/***********************************************************************
**                                                                    **
**          /----------------------------------------------\          **
**         |  Delphes, a framework for the fast simulation  |         **
**         |       of a  generic collider experiment        |         **
**          \----------------------------------------------/          **
**                                                                    **
**                                                                    **
**   This package uses:                                               **
**   ------------------                                               **
**   FastJet algorithm: Phys. Lett. B641 (2006) [hep-ph/0512210]      ** 
**   Hector: JINST 2:P09005 (2007) [physics.acc-ph:0707.1198v2]       ** 
**   FROG: [hep-ex/0901.2718v1]                                       **
**                                                                    **
** ------------------------------------------------------------------ **
**                                                                    **
**   Main authors:                                                    **
**   -------------                                                    **
**                                                                    **
**                Severine Ovyn                Xavier Rouby           ** 
**          severine.ovyn@uclouvain.be      xavier.rouby@cern         ** 
**                                                                    ** 
**         Center for Particle Physics and Phenomenology (CP3)        ** 
**                Universite catholique de Louvain (UCL)              **       
**                     Louvain-la-Neuve, Belgium                      **       
**                                                                    **
**                      Copyright (C) 2008-2009,                      **
**                        All rights reserved.                        **  
**                                                                    **
***********************************************************************/

/// \file Delphes.cpp
/// \brief Executable for Delphes

#include "TChain.h"
#include "TApplication.h"
#include "TStopwatch.h"
#include "TFile.h"

#include "ExRootTreeReader.h"
#include "ExRootTreeWriter.h"
#include "ExRootTreeBranch.h"
#include "ExRootProgressBar.h"

#include "DataConverter.h"
#include "LHEFConverter.h"
#include "HepMCConverter.h"
#include "HEPEVTConverter.h"
#include "STDHEPConverter.h"
#include "LHCOConverter.h"

#include "SmearUtil.h"
#include "CaloUtil.h"
#include "BFieldProp.h"
#include "TriggerUtil.h"
#include "VeryForward.h"
#include "JetsUtil.h"
#include "FrogUtil.h"

#include <vector>
#include <iostream>

using namespace std;

//------------------------------------------------------------------------------
void todo(string filename) {
  ifstream infile(filename.c_str());
  cout << "** TODO list ..." << endl;
  while(infile.good()) {
    string temp;
    getline(infile,temp);
    cout << "*" << temp << endl;
  }
  cout << "** done...\n"; 
}

//------------------------------------------------------------------------------

int main(int argc, char *argv[])
{
  
  int appargc = 2;
  char *appName= new char[20];
  char *appOpt= new char[20];
  sprintf(appName,"Delphes");
  sprintf(appOpt,"-b");
  char *appargv[] = {appName,appOpt};
  TApplication app(appName, &appargc, appargv);
  delete [] appName;
  delete [] appOpt;
  
  if(argc != 3 && argc != 4 && argc != 5) {
    cout << " Usage: " << argv[0] << " input_file output_file [detector_card] [trigger_card] " << endl;
    cout << " input_list - list of files in Ntpl, StdHep of LHEF format," << endl;
    cout << " output_file - output file." << endl;
    cout << " detector_card - Datacard containing resolution variables for the detector simulation (optional) "<<endl;
    cout << " trigger_card - Datacard containing the trigger algorithms (optional) "<<endl;
    exit(1);
  }
  
  
  
  
  cout << endl << endl;
  
  cout <<"*********************************************************************"<< endl;
  cout <<"*********************************************************************"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**                            Welcome to                           **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**     .ddddddd-            lL             hH                      **"<< endl;
  cout <<"**     -Dd` `dD:           Ll             hH`                      **"<< endl;
  cout <<"**     dDd   dDd    eeee.  lL  .pp+pp    Hh+hhh`   -eeee- `sssss   **"<< endl;
  cout <<"**    -Dd   `DD   ee. ee  Ll   .Pp. PP   Hh. HH.  ee. ee  sSs      **"<< endl;
  cout <<"**    dD`   dDd  eEeee:   lL.  pP.  pP  hH   hH` eEeee:` -sSSSs.   **"<< endl;
  cout <<"**   .Dd  :dd    eE.     LlL   PpppPP   Hh  Hh   eE         sSS    **"<< endl;
  cout <<"**   dddddd:.     eee+:  lL.  pp.      hh.  hh    eee+  sssssS     **"<< endl;
  cout <<"**                            Pp                                   **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**           Delphes, a framework for the fast simulation          **"<< endl;
  cout <<"**                 of a  generic collider experiment               **"<< endl;
  cout <<"**                    arXiv:0903.2225v1 [hep-ph]                   **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**                  --- Version 1.6 of Delphes ---                 **"<< endl;
  cout <<"**                Last date of change:    7 May 2009               **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**     This package uses:                                          **"<< endl;
  cout <<"**     ------------------                                          **"<< endl;
  cout <<"**     FastJet algorithm: Phys. Lett. B641 (2006) [hep-ph/0512210] **"<< endl;
  cout <<"**     Hector: JINST 2:P09005 (2007) [physics.acc-ph:0707.1198v2]  **"<< endl;
  cout <<"**     FROG:                               [hep-ex/0901.2718v1]    **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**-----------------------------------------------------------------**"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**   Main authors:                                                 **"<< endl;
  cout <<"**   -------------                                                 **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**              Séverine Ovyn               Xavier Rouby           **"<< endl;
  cout <<"**       severine.ovyn@uclouvain.be      xavier.rouby@cern         **"<< endl;
  cout <<"**       Center for Particle Physics and Phenomenology (CP3)       **"<< endl;
  cout <<"**       Universite Catholique de Louvain (UCL)                    **"<< endl;
  cout <<"**       Louvain-la-Neuve, Belgium                                 **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**-----------------------------------------------------------------**"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**   Former Delphes versions and documentation can be found on :   **"<< endl;
  cout <<"**               http://www.fynu.ucl.ac.be/delphes.html            **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"**   Disclaimer: this program is a beta version of Delphes and     **"<< endl;
  cout <<"** therefore comes without guarantees. Beware of errors and please **"<< endl;
  cout <<"**        give us your feedbacks about potential bugs              **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"*********************************************************************"<< endl;
  cout <<"*********************************************************************"<< endl;
  
  // 1. ********** initialisation ***********
  
  srand (time (NULL));         /* Initialisation du générateur */
  TStopwatch globalwatch, loopwatch, triggerwatch, frogwatch, lhcowatch;
  globalwatch.Start();
  
  
  //read the output TROOT file
  string inputFileList(argv[1]), outputfilename(argv[2]);
  if(outputfilename.find(".root") > outputfilename.length()) {
    cout <<"**    ERROR: 'output_file' should be a .root file. Exiting...      **"<< endl;
    exit(1);
  }
  //create output log-file name
  string forLog = outputfilename;
  string LogName = forLog.erase(forLog.find(".root"));
  LogName = LogName+"_run.log";
  
  TFile *outputFile = TFile::Open(outputfilename.c_str(), "RECREATE"); // Creates the file, but should be closed just after
  outputFile->Close();
  
  string line;
  ifstream infile(inputFileList.c_str());
  infile >> line; // the first line determines the type of input files
  
  //read the datacard input file
  string DetDatacard("data/DetectorCard.dat"); //for detector smearing parameters
  string TrigDatacard("data/TriggerCard.dat"); //for trigger selection
  
  string lineCard1,lineCard2;
  bool detecCard=false,trigCard=false;
  if(argv[3]) 
    {  
      ifstream infile1(argv[3]);
      infile1 >> lineCard1; // the first line determines the type of input files
      if(strstr(lineCard1.c_str(),"DETECTOR") && detecCard==true) 
	cerr <<"**         ERROR: A DETECTOR card has already been loaded          **"<< endl;
      else if(strstr(lineCard1.c_str(),"DETECTOR") && detecCard==false){DetDatacard =argv[3]; detecCard=true;}
      else if(strstr(lineCard1.c_str(),"TRIGGER") && trigCard==true)
	cerr <<"**         ERROR: A TRIGGER card has already been loaded           **"<< endl;
      else if(strstr(lineCard1.c_str(),"TRIGGER") && trigCard==false){TrigDatacard =argv[3]; trigCard=true;}
    }
  if(argv[4])
    {  
      ifstream infile2(argv[4]);
      infile2 >> lineCard2; // the first line determines the type of input files
      if(strstr(lineCard2.c_str(),"DETECTOR") && detecCard==true)
	cerr <<"**         ERROR: A DETECTOR card has already been loaded          **"<< endl;
      else if(strstr(lineCard2.c_str(),"DETECTOR") && detecCard==false){DetDatacard =argv[4]; detecCard=true;}
      else if(strstr(lineCard2.c_str(),"TRIGGER") && trigCard==true)
	cerr <<"**         ERROR: A TRIGGER card has already been loaded           **"<< endl;
      else if(strstr(lineCard2.c_str(),"TRIGGER") && trigCard==false){TrigDatacard =argv[4]; trigCard=true;}
    }
  
  //Smearing information
  RESOLution *DET = new RESOLution();
  cout <<"**                                                                 **"<< endl;
  cout <<"**        ####### Start reading DETECTOR parameters #######        **"<< endl;
  cout << left  << setw(40) <<"**        Opening configuration card: "<<""
       << left  << setw(27) << DetDatacard                            <<""
       << right << setw(2) <<"**"<<""<<endl;
  DET->ReadDataCard(DetDatacard);
  DET->Logfile(LogName);
  cout << left  << setw(40) <<"**        Parameters summarised in: "<<""
       << left  << setw(27) << LogName                            <<""
       << right << setw(2) <<"**"<<""<<endl;
  cout <<"**                                                                 **"<< endl;
  
  //Trigger information
  cout <<"**        ########### Start reading TRIGGER card ##########        **"<< endl;
  if(trigCard==false)
    {
      cout <<"**        WARNING: Datacard  not found, use default card           **" << endl;
      TrigDatacard="data/TriggerCard.dat";
    }
  TriggerTable *TRIGT = new TriggerTable();
  TRIGT->TriggerCardReader(TrigDatacard.c_str());
  TRIGT->PrintTriggerTable(LogName);
  if(DET->FLAG_trigger == 1)
    {
      cout << left  << setw(40) <<"**        Opening configuration card: "<<""
           << left  << setw(27) << TrigDatacard                            <<""
           << right << setw(2) <<"**"<<""<<endl;
      cout <<"**                                                                 **"<< endl;
    }
  
  //Propagation of tracks in the B field
  TrackPropagation *TRACP = new TrackPropagation(DET); 
  
  //Jet information
  JetsUtil *JETRUN = new JetsUtil(DET);
  
  //VFD information
  VeryForward * VFD = new VeryForward(DET);
  
  // data converters
  cout <<"**                                                                 **"<<endl;
  cout <<"**        ####### Start convertion to TRoot format ########        **"<< endl;
  
  if(line.length() == 1+line.find_last_of(".hep"))
    {                           
      cout <<"**                 StdHEP file format detected                     **"<<endl;
      cout <<"**                This can take several minutes                    **"<< endl;
      STDHEPConverter converter(inputFileList,outputfilename);//case ntpl file in input list
    }
  else if(line.length() == 1+line.find_last_of(".lhe"))
    {
      cout <<"**                   LHEF file format detected                     **"<<endl;
      cout <<"**                 This can take several minutes                   **"<< endl;
      LHEFConverter converter(inputFileList,outputfilename);//case ntpl file in input list
    }
  else if(line.length() == 1+line.find_last_of(".root"))
    {
      cout <<"**                   h2root file format detected                   **"<<endl;
      cout <<"**                  This can take several minutes                  **"<< endl;
      HEPEVTConverter converter(inputFileList,outputfilename);//case ntpl file in input list
    }
  else if(line.length() == 1+line.find_last_of(".hepmc"))
    {
      cout <<"**                HepMC ASCII file format detected                 **"<<endl;
      cout <<"**                  This can take several minutes                  **"<< endl;
      HepMCConverter converter(inputFileList,outputfilename);
    }
  else {
    cerr << left  << setw(4) <<"**  "<<""
	 << left  << setw(63) << line.c_str() <<""
	 << right << setw(2) <<"**"<<endl;
    cerr <<"**         ERROR: File format not identified --  Exiting...        **"<< endl;
    cout <<"**                                                                 **"<< endl;
    cout <<"*********************************************************************"<< endl;
    return -1;};
  cout <<"**                       Exiting conversion...                     **"<< endl;
  
  TChain chain("GEN");
  chain.Add(outputfilename.c_str());
  ExRootTreeReader *treeReader = new ExRootTreeReader(&chain);
  const TClonesArray *branchGen = treeReader->UseBranch("Particle");
  
  TIter itGen((TCollection*)branchGen);
  
  //Output file : contents of the analysis object data
  ExRootTreeWriter *treeWriter = new ExRootTreeWriter(outputfilename, "Analysis");
  ExRootTreeBranch *branchTauJet = treeWriter->NewBranch("TauJet", TRootTauJet::Class());
  ExRootTreeBranch *branchJet = treeWriter->NewBranch("Jet", TRootJet::Class());
  ExRootTreeBranch *branchElectron = treeWriter->NewBranch("Electron", TRootElectron::Class());
  ExRootTreeBranch *branchMuon = treeWriter->NewBranch("Muon", TRootMuon::Class());
  ExRootTreeBranch *branchPhoton = treeWriter->NewBranch("Photon", TRootPhoton::Class());
  ExRootTreeBranch *branchTrack = treeWriter->NewBranch("Tracks", TRootTracks::Class());
  ExRootTreeBranch *branchETmis = treeWriter->NewBranch("ETmis", TRootETmis::Class());
  ExRootTreeBranch *branchCalo = treeWriter->NewBranch("CaloTower", TRootCalo::Class());
  ExRootTreeBranch *branchZDC = treeWriter->NewBranch("ZDChits", TRootZdcHits::Class());
  ExRootTreeBranch *branchRP220 = treeWriter->NewBranch("RP220hits", TRootRomanPotHits::Class());
  ExRootTreeBranch *branchFP420 = treeWriter->NewBranch("FP420hits", TRootForwardTaggerHits::Class());
  
  TRootETmis *elementEtmis;
  TRootElectron *elementElec;
  TRootMuon *elementMu;
  TRootPhoton *elementPhoton;
  TRootTracks * elementTrack;
  TRootCalo *elementCalo;
  
  TLorentzVector genMomentum(0,0,0,0);        // four-momentum at the vertex
  TLorentzVector genMomentumBfield(0,0,0,0);  // four-momentum at the exit of the tracks
  TLorentzVector momentumCaloSegmentation(0,0,0,0);    // four-momentum in the calo, after applying the calo segmentation
  LorentzVector jetMomentum;
  
  vector<fastjet::PseudoJet> input_particles;//for FastJet algorithm
  vector<fastjet::PseudoJet> sorted_jets;
  vector<TRootTracks> TrackCentral;  
  vector<PhysicsTower> towers;
  vector<D_Particle> electron;
  vector<D_Particle> muon;
  vector<D_Particle> gamma;
 
  vector<int> NTrackJet;

  TSimpleArray<TRootC::GenParticle> NFCentralQ;
  
  D_CaloList list_of_calorimeters;
  D_CaloElement CentralCalo("centralcalo", 
			    -DET->CEN_max_calo_cen, DET->CEN_max_calo_cen,
			    DET->ELG_Ccen,  DET->ELG_Ncen,  DET->ELG_Scen,
			    DET->HAD_Chcal, DET->HAD_Nhcal, DET->HAD_Shcal);
  D_CaloElement ForwardCalo("forwardcalo",
			    DET->CEN_max_calo_cen, DET->CEN_max_calo_fwd, 
			    DET->ELG_Cfwd,  DET->ELG_Nfwd,  DET->ELG_Sfwd,
			    DET->HAD_Chf,   DET->HAD_Nhf,   DET->HAD_Shf  );
  D_CaloElement BackwardCalo("backwardcalo",
			     -DET->CEN_max_calo_fwd, -DET->CEN_max_calo_cen,
			     DET->ELG_Cfwd,  DET->ELG_Nfwd,  DET->ELG_Sfwd,
			     DET->HAD_Chf,   DET->HAD_Nhf,   DET->HAD_Shf  );
  //D_CaloElement CastorCalo("castor",5.5,6.6,1,0,0,1,0,0);
  list_of_calorimeters.addElement(CentralCalo);
  list_of_calorimeters.addElement(ForwardCalo);
  list_of_calorimeters.addElement(BackwardCalo);
  //list_of_calorimeters.addElement(CastorCalo);
  list_of_calorimeters.sortElements();
  
  
  // 2. ********** Loop over all events ***********
  Long64_t entry, allEntries = treeReader->GetEntries();
  cout <<"**                                                                 **"<<endl;
  cout <<"**        ####### Start fast detector simulation ########          **"<< endl;
  cout << left  << setw(52) <<"**              Total number of events to run: "<<""
       << left  << setw(15) << allEntries <<""
       << right << setw(2) <<"**"<<endl;
  
  ExRootProgressBar *Progress = new ExRootProgressBar(allEntries);
  
  loopwatch.Start();
  
  // loop on all events
  for(entry = 0; entry < allEntries; ++entry)
    {
      Progress->Update(entry);
      TLorentzVector PTmis(0,0,0,0);
      treeReader->ReadEntry(entry);
      treeWriter->Clear();
      
      electron.clear();
      muon.clear();
      gamma.clear();
      NFCentralQ.Clear();
      
      TrackCentral.clear();
      towers.clear();
      input_particles.clear();
      NTrackJet.clear();     
      
      
      D_CaloTowerList list_of_active_towers; 
      D_CaloTowerList list_of_towers_with_photon; // to speed up the code: will only look in interesting towers for gamma candidates
       
      
      // 2.1a Loop over all particles in event, to fill the towers
      itGen.Reset();
      TRootC::GenParticle *particleG; 
      while( (particleG = (TRootC::GenParticle*) itGen.Next()) ) 
	{
	  TRootGenParticle *particle = new TRootGenParticle(particleG);
	  int pid = abs(particle->PID);
	  particle->Charge=ChargeVal(particle->PID);
	  particle->setFractions(); // init
	  
	  
	  // 2.1a.1********************* preparation for the b-tagging
	  //// This subarray is needed for the B-jet algorithm
	  // optimization for speed : put first PID condition, then ETA condition, then either pt or status
	  if( (pid <= pB || pid == pGLUON) &&// is it a light quark or a gluon, i.e. is it one of these : u,d,c,s,b,g ?
              fabs(particle->Eta) < DET->CEN_max_tracker &&
              particle->Status != 1 &&
              particle->PT > DET->PT_QUARKS_MIN ) 
	    {
	        NFCentralQ.Add(particleG);
	    }
	  
	  // 2.1a.2********************* visible particles only
	  if( (particle->Status == 1) && (pid != pNU1) && (pid != pNU2) && (pid != pNU3) )
	    {
	      // 2.1a.2.1 Central solenoidal magnetic field 
	      TRACP->bfield(particle); // fills in particle->EtaCalo et particle->PhiCalo
	      // 2.1a.2.2 Filling the calorimetric towers -- includes also forward detectors ?
	      // first checks if the charged particles reach the calo!
	      if( DET->FLAG_bfield || 
		  particle->Charge==0 ||
		  (!DET->FLAG_bfield && particle->Charge!=0 && particle->PT > DET->TRACK_ptmin)) 
		if(
		   (particle->EtaCalo > list_of_calorimeters.getEtamin() ) &&
		   (particle->EtaCalo < list_of_calorimeters.getEtamax() )
		   ) 
		  {
		    float iEta=UNDEFINED, iPhi=UNDEFINED;
		    DET->BinEtaPhi(particle->PhiCalo,particle->EtaCalo,iPhi,iEta); // fills in iPhi and iEta
		    if (iEta != UNDEFINED && iPhi != UNDEFINED) 
		      {
			D_CaloTower tower(iEta,iPhi);	                               // new tower
			tower.Set_Eem_Ehad_E_ET(particle->E*particle->getFem() , particle->E*particle->getFhad() );
			list_of_active_towers.addTower(tower);
			// this list may contain several times the same calotower, as several particles 
			// may leave some energy in the same calotower
			// After the loop on particles, identical cells in the list should be merged 
		      } // iEta and iPhi must be defined
		  }
	    
	      // 2.1a.2.3 charged particles in tracker: energy flow
	      // if bfield not simulated, pt should be high enough to be taken into account
	      // it is supposed here that DET->MAX_calo > DET->CEN_max_tracker > DET->CEN_max_mu > 0
	      if( particle->Charge !=0 &&
		  fabs(particle->EtaCalo)< DET->CEN_max_tracker && // stays in the tracker -> track available
		  ( DET->FLAG_bfield || 
		    (!DET->FLAG_bfield && particle->PT > DET->TRACK_ptmin)
		    )
		  ) 
		{	
		  // 2.1a.2.3.1 Filling the particle properties + smearing
		  // Hypothesis: the final eta/phi are the ones from the generator, thanks to the track reconstruction
		  // This is the EnergyFlow hypothesis
		  particle->SetEtaPhi(particle->Eta,particle->Phi);
		  float sET=UNDEFINED; // smeared ET, computed from the smeared E -> needed for the tracks
		  
		  // 2.1a.2.3.2 Muons
		  if (pid == pMU && fabs(particle->EtaCalo)< DET->CEN_max_mu) 
		    {
		      TLorentzVector p;
		      float sPT = gRandom->Gaus(particle->PT, DET->MU_SmearPt*particle->PT );
		      if (sPT > 0 && sPT > DET->PTCUT_muon) 
			{
			  p.SetPtEtaPhiE(sPT,particle->Eta,particle->Phi,sPT*cosh(particle->Eta));
			  muon.push_back(D_Particle(p,pMU,particle->EtaCalo,particle->PhiCalo));
			}
		      sET = (sPT >0)? sPT : 0;
		    }  
		  // 2.1a.2.3.3 Electrons
		  else if (pid == pE) 
		    {
		      // Finds in which calorimeter the particle has gone, to know its resolution
		      
		      D_CaloElement currentCalo = list_of_calorimeters.getElement(particle->EtaCalo);
		      if(currentCalo.getName() == dummyCalo.getName()) 
			{
			  cout << "** Warning: the calo coverage behind the tracker is not complete! **" << endl; 
			}
		      
		      // final smeared EM energy   // electromagnetic fraction F_em =1 for electrons;
		      float sE  = currentCalo.getElectromagneticResolution().Smear(particle->E);
		      if (sE>0) 
			{
			  sET = sE/cosh(particle->Eta); 
			  // NB: ET is found via the calorimetry and not via the track curvature
			  
			  TLorentzVector p;
			  p.SetPtEtaPhiE(sET,particle->Eta,particle->Phi,sE);
			  if (sET > DET->PTCUT_elec)
			    electron.push_back(D_Particle(p,particle->PID,particle->EtaCalo,particle->PhiCalo));
			} 
		      else { sET=0;} // if negative smeared energy -- needed for the tracks
		    }  
		  // 2.1a.2.3.4 Other charged particles : smear them for the tracks!
		  else 
		    {  //other particles
		      D_CaloElement currentCalo = list_of_calorimeters.getElement(particle->EtaCalo);
		      float sEem  = currentCalo.getElectromagneticResolution().Smear(particle->E * particle->getFem());
		      float sEhad = currentCalo.getHadronicResolution().Smear(particle->E * particle->getFhad());
		      float sE = ( (sEem>0)? sEem : 0 ) + ( (sEhad>0)? sEhad : 0 );
		      sET = sE/cosh(particle->EtaCalo);
		    }
	      
		  // 2.1a.2.3.5 Tracks
		  if( (rand()%100) < DET->TRACK_eff && sET!=0) 
		    {
		      elementTrack = (TRootTracks*) branchTrack->NewEntry();
		      elementTrack->Set(particle->Eta, particle->Phi, particle->EtaCalo, particle->PhiCalo, sET, particle->Charge);
		      TrackCentral.push_back(*elementTrack); // tracks at vertex!
		      // TODO!!! apply a smearing on the position of the origin of the track
		      // TODO!!! elementTracks->SetPositionOut(Xout,Yout,Zout);
		    }
		} // 2.1a.2.3 : if tracker/energy-flow
	      // 2.1a.2.4 Photons
	      // stays in the tracker -> track available -> gamma ID
	      else if( (pid == pGAMMA) && fabs(particle->EtaCalo)< DET->CEN_max_tracker ) 
		{
		  float iEta=UNDEFINED, iPhi=UNDEFINED;
		  DET->BinEtaPhi(particle->PhiCalo,particle->EtaCalo,iPhi,iEta); // fills in iPhi and iEta
		  D_CaloTower tower(iEta,iPhi); 
		  // stores the list of towers where to apply the photon ID algorithm. Just a trick for a faster search
		  list_of_towers_with_photon.addTower(tower); 
		}
	      // 2.1a.2.5 : very forward detectors
	      else
		{
		  if (DET->FLAG_RP==1) 
		    {
		      // for the moment, only protons are transported
		      // BUT !!! could be a beam of other particles! (heavy ions?)
		      // BUT ALSO !!! if very forward muons, or others!
		      VFD->RomanPots(treeWriter,branchRP220,branchFP420,particle);
		    }
		  // 2.1a.2.6: Zero degree calorimeter
		  if(DET->FLAG_vfd==1) 
		    {
		      VFD->ZDC(treeWriter,branchZDC,particle);
		    }
		}
	    
	    } // 2.1a.2 : if visible particle
	  delete particle;
        }// loop on all particles 2.1a
      
      
      // 2.1b loop on all (activated) towers
      // at this stage, list_of_active_towers may contain several times the same tower
      // first step is to merge identical towers, by matching their (iEta,iPhi)  
      
      list_of_active_towers.sortElements();
      list_of_active_towers.mergeDuplicates();
      
      // Calotower smearing 
      list_of_active_towers.smearTowers(list_of_calorimeters);
      
      for(unsigned int i=0; i<list_of_active_towers.size(); i++) 
	{
	  float iEta = list_of_active_towers[i].getEta();
	  float iPhi = list_of_active_towers[i].getPhi();
	  float e = list_of_active_towers[i].getE(); 
	  if(iEta != UNDEFINED && iPhi != UNDEFINED && e!=0) 
	    {
	      elementCalo = (TRootCalo*) branchCalo->NewEntry();
	      elementCalo->set(list_of_active_towers[i]);
	      // not beautiful : should be improved!
	      TLorentzVector p;
	      p.SetPtEtaPhiE(list_of_active_towers[i].getET(), iEta, iPhi, e );
	      PhysicsTower Tower(LorentzVector(p.Px(),p.Py(),p.Pz(),p.E()));
	      towers.push_back(Tower);
	    }
	} // loop on towers
      
	  // 2.1c photon ID
	  // list_of_towers_with_photon is the list of towers with photon candidates
	  // already smeared !
	  // sorts the vector and smears duplicates 
      list_of_towers_with_photon.mergeDuplicates(); 
      for(unsigned int i=0; i<list_of_towers_with_photon.size(); i++) { 
	  float eta = list_of_towers_with_photon[i].getEta(); 
	  float phi = list_of_towers_with_photon[i].getPhi();
	  D_CaloTower cal(list_of_active_towers.getElement(eta,phi));
	  if(cal.getEta() != UNDEFINED && cal.getPhi() != UNDEFINED &&  cal.getE() > 0) 
	    {
	      TLorentzVector p;
	      p.SetPtEtaPhiE(cal.getET(), eta,phi,cal.getE() );
	      if (cal.getET() > DET->PTCUT_gamma) { gamma.push_back(D_Particle(p,pGAMMA,p.Eta(),p.Phi())); }
	    }
	} // for -- list of photons
      
      // 2.2 ********** Output preparation & complex objects  ***********
      // 2.2.1 ********************* sorting collections by decreasing pt
      DET->SortedVector(electron); 
      float iPhiEl=0,iEtaEl=0,ptisoEl=0;
      for(unsigned int i=0; i < electron.size(); i++) 
	{
	  elementElec = (TRootElectron*) branchElectron->NewEntry();
	  elementElec->Set(electron[i].Px(),electron[i].Py(),electron[i].Pz(),electron[i].E());
	  elementElec->EtaCalo = electron[i].EtaCalo(); 
	  elementElec->PhiCalo = electron[i].PhiCalo();
	  elementElec->Charge = sign(electron[i].PID());
	  elementElec->IsolFlag = DET->Isolation(electron[i],TrackCentral,DET->ISOL_PT,DET->ISOL_Cone,ptisoEl);
	  elementElec->IsolPt = ptisoEl;
	  DET->BinEtaPhi(elementElec->PhiCalo,elementElec->EtaCalo,iPhiEl,iEtaEl); 
 	  D_CaloTower calElec(list_of_active_towers.getElement(iEtaEl,iPhiEl));
	  elementElec->EHoverEE = calElec.getEhad()/calElec.getEem();
	}			
      
      DET->SortedVector(muon);
      float iPhiMu=0,iEtaMu=0,ptisoMu=0;
      for(unsigned int i=0; i < muon.size(); i++) 
	{
	  elementMu = (TRootMuon*) branchMuon->NewEntry();
	  elementMu->Charge = sign(muon[i].PID());
	  elementMu->Set(muon[i].Px(),muon[i].Py(),muon[i].Pz(),muon[i].E());
	  elementMu->EtaCalo = muon[i].EtaCalo(); 
	  elementMu->PhiCalo = muon[i].PhiCalo();
	  elementMu->IsolFlag = DET->Isolation(muon[i],TrackCentral,DET->ISOL_PT,DET->ISOL_Cone,ptisoMu); 
	  elementMu->IsolPt = ptisoMu;
	  DET->BinEtaPhi(elementMu->PhiCalo,elementMu->EtaCalo,iPhiMu,iEtaMu);
	  D_CaloTower calMuon(list_of_active_towers.getElement(iEtaMu,iPhiMu));
	  if( calMuon.getEem() !=0 ) elementMu->EHoverEE = calMuon.getEhad()/calMuon.getEem();
	  else elementMu->EHoverEE = UNDEFINED;
	  elementMu->EtRatio = DET->CaloIsolation(muon[i], list_of_active_towers);
	}

      DET->SortedVector(gamma);
      for(unsigned int i=0; i < gamma.size(); i++) 
	{
	  elementPhoton = (TRootPhoton*) branchPhoton->NewEntry();
	  elementPhoton->Set(gamma[i].Px(),gamma[i].Py(),gamma[i].Pz(),gamma[i].E());
	  D_CaloTower calGamma(list_of_active_towers.getElement(gamma[i].EtaCalo(),gamma[i].PhiCalo()));
	  elementPhoton->EHoverEE = calGamma.getEhad()/calGamma.getEem();
	}
      
      // 2.2.2 ************* computes the Missing Transverse Momentum
      TLorentzVector Att(0.,0.,0.,0.);
      for(unsigned int i=0; i < towers.size(); i++)
        {
	  Att.SetPxPyPzE(towers[i].fourVector.px, towers[i].fourVector.py, towers[i].fourVector.pz, towers[i].fourVector.E);
	  if(fabs(Att.Eta()) < DET->CEN_max_calo_fwd)
	    {
	      PTmis = PTmis + Att;
	      // create a fastjet::PseudoJet with these components and put it onto
	      // back of the input_particles vector
	      input_particles.push_back(fastjet::PseudoJet(towers[i].fourVector.px,towers[i].fourVector.py,towers[i].fourVector.pz,towers[i].fourVector.E));
	    }
        }
      elementEtmis = (TRootETmis*) branchETmis->NewEntry();
      elementEtmis->ET = (PTmis).Pt();
      elementEtmis->Phi = (-PTmis).Phi();
      elementEtmis->Px = (-PTmis).Px();
      elementEtmis->Py = (-PTmis).Py();
      
      // 2.2.3 ************* jets, B-tag, tau jets
      vector<int> NTrackJet; //for number of tracks
      vector<float> EHADEEM; //for energyHad over energyEm
      sorted_jets=JETRUN->RunJets(input_particles, TrackCentral,NTrackJet,EHADEEM,list_of_active_towers);
      JETRUN->RunJetBtagging(treeWriter, branchJet,sorted_jets,NFCentralQ,NTrackJet,EHADEEM);
      JETRUN->RunTauJets(treeWriter,branchTauJet,sorted_jets,towers, TrackCentral,NTrackJet,EHADEEM);
      
      treeWriter->Fill();
    } // 2. Loop over all events ('for' loop)
  
  cout <<"**                 Exiting detector simulation...                  **"<< endl;
  
  
  treeWriter->Write();
  delete treeWriter;
  loopwatch.Stop();
  
  
  
  // 3. ********** Trigger  & Frog ***********
  // 3.1 ************ running the trigger in case the FLAG trigger is put to 1 in the datacard
  triggerwatch.Start();
  if(DET->FLAG_trigger == 1)
    {
      cout <<"**                                                                 **"<<endl;
      cout <<"**        ########### Start Trigger selection ###########          **"<< endl;
      
      // input
      TChain chainT("Analysis");
      chainT.Add(outputfilename.c_str());
      ExRootTreeReader *treeReaderT = new ExRootTreeReader(&chainT);
      
      // output
      TClonesArray *branchElecTrig = treeReaderT->UseBranch("Electron");
      TClonesArray *branchMuonTrig = treeReaderT->UseBranch("Muon");
      TClonesArray *branchJetTrig = treeReaderT->UseBranch("Jet");
      TClonesArray *branchTauJetTrig = treeReaderT->UseBranch("TauJet");
      TClonesArray *branchPhotonTrig = treeReaderT->UseBranch("Photon");
      TClonesArray *branchETmisTrig = treeReaderT->UseBranch("ETmis");
      
      ExRootTreeWriter *treeWriterT = new ExRootTreeWriter(outputfilename, "Trigger");
      ExRootTreeBranch *branchTrigger = treeWriterT->NewBranch("TrigResult", TRootTrigger::Class());
      
      
      Long64_t entryT, allEntriesT = treeReaderT->GetEntries();
      // loop on all entries
      for(entryT = 0; entryT < allEntriesT; ++entryT) {
	treeWriterT->Clear();
	treeReaderT->ReadEntry(entryT);
	TRIGT->GetGlobalResult(branchElecTrig, branchMuonTrig,branchJetTrig, branchTauJetTrig,branchPhotonTrig, branchETmisTrig,branchTrigger);
	treeWriterT->Fill();
      } // loop on all entries
      cout <<"**                 Exiting trigger simulation...                   **"<< endl;
      
      treeWriterT->Write();
      delete treeWriterT;
      delete treeReaderT;
    } // trigger
  triggerwatch.Stop();
  
  
  // 3.2 ************** FROG display
  frogwatch.Start();
  if(DET->FLAG_frog == 1) {
    cout <<"**                                                                 **"<<endl;
    cout <<"**        ################## Start FROG #################          **"<< endl;
    
    FrogDisplay *FROG = new FrogDisplay(DET);
    FROG->BuildEvents(outputfilename);
    FROG->BuildGeom();
    delete FROG;
    cout <<"**                  Exiting FROG preparation...                    **"<< endl;
  }
  frogwatch.Stop();
  
  // 3.3 *************** LHCO output
  lhcowatch.Start();
  if(DET->FLAG_lhco == 1){
    cout <<"**                                                                 **"<<endl;
    cout <<"**        ############ Start LHCO convertion ############          **"<< endl;
    
    //LHCOConverter *LHCO = new LHCOConverter(outputfilename,LogNameLHCO);
    LHCOConverter *LHCO = new LHCOConverter(outputfilename,"");
    LHCO->CopyRunLogFile();
    LHCO->ConvertExRootAnalysisToLHCO();
    delete LHCO;
    cout <<"**                  Exiting LHCO converstion...                    **"<< endl;
  }
  lhcowatch.Stop();
  
  
  
  // 4. ********** End & Exit ***********
  
  globalwatch.Stop();
  cout <<"**                                                                 **"<< endl;
  cout <<"**        ################## Time report #################         **"<< endl;
  cout << left  << setw(32) <<"**              Time report for "<<""
       << left  << setw(15) << allEntries <<""
       << right << setw(22) <<"events         **"<<endl;
  cout <<"**                                                                 **"<< endl;
  cout << left  << setw(10) <<"**"<<""
       << left  << setw(15) <<"Time (s):"<<""
       << right << setw(15) <<"CPU"<<""
       << right << setw(15) <<"Real"<<""
       << right << setw(14)  <<"**"<<endl;
  cout << left  << setw(10) <<"**"<<""
       << left  << setw(15) <<" +  Global:"<<""
       << right << setw(15) <<globalwatch.CpuTime()<<""
       << right << setw(15) <<globalwatch.RealTime()<<""
       << right << setw(14)  <<"**"<<endl;
  cout << left  << setw(10) <<"**"<<""
       << left  << setw(15) <<" +  Events:"<<""
       << right << setw(15) <<loopwatch.CpuTime()<<""
       << right << setw(15) <<loopwatch.RealTime()<<""
       << right << setw(14)  <<"**"<<endl;
  if(DET->FLAG_trigger == 1)
    {
      cout << left  << setw(10) <<"**"<<""
	   << left  << setw(15) <<" +  Trigger:"<<""
	   << right << setw(15) <<triggerwatch.CpuTime()<<""
	   << right << setw(15) <<triggerwatch.RealTime()<<""
	   << right << setw(14)  <<"**"<<endl;
    }
  if(DET->FLAG_frog == 1)
    {
      cout << left  << setw(10) <<"**"<<""
	   << left  << setw(15) <<" +  Frog:"<<""
	   << right << setw(15) <<frogwatch.CpuTime()<<""
	   << right << setw(15) <<frogwatch.RealTime()<<""
	   << right << setw(14)  <<"**"<<endl;
    }
  if(DET->FLAG_lhco == 1)
    {
      cout << left  << setw(10) <<"**"<<""
           << left  << setw(15) <<" +  LHCO:"<<""
           << right << setw(15) <<lhcowatch.CpuTime()<<""
           << right << setw(15) <<lhcowatch.RealTime()<<""
           << right << setw(14)  <<"**"<<endl;
    }

  
  cout <<"**                                                                 **"<< endl;
  cout <<"**                        Exiting Delphes ...                      **"<< endl;
  cout <<"**                                                                 **"<< endl;
  cout <<"*********************************************************************"<< endl;
  cout <<"*********************************************************************"<< endl;
  
  
  delete treeReader;
  delete DET;
  delete TRIGT;
  delete TRACP;
  delete JETRUN;
  delete VFD;
  
  //  todo("TODO");
}