0], pmom[1], pmom[2], e,
+                vpos[0], vpos[1], vpos[2], tof, polar[0], polar[1], polar[2],
+                mech, ntr, weight, is);
+    } else {
+       AliWarning(Form("Particle type %d not defined in PDG Database !", pdg));
+       AliWarning("Particle skipped !");
     }
-  } 
-  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++;
 }
 
 //_____________________________________________________________________________
-void AliStack::SetTrack(Int_t done, Int_t parent, Int_t pdg,
+void AliStack::PushTrack(Int_t done, Int_t parent, Int_t pdg,
                      Double_t px, Double_t py, Double_t pz, Double_t e,
                      Double_t vx, Double_t vy, Double_t vz, Double_t tof,
                      Double_t polx, Double_t poly, Double_t polz,
-                     AliMCProcess mech, Int_t &ntr, Float_t weight)
+                     TMCProcess mech, Int_t &ntr, Double_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
   // kS          generation status code
@@ -248,269 +199,367 @@ void AliStack::SetTrack(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 kS=0;
   const Int_t kFirstDaughter=-1;
   const Int_t kLastDaughter=-1;
-  
-  TClonesArray &particles = *fParticles;
+
+
   TParticle* particle
-    = new(particles[fLoadPoint++]) 
-      TParticle(pdg, kS, parent, -1, kFirstDaughter, kLastDaughter,
+    = new(fParticles[fLoadPoint++]) 
+      TParticle(pdg, is, parent, -1, kFirstDaughter, kLastDaughter,
                px, py, pz, e, vx, vy, vz, tof);
-   
+                
   particle->SetPolarisation(polx, poly, polz);
   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 = (TParticle*) fParticleMap->At(parent);
-    if (particle) {
-      particle->SetLastDaughter(fNtrack);
-      if(particle->GetFirstDaughter()<0) particle->SetFirstDaughter(fNtrack);
-    }
-    else {
-      printf("Error in AliStack::SetTrack: 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 = GetParticleMapEntry(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++;
 }
 
 //_____________________________________________________________________________
-void AliStack::GetNextTrack(Int_t &mtrack, Int_t &ipart, Float_t *pmom,
-                         Float_t &e, Float_t *vpos, Float_t *polar,
-                         Float_t &tof)
+TParticle*  AliStack::PopNextTrack(Int_t& itrack)
 {
   //
-  // Return next track from stack of particles
+  // Returns next track from stack of particles
   //
   
 
   TParticle* track = GetNextParticle();
-//    cout << "GetNextTrack():" << fCurrent << fNprimary << endl;
-
-  if(track) {
-    mtrack=fCurrent;
-    ipart=track->GetPdgCode();
-    pmom[0]=track->Px();
-    pmom[1]=track->Py(); 
-    pmom[2]=track->Pz();
-    e      =track->Energy();
-    vpos[0]=track->Vx();
-    vpos[1]=track->Vy();
-    vpos[2]=track->Vz();
-    TVector3 pol;
-    track->GetPolarisation(pol);
-    polar[0]=pol.X();
-    polar[1]=pol.Y();
-    polar[2]=pol.Z();
-    tof=track->T();
+
+  if (track) {
+    itrack = fCurrent;
     track->SetBit(kDoneBit);
-//      cout << "Filled params" << endl;
   }
-  else 
-    mtrack=-1;
+  else
+    itrack = -1;
+  
+  fCurrentTrack = track;
+  return track;
+}
 
+//_____________________________________________________________________________
+TParticle*  AliStack::PopPrimaryForTracking(Int_t i)
+{
+  //
+  // Returns i-th primary particle if it is flagged to be tracked,
+  // 0 otherwise
   //
-  // stop and start timer when we start a primary track
-  Int_t nprimaries = fNprimary;
-  if (fCurrent >= nprimaries) return;
-  if (fCurrent < nprimaries-1) { 
-    fTimer.Stop();
-    track=(TParticle*) fParticleMap->At(fCurrent+1);
-    //    track->SetProcessTime(fTimer.CpuTime());
+  
+  TParticle* particle = Particle(i);
+  
+  if (!particle->TestBit(kDoneBit)) {
+    fCurrentTrack = particle;
+    return particle;
   }
-  fTimer.Start();
-}
-
+  else
+    return 0;
+}      
 
 //_____________________________________________________________________________
-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=(TParticle*) particles.At(i))) { 
-          part->ResetBit(kDaughtersBit);
-          part->SetFirstDaughter(-1);
-          part->SetLastDaughter(-1);
+      // Preset map, to be removed later
+      if(i<=fHgwmk) fTrackLabelMap[i]=i ; 
+      else {
+         fTrackLabelMap[i] = -99;
+         if((part=GetParticleMapEntry(i))) {
+//
+//        Check of this track should be kept for physics reasons 
+             if (KeepPhysics(part)) KeepTrack(i);
+//
+             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 = (TParticle *)particles.At(fHgwmk+1);
-  particles.At(part->GetFirstMother())->ResetBit(kDaughtersBit);
+  part = GetParticleMapEntry(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 = (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 = GetParticleMapEntry(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 = (TParticle *)particles.At(i);
-    parent = part->GetFirstMother();
-    if(parent>=0) {
-      father = (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 = GetParticleMapEntry(i);
+      parent = part->GetFirstMother();
+      if(parent>=0) {
+         father = GetParticleMapEntry(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->GetHitLists();
-  TIter next(hitLists);
-  TCollection *hitList;
-  while((hitList = (TCollection*)next())) {
-    TIter nexthit(hitList);
-    AliHit *hit;
-    while((hit = (AliHit*)nexthit())) {
-      hit->SetTrack(map[hit->GetTrack()]);
-    }
   }
-
-  // 
-  // This for detectors which have a special mapping mechanism
-  // for hits, such as TPC and TRD
   //
-
-   TObjArray* modules = gAlice->Modules();
-   TIter nextmod(modules);
-   AliModule *detector;
-   while((detector = (AliModule*)nextmod())) {
-     detector->RemapTrackHitIDs(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 = GetParticleMapEntry(i);
+      fParticleFileMap[i]=static_cast<Int_t>(TreeK()->GetEntries());
+      TreeK()->Fill();
+      fParticleMap[i]=fParticleBuffer=0;
+  }
   
-   // 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 = 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=fHgwmk+1; i<nkeep; ++i) {
-     fParticleBuffer = (TParticle*) particles.At(i);
-     fParticleFileMap[i]=(Int_t) fTreeK->GetEntries();
-     fTreeK->Fill();
-     particles[i]=fParticleBuffer=0;
-   }
 
-   for (i=nkeep; i<fNtrack; ++i) particles[i]=0;
+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;
 
-   Int_t toshrink = fNtrack-fHgwmk-1;
-   fLoadPoint-=toshrink;
-   for(i=fLoadPoint; i<fLoadPoint+toshrink; ++i) fParticles->RemoveAt(i);
+  //
+  // 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] = GetParticleMapEntry(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 = GetParticleMapEntry(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;
+}
 
-   fNtrack=nkeep;
-   fHgwmk=nkeep-1;
-   //   delete [] map;
+Bool_t AliStack::KeepPhysics(const TParticle* part)
+{
+    //
+    // Some particles have to kept on the stack for reasons motivated
+    // by physics analysis. Decision is put here.
+    //
+    Bool_t keep = kFALSE;
+    //
+    // Keep first-generation daughter from primaries with heavy flavor 
+    //
+    Int_t parent = part->GetFirstMother();
+    if (parent >= 0 && parent <= fHgwmk) {
+       TParticle* father = GetParticleMapEntry(parent);
+       Int_t kf = father->GetPdgCode();
+       kf = TMath::Abs(kf);
+       Int_t kfl = kf;
+       // meson ?
+       if  (kfl > 10) kfl/=100;
+       // baryon
+       if (kfl > 10) kfl/=10;
+       if (kfl > 10) kfl/=10;
+       if (kfl >= 4) {
+           keep = kTRUE;
+       }
+    }
+    return keep;
 }
 
 //_____________________________________________________________________________
 void AliStack::FinishEvent()
 {
-  //
-  // Write out the kinematics that was not yet filled
-  //
+//
+// Write out the kinematics that was not yet filled
+//
   
-  // Update event header
-
+// Update event header
 
-  if (!fTreeK) {
+  if (!TreeK()) {
 //    Fatal("FinishEvent", "No kinematics tree is defined.");
 //    Don't panic this is a probably a lego run
       return;
-      
   }  
   
   CleanParents();
-  if(fTreeK->GetEntries() ==0) {
+   if(TreeK()->GetEntries() ==0) {
     // set the fParticleFileMap size for the first time
     fParticleFileMap.Set(fHgwmk+1);
   }
 
   Bool_t allFilled = kFALSE;
-  TObject *part;
-  for(Int_t i=0; i<fHgwmk+1; ++i) 
-    if((part=fParticleMap->At(i))) {
-      fParticleBuffer = (TParticle*) part;
-      fParticleFileMap[i]= (Int_t) fTreeK->GetEntries();
-      fTreeK->Fill();
-      //PH      (*fParticleMap)[i]=fParticleBuffer=0;      
+  TParticle *part;
+  for(Int_t i=0; i<fHgwmk+1; ++i) {
+    if((part=GetParticleMapEntry(i))) {
+      fParticleBuffer = part;
+      fParticleFileMap[i]= static_cast<Int_t>(TreeK()->GetEntries());
+      TreeK()->Fill();
       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 {
+    else 
+    {
       // // printf("Why = 0 part # %d?\n",i); => We know.
       // break;
-         // we don't break now in order to be sure there is no
-        // particle !=0 left.
-        // To be removed later and replaced with break.
-      if(!allFilled) allFilled = kTRUE;
-    } 
-//    cout << "Nof particles: " << fNtrack << endl;
-  //Reset();   
+      // we don't break now in order to be sure there is no
+      // particle !=0 left.
+      // To be removed later and replaced with break.
+       if(!allFilled) allFilled = kTRUE;
+    }
+  }
 } 
-
 //_____________________________________________________________________________
+
 void AliStack::FlagTrack(Int_t track)
 {
   //
@@ -521,7 +570,7 @@ void AliStack::FlagTrack(Int_t track)
 
   Int_t curr=track;
   while(1) {
-    particle=(TParticle*)fParticleMap->At(curr);
+    particle = GetParticleMapEntry(curr);
     
     // If the particle is flagged the three from here upward is saved already
     if(particle->TestBit(kKeepBit)) return;
@@ -541,16 +590,16 @@ 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;
   fNprimary=0;
   fHgwmk=0;
@@ -559,37 +608,40 @@ void  AliStack::Reset(Int_t size)
   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);
 }
 
 //_____________________________________________________________________________
-void AliStack::SetHighWaterMark(Int_t nt)
+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;
 }
 
 //_____________________________________________________________________________
@@ -597,34 +649,83 @@ 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;
-    if (i<fNprimary)
-       entry = i+fNtrack-fNprimary;
-    else 
-       entry = i-fNprimary;
+    Int_t entry = TreeKEntry(i);
     // check whether algorithmic way and 
     // 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]))
     } 
-      
-    fTreeK->GetEntry(entry);
-    new ((*fParticles)[nentries]) TParticle(*fParticleBuffer);
-    fParticleMap->AddAt((*fParticles)[nentries],i);
+    // Load particle at entry into fParticleBuffer
+    TreeK()->GetEntry(entry);
+    // Add to the TClonesarray
+    new (fParticles[nentries]) TParticle(*fParticleBuffer);
+    // Store a pointer in the TObjArray
+    fParticleMap.AddAt(fParticles[nentries],i);
   }
-  //PH  return (TParticle *) (*fParticleMap)[i];
-  return (TParticle *) fParticleMap->At(i);
+  return GetParticleMapEntry(i);
 }
 
+//_____________________________________________________________________________
+TParticle* AliStack::ParticleFromTreeK(Int_t id) const
+{
+// 
+// return pointer to TParticle with label id
+//
+  Int_t entry;
+  if ((entry = TreeKEntry(id)) < 0) return 0;
+  if (fTreeK->GetEntry(entry)<=0) return 0;
+  return fParticleBuffer;
+}
+
+//_____________________________________________________________________________
+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
+//
+// 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;
+  else 
+    entry = id-fNprimary;
+  return entry;
+}
+
+//_____________________________________________________________________________
+Int_t AliStack::GetCurrentParentTrackNumber() const
+{
+  //
+  // Return number of the parent of the current track
+  //
+  
+  TParticle* current = GetParticleMapEntry(fCurrent);
+
+  if (current) 
+    return current->GetFirstMother();
+  else {
+    AliWarning("Current track not found in the stack");
+    return -1;
+  }  
+}
 //_____________________________________________________________________________
 Int_t AliStack::GetPrimary(Int_t id)
 {
@@ -648,9 +749,7 @@ void AliStack::DumpPart (Int_t i) const
   //
   // Dumps particle i in the stack
   //
-  
-  //PH  ((TParticle*) (*fParticleMap)[i])->Print();
-  ((TParticle*) fParticleMap->At(i))->Print();
+  GetParticleMapEntry(i)->Print();
 }
 
 //_____________________________________________________________________________
@@ -662,8 +761,7 @@ void AliStack::DumpPStack ()
 
   Int_t i;
 
-  printf(
-        "\n\n=======================================================================\n");
+  printf("\n\n=======================================================================\n");
   for (i=0;i<fNtrack;i++) 
     {
       TParticle* particle = Particle(i);
@@ -675,13 +773,12 @@ void AliStack::DumpPStack ()
         Warning("DumpPStack", "No particle with id %d.", i); 
     }   
 
-  printf(
-        "\n=======================================================================\n\n");
+  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]);
 }
 
 
@@ -693,12 +790,11 @@ 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 = (TParticle*) particles[i];
+      TParticle* particle = GetParticleMapEntry(i);
       if (particle) {
         printf("-> %d ",i); particle->Print();
         printf("--------------------------------------------------------------\n");
@@ -712,6 +808,15 @@ void AliStack::DumpLoadedStack() const
         "\n=======================================================================\n\n");
 }
 
+//_____________________________________________________________________________
+void  AliStack::SetCurrentTrack(Int_t track)
+{ 
+  fCurrent = track; 
+  if (fCurrent < fNprimary) fCurrentTrack = Particle(track);
+}
+
+
+//_____________________________________________________________________________
 //
 // protected methods
 //
@@ -724,11 +829,10 @@ void AliStack::CleanParents()
   // Set parent/daughter relations
   //
   
-  TObjArray &particles = *fParticleMap;
   TParticle *part;
   int i;
   for(i=0; i<fHgwmk+1; i++) {
-    part = (TParticle *)particles.At(i);
+    part = GetParticleMapEntry(i);
     if(part) if(!part->TestBit(kDaughtersBit)) {
       part->SetFirstDaughter(-1);
       part->SetLastDaughter(-1);
@@ -748,11 +852,9 @@ TParticle* AliStack::GetNextParticle()
   // search secondaries
   //for(Int_t i=fNtrack-1; i>=0; i--) {
   for(Int_t i=fNtrack-1; i>fHgwmk; i--) {
-      particle = (TParticle*) fParticleMap->At(i);
+      particle = GetParticleMapEntry(i);
       if ((particle) && (!particle->TestBit(kDoneBit))) {
          fCurrent=i;    
-         //cout << "GetNextParticle() - secondary " 
-         // << fNtrack << " " << fHgwmk << " " << fCurrent << endl;
          return particle;
       }   
   }    
@@ -760,92 +862,190 @@ TParticle* AliStack::GetNextParticle()
   // take next primary if all secondaries were done
   while (fCurrentPrimary>=0) {
       fCurrent = fCurrentPrimary;    
-      particle = (TParticle*) fParticleMap->At(fCurrentPrimary--);
+      particle = GetParticleMapEntry(fCurrentPrimary--);
       if ((particle) && (!particle->TestBit(kDoneBit))) {
-         //cout << "GetNextParticle() - primary " 
-         //   << fNtrack << " " << fHgwmk << " " << fCurrent << endl;
          return particle;
       } 
   }
   
   // nothing to be tracked
   fCurrent = -1;
-    //cout << "GetNextParticle() - none  " 
-    //   << fNtrack << " " << fHgwmk << " " << fCurrent << endl;
+  
   return particle;  
 }
-
 //__________________________________________________________________________________________
-void AliStack::MakeTree(Int_t event, const char *file)
-{
-//
-//  Make Kine tree and creates branch for writing particles
-//  
-  TBranch *branch=0;
-  // Make Kinematics Tree
-  char hname[30];
-//    printf("\n MakeTree called %d", event);
-  if (!fTreeK) {
-    sprintf(hname,"TreeK%d",event);
-    fTreeK = new TTree(hname,"Kinematics");
-    //  Create a branch for particles
-    branch = fTreeK->Branch("Particles", "TParticle", &fParticleBuffer, 4000);          
-    fTreeK->Write(0,TObject::kOverwrite);
-  }
-}
 
-//_____________________________________________________________________________
-void AliStack::BeginEvent(Int_t event)
+void AliStack::ConnectTree(TTree* tree)
 {
-// start a new event
 //
+//  Creates branch for writing particles
 //
-    fNprimary = 0;
-    fNtrack   = 0;
+
+  fTreeK = tree;
     
-    char hname[30];
-    if(fTreeK) {
-       fTreeK->Reset();
-       sprintf(hname,"TreeK%d",event);
-       fTreeK->SetName(hname);
-    }
-}
+  AliDebug(1, "Connecting TreeK");
+  if (fTreeK == 0x0)
+   {
+    if (TreeK() == 0x0)
+     {
+      AliFatal("Parameter is NULL");//we don't like such a jokes
+      return;
+     }
+    return;//in this case TreeK() calls back this method (ConnectTree) 
+           //tree after setting fTreeK, the rest was already executed
+           //it is safe to return now
+   }
 
-//_____________________________________________________________________________
-void AliStack::FinishRun()
-{
-// Clean TreeK information
-    if (fTreeK) {
-       delete fTreeK; fTreeK = 0;
-    }
+ //  Create a branch for particles   
+  
+  AliDebug(2, Form("Tree name is %s",fTreeK->GetName()));
+   
+  if (fTreeK->GetDirectory())
+   {
+     AliDebug(2, Form("and dir is %s",fTreeK->GetDirectory()->GetName()));
+   }    
+  else
+    AliWarning("DIR IS NOT SET !!!");
+  
+  TBranch *branch=fTreeK->GetBranch("Particles");
+  if(branch == 0x0)
+   {
+    branch = fTreeK->Branch("Particles", "TParticle", &fParticleBuffer, 4000);
+    AliDebug(2, "Creating Branch in Tree");
+   }  
+  else
+   {
+    AliDebug(2, "Branch Found in Tree");
+    branch->SetAddress(&fParticleBuffer);
+   }
+  if (branch->GetDirectory())
+   {
+    AliDebug(1, Form("Branch Dir Name is %s",branch->GetDirectory()->GetName()));
+   } 
+  else
+    AliWarning("Branch Dir is NOT SET");
 }
 
 //_____________________________________________________________________________
-Bool_t AliStack::GetEvent(Int_t event)
+
+Bool_t AliStack::GetEvent()
 {
 //
 // Get new event from TreeK
 
     // Reset/Create the particle stack
-    if (fTreeK) delete fTreeK;
-    
-    // Get Kine Tree from file
-    char treeName[20];
-    sprintf(treeName,"TreeK%d",event);
-    fTreeK = (TTree*)gDirectory->Get(treeName);
-
-    if (fTreeK) 
-      fTreeK->SetBranchAddress("Particles", &fParticleBuffer);
-    else {
-      Error("GetEvent","cannot find Kine Tree for event:%d\n",event);
-      return kFALSE;
-    }
-//      printf("\n primaries %d", fNprimary);
-//      printf("\n tracks    %d", fNtrack);    
-      
-    Int_t size = (Int_t)fTreeK->GetEntries();
+    Int_t size = (Int_t)TreeK()->GetEntries();
     ResetArrays(size);
     return kTRUE;
 }
+//_____________________________________________________________________________
+
+Bool_t AliStack::IsStable(Int_t pdg) const
+{
+  //
+  // 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 ?
+}