//
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//
// Hadrontherapy advanced example for Geant4
// See more at: https://twiki.cern.ch/twiki/bin/view/Geant4/AdvancedExamplesHadrontherapy

#include "G4SteppingManager.hh"
#include "G4TrackVector.hh"
#include "HadrontherapySteppingAction.hh"
#include "G4ios.hh"
#include "G4SteppingManager.hh"
#include "G4Track.hh"
#include "G4Step.hh"
#include "G4StepPoint.hh"
#include "G4TrackStatus.hh"
#include "G4TrackVector.hh"
#include "G4ParticleDefinition.hh"
#include "G4ParticleTypes.hh"
#include "G4UserEventAction.hh"
#include "G4TransportationManager.hh"
#include "G4VSensitiveDetector.hh"
#include "HadrontherapyRunAction.hh"
#include "HadrontherapyAnalysisManager.hh"
#include "G4SystemOfUnits.hh"

/////////////////////////////////////////////////////////////////////////////
HadrontherapySteppingAction::HadrontherapySteppingAction( HadrontherapyRunAction *run)
{
    runAction = run;
}

/////////////////////////////////////////////////////////////////////////////
HadrontherapySteppingAction::~HadrontherapySteppingAction()
{
}

/////////////////////////////////////////////////////////////////////////////
void HadrontherapySteppingAction::UserSteppingAction(const G4Step* aStep)
{
G4StepPoint* PreStep = aStep->GetPreStepPoint();
G4StepPoint* PostStep = aStep->GetPostStepPoint();

G4double PreStepX =PreStep->GetPosition().x();
G4double PreStepY =PreStep->GetPosition().y();
G4double PreStepZ =PreStep->GetPosition().z();
G4double parentID =aStep->GetTrack()->GetParentID();
G4double trackID =aStep->GetTrack()->GetTrackID();

G4double PostStepX =PostStep->GetPosition().x();
G4double PostStepY =PostStep->GetPosition().y();
G4double PostStepZ  =PostStep->GetPosition().z();

// positions in the global coordinate system:
//G4ThreeVector posPreStep  = PreStep->GetPosition();
// G4ThreeVector posPostStep = PostStep->GetPosition();

G4TouchableHandle touchPreStep = PreStep->GetTouchableHandle();
G4TouchableHandle touchPostStep = PostStep->GetTouchableHandle();
//To get the current volume:
G4VPhysicalVolume* volumePre = touchPreStep->GetVolume();
G4VPhysicalVolume* volumePost =touchPostStep->GetVolume();

//To get its name:
G4String namePre = volumePre->GetName();
 G4String namePost;

if(volumePost){
 namePost = volumePost->GetName(); 
     }


G4int eventNum = G4RunManager::GetRunManager() -> GetCurrentEvent() -> GetEventID();
G4double eKin = aStep -> GetPreStepPoint() -> GetKineticEnergy();
G4double PosX = aStep->GetTrack()->GetPosition().x();
G4double PosY = aStep->GetTrack()->GetPosition().y();
G4double PosZ = aStep->GetTrack()->GetPosition().z();
G4String material= aStep -> GetTrack() -> GetMaterial() -> GetName();
G4String volume=  aStep->GetTrack()->GetVolume()->GetName();
G4Track* theTrack = aStep->GetTrack();	

 if((namePre== "collimator")||(namePre== "PhysicExternalMagnet_1Down")||(namePre== "PhysicExternalMagnet_1")||(namePre== "PhysicMagnet_1Right")||(namePre== "PhysicMagnet_1Left")||(namePre== "PhysicExternalMagnet_2")||(namePre== "PhysicExternalMagnet_2Down")||(namePre== "PhysicMagnet_2Right")||(namePre== "PhysicMagnet_2Left")||(namePre== "PhysicExternalMagnet_3")||(namePre== "PhysicExternalMagnet_3Down")||(namePre== "PhysicMagnet_3Right")||(namePre== "PhysicMagnet_3Left")||(namePre== "PhysicExternalMagnet_4")||(namePre== "PhysicExternalMagnet_4Down")||(namePre=="physQuadChamberWall")||(namePre== "PhysicMagnet_4Right")||(namePre== "PhysicMagnet_4Left")||(namePre=="ExternalChamber")||(namePre=="collimatorFinal")||(namePre=="ExternalSlit")||(namePre=="PhysFourthQuad")||(namePre=="PhysThirdQuad")||(namePre=="PhysSecondQuad")||(namePre=="PhysFirstQuad")) 
     {
       theTrack -> SetTrackStatus(fKillTrackAndSecondaries);	        
    }
 
 // G4TransportationManager* tManager = G4TransportationManager::GetTransportationManager();
  //G4VPhysicalVolume* pW = tManager->GetParallelWorld ("DetectorROGeometry");

  //G4Navigator* gNav = tManager->GetNavigator(pW);
  
 // G4VPhysicalVolume* currentVol = gNav->LocateGlobalPointAndSetup(aStep->GetTrack()->GetPosition());

 // G4cout << "Step: " << currentVol->GetName() << " " << aStep->GetTrack()->GetPosition() << G4endl;
  //G4cout << "G4LogicalVolume: = " << currentVol->GetLogicalVolume()->GetName() << G4endl;
  //if (currentVol->GetLogicalVolume()->GetSensitiveDetector())
   // G4cout << "Sensitive Detector: " << currentVol->GetLogicalVolume()->GetSensitiveDetector()->GetName() << G4endl;


   
//////////////////////////////////////////////////////////////////////////////////////////////////////////////
////  A METHOD TO RETRIEVE INFORMATIONS ABOUT SECONDARY ELECTRONS IN DIFFERENT POINTS OF FARADAY CUP      ////
//////////////////////////////////////////////////////////////////////////////////////////////////////////////
  

    
   
  //if( (aStep->GetTLocateGlobalPointAndSeturack()->GetVolume()->GetName() == "PVirtualMag") 
 if((aStep->GetTrack()->GetVolume()->GetName()=="PVirtualMag") && aStep->GetTrack()->GetDefinition()->GetParticleName() == "e-")
    {
      std::ofstream WriteDataIn("new200.out", std::ios::app);
      WriteDataIn	<<   eKin             << '\t' << "   "
			<<   eventNum         << '\t' << "   "
			<<   PosX             << '\t' << "   "
			<<   PosY             << '\t' << "   "
			<<   PosZ             << '\t' << "   "
	//<<   material         << '\t' << "   "
	//              <<   volume           << '\t' << "   "
			<<   G4endl;


}

// USEFULL METHODS TO RETRIEVE INFORMATION DURING THE STEPS

      /*    G4cout << "ENERGIA:   " << aStep->GetTrack()->GetKineticEnergy() 
    << "   VOLUME  " << aStep->GetTrack()->GetVolume()->GetName()
    << "   MATERIALE    " <<  aStep -> GetTrack() -> GetMaterial() -> GetName()
    << "   EVENTO     " << G4RunManager::GetRunManager()->GetCurrentEvent() -> GetEventID()
    << "   POS     " << aStep->GetTrack()->GetPosition().x()
    << G4endl;*/
    
   
if ((namePre=="PhysicEntranceWindow")   &&  
    (aStep->GetTrack()->GetDefinition()->GetParticleName() == "e-") && (PreStep->GetStepStatus() == fGeomBoundary))
{       
       std::ofstream WriteDataIn("finestra.out", std::ios::app);
       WriteDataIn	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PreStepX            << '\t' << "   "
			<<   PreStepY            << '\t' << "   "
			<<   PreStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;

       //theTrack -> SetTrackStatus(fKillTrackAndSecondaries);
       
      }
   
 if ((namePre=="PhysicCup")   &&  (aStep->GetTrack()->GetDefinition()->GetParticleName() == "e-") && (PreStep->GetStepStatus() == fGeomBoundary))
{
      
       std::ofstream WriteDataBack("fondo.out", std::ios::app);
       WriteDataBack	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PreStepX            << '\t' << "   "
			<<   PreStepY            << '\t' << "   "
			<<   PreStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;
      
    
       //theTrack -> SetTrackStatus(fKillTrackAndSecondaries);
 }

                                                            ////////////////////////////////////  VIRTUAL WINDOW  //////////////////////////////////////////////////   

 if (((namePost=="PhysicVirtualWindow") && (namePre!="PhysicVirtualWindow"))  &&  
 (aStep->GetTrack()->GetDefinition()->GetParticleName() == "e-") && (PreStep->GetStepStatus() == fGeomBoundary)) //To check that the particle has just entered in the current volume (i.e. it is at the first step in the volume; the preStepPoint is at the boundary):
{  //(namePost=="VirtualWindow") && 
      
     if ((PostStepX - PreStepX)>0)
      { 
  
//To check that the particle is leaving the current volume (i.e. it is at the last step in the volume; the postStepPoint is at the boundary):
// if (PostStep->GetStepStatus() == fGeomBoundary)

      
      
 
       std::ofstream WriteDataIn("DatiFCWindowIn.out", std::ios::app);
       WriteDataIn	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PostStepX            << '\t' << "   "
			<<   PostStepY            << '\t' << "   "
			<<   PostStepZ            << '\t' << "   "
                        //<<   direction.x()            << '\t'  << "   "
                        //<<   direction.y()            << '\t'  << "   "
                        //<<   direction.z()            << '\t'  << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;
       
      }
    
      else //if  ((PostStepX - PreStepX)<0)
     {
      
//G4cout<<"ecco il nome del volume nella condizione Out  "<< namePre<<"   "<<namePost<<G4endl;
      
       std::ofstream WriteDataBack("DatiFCWindowBack.out", std::ios::app);
       WriteDataBack	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PostStepX            << '\t' << "   "
			<<   PostStepY            << '\t' << "   "
			<<   PostStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;
      
     }
}



                                                           /////////////////////////////////////////  proton in window //////////////////////////////////////////////////

/*
if ((namePost=="SpectrumPVolume") && (namePre!="SpectrumPVolume")  &&  
   (aStep->GetTrack()->GetDefinition()->GetParticleName() == "proton"))//&& (PreStep->GetStepStatus() == fGeomBoundary)To check that the particle has just entered in the current volume (i.e. it is at the first step in the volume; the preStepPoint is at the boundary):
{  //(namePost=="VirtualVolumeWindow") && 
      
    
  
//To check that the particle is leaving the current volume (i.e. it is at the last step in the volume; the postStepPoint is at the boundary):
// if (PostStep->GetStepStatus() == fGeomBoundary)

      
*/
/*     
     
       std::ofstream WriteDataP("DatiFCWindowProton.out", std::ios::app);
       WriteDataP	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PostStepX            << '\t' << "   "
			<<   PostStepY            << '\t' << "   "
			<<   PostStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;
       
      }
*/
 
if (((namePost=="PhysicVirtualWindow") && (namePre!="PhysicVirtualWindow"))  &&  
    (aStep->GetTrack()->GetDefinition()->GetParticleName() == "proton"))//&& (PreStep->GetStepStatus() == fGeomBoundary)) //To check that the particle has just entered in the current volume (i.e. it is at the first step in the volume; the preStepPoint is at the boundary):
{  //(namePost=="VirtualVolumeWindow") && 
      
    
  
//To check that the particle is leaving the current volume (i.e. it is at the last step in the volume; the postStepPoint is at the boundary):
// if (PostStep->GetStepStatus() == fGeomBoundary)

      
      
      
// 
      
       std::ofstream WriteData("DatiFCAfterWindowProton.out", std::ios::app);
       WriteData	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PostStepX            << '\t' << "   "
			<<   PostStepY            << '\t' << "   "
			<<   PostStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;
       
      }




                                                         //////////////////////////////////////////////////  GUARD RING  ///////////////////////////////////////////////////////////////
      
    
if ((namePre=="PhysicGuardRing")  &&  
     (aStep->GetTrack()->GetDefinition()->GetParticleName() == "e-")&& (PreStep->GetStepStatus() == fGeomBoundary))
{
      
     if ((PostStepX - PreStepX)>0)
    {      
     
      
       std::ofstream WriteDataIn("DatiFCGuardRingIn.out", std::ios::app);
       WriteDataIn	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PreStepX            << '\t' << "   "
			<<   PreStepY            << '\t' << "   "
			<<   PreStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
			<< G4endl;
       
     }
    
   else
     {
      

       std::ofstream WriteDataBack("DatiFCGuardRingBack.out", std::ios::app);
       WriteDataBack	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PreStepX            << '\t' << "   "
			<<   PreStepY            << '\t' << "   "
			<<   PreStepZ            << '\t' << "   "
			<<   parentID            << '\t' << "   "
			<< G4endl;
      
     }
} 

                                                           ////////////////////////////////////////  VIRTUAL MIDDLE  ///////////////////////////////////////////////////////////////
    
 if (((namePost=="PhysicVirtualMiddle") && (namePre!="PhysicVirtualMiddle"))  &&
 (aStep->GetTrack()->GetDefinition()->GetParticleName() == "e-") && (PreStep->GetStepStatus() == fGeomBoundary))
{
      
     if ((PostStepX - PreStepX)>0)
    {      
      
      
// 
      
       std::ofstream WriteMDataIn("DatiFCMiddleIn.out", std::ios::app);
       WriteMDataIn	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PostStepX            << '\t' << "   "
			<<   PostStepY            << '\t' << "   "
			<<   PostStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;
       
     }
    
   else
     {
      
       std::ofstream WriteMDataBack("DatiFCMiddleBack.out", std::ios::app);
       WriteMDataBack	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PostStepX            << '\t' << "   "
			<<   PostStepY            << '\t' << "   "
			<<   PostStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;
      
     }
} 

                                                         /////////////////////////////////////// VIRTUAL BOTTOM  ///////////////////////////////////////////////////////////////    

 if (((namePost=="PhysicVirtualBottom") && (namePre!="PhysicVirtualBottom")) && 
 (aStep->GetTrack()->GetDefinition()->GetParticleName() == "e-")&& (PreStep->GetStepStatus() == fGeomBoundary))
{
      
     if ((PostStepX - PreStepX)>0)
    {      
      
       std::ofstream WriteDataIn("DatiFCBottomIn.out", std::ios::app);
       WriteDataIn	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PostStepX            << '\t' << "   "
			<<   PostStepY            << '\t' << "   "
			<<   PostStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;
       
     }
    
   else
     {
      
//G4cout<<"ecco il nome del volume nella condizione Back  "<< namePre<<"   "<<namePost<<G4endl;
      
       std::ofstream WriteDataBack("DatiFCBottomBack.out", std::ios::app);
       WriteDataBack	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PostStepX            << '\t' << "   "
			<<   PostStepY            << '\t' << "   "
			<<   PostStepZ            << '\t' << "   "
                        //<<   direction.x()            << '\t'  << "   "
                        //<<   direction.y()            << '\t'  << "   "
                        //<<   direction.z()            << '\t'  << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;
      
     }
} 



                                                         //////////////////////////////////////////////////  Dose Calculation  ///////////////////////////////////////////////////////////////

//namePre!=("Cup")
 if (((namePost=="PhysicCup") && (namePre!="PhysicCup")) &&
     (aStep->GetTrack()->GetDefinition()->GetParticleName() == "proton") && (PreStep->GetStepStatus() == fGeomBoundary)) //|| (namePre=="Cup") && )
{

 std::ofstream Carica("CaricaRaccolta.out", std::ios::app);
                 Carica	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PostStepX            << '\t' << "   "
			<<   PostStepY            << '\t' << "   "
			<<   PostStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;


}

//namePre!=("PhysicFaradayCupBottom")
 if (((namePost=="PhysicFaradayCupBottom") && (namePre!="PhysicFaradayCupBottom"))&& 
    (aStep->GetTrack()->GetDefinition()->GetParticleName() == "proton") && (PreStep->GetStepStatus() == fGeomBoundary)) // || (namePre=="cup") && )
{

 std::ofstream CaricaLatFC("CaricaRaccoltaLatFC.out", std::ios::app);
                 CaricaLatFC	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PostStepX            << '\t' << "   "
			<<   PostStepY            << '\t' << "   "
			<<   PostStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;


}



 if (((namePre=="PhysicFaradayCupBottom") || (namePre=="PhysicCup")) && ((aStep->GetTrack()->GetDefinition()->GetParticleName() == "e-") && (PreStep->GetStepStatus() == fGeomBoundary)))
{
      
     if ((PostStepX - PreStepX)>0)
    {      
      
       std::ofstream WriteDataIn("DatiFCConeBottomCupIn.out", std::ios::app);
       WriteDataIn	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PreStepX            << '\t' << "   "
			<<   PreStepY            << '\t' << "   "
			<<   PreStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
			<< G4endl;
       
     }
    
   else
     {
      
//G4cout<<"ecco il nome del volume nella condizione Back  "<< namePre<<"   "<<namePost<<G4endl;
      
       std::ofstream WriteDataBack("DatiFCConeBottomCupBack.out", std::ios::app);
       WriteDataBack	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PreStepX            << '\t' << "   "
			<<   PreStepY            << '\t' << "   "
			<<   PreStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
			<< G4endl;
      
     }
}

                                                    /////////////////////////////////////////////////  VIRTUAL OVER BOTTOM  ///////////////////////////////////////////////////////////////
    
   
if ((namePre=="PhysicVirtualOverBottom")  &&  
    (aStep->GetTrack()->GetDefinition()->GetParticleName() == "e-")&& (PreStep->GetStepStatus() == fGeomBoundary))
{
      
     if ((PostStepX - PreStepX)>0)
    {      
      
      
// 
      
       std::ofstream WriteDataIn("DatiFCOverBottomIn.out", std::ios::app);
       WriteDataIn	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PreStepX            << '\t' << "   "
			<<   PreStepY            << '\t' << "   "
			<<   PreStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;
       
     }
    
   else
     {
      
//G4cout<<"ecco il nome del volume nella condizione Back  "<< namePre<<"   "<<namePost<<G4endl;
      
       std::ofstream WriteDataBack("DatiFCOverBottomBack.out", std::ios::app);
       WriteDataBack	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PreStepX            << '\t' << "   "
			<<   PreStepY            << '\t' << "   "
			<<   PreStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;
      
     }
     
     
}


                                                    /////////////////////////////////////////////  VIRTUAL LATERAL  ///////////////////////////////////////////////////////////////
   

if (((namePost=="PhysicVirtualLateral") && (namePre!="PhysicVirtualLateral"))&&
    (aStep->GetTrack()->GetDefinition()->GetParticleName() == "e-") && (PreStep->GetStepStatus() == fGeomBoundary))
{
     
      
       std::ofstream WriteDataIn("DatiFCLateral.out", std::ios::app);
       WriteDataIn	<<      eKin             << '\t' << "   "
			<<   eventNum            << '\t' << "   "
			<<   PostStepX            << '\t' << "   "
			<<   PostStepY            << '\t' << "   "
			<<   PostStepZ            << '\t' << "   "
			<<   parentID            << '\t'  << "   "
                        <<    trackID            << '\t'  << "   "
			<< G4endl;

       
     }



    if( aStep->GetTrack()->GetVolume()->GetName() == "NewDetectorPhys"){
#ifdef G4ANALYSIS_USE_ROOT
	G4ParticleDefinition *def = aStep->GetTrack()->GetDefinition();
	G4double secondaryParticleKineticEnergy =  aStep->GetTrack()->GetKineticEnergy();     
	G4String particleType = def->GetParticleType(); // particle type = nucleus for d, t, He3, alpha, and heavier nuclei
	G4String particleName = def->GetParticleName(); // e.g. for alpha: the name = "alpha" and type = "nucleus"
	if(particleType == "nucleus") {
	    G4int A = def->GetBaryonNumber();
	    G4double Z = def->GetPDGCharge();
	    G4double posX = aStep->GetTrack()->GetPosition().x() / cm;
	    G4double posY = aStep->GetTrack()->GetPosition().y() / cm;
	    G4double posZ = aStep->GetTrack()->GetPosition().z() / cm;
	    G4double energy = secondaryParticleKineticEnergy / A / MeV;

	    HadrontherapyAnalysisManager* analysisMgr =  HadrontherapyAnalysisManager::GetInstance();   
	    analysisMgr->FillFragmentTuple(A, Z, energy, posX, posY, posZ);
	} else if(particleName == "proton") {   // proton (hydrogen-1) is a special case
	    G4double posX = aStep->GetTrack()->GetPosition().x() / cm ;
	    G4double posY = aStep->GetTrack()->GetPosition().y() / cm ;
	    G4double posZ = aStep->GetTrack()->GetPosition().z() / cm ;
	    G4double energy = secondaryParticleKineticEnergy * MeV;    // Hydrogen-1: A = 1, Z = 1
	    HadrontherapyAnalysisManager::GetInstance()->FillFragmentTuple(1, 1.0, energy, posX, posY, posZ);
	}

	G4String secondaryParticleName =  def -> GetParticleName();  
	//G4cout <<"Particle: " << secondaryParticleName << G4endl;
	//G4cout <<"Energy: " << secondaryParticleKineticEnergy << G4endl;
	HadrontherapyAnalysisManager* analysis =  HadrontherapyAnalysisManager::GetInstance();   
	//There is a bunch of stuff recorded with the energy 0, something should perhaps be done about this.
	if(secondaryParticleName == "proton") {
	    analysis->hydrogenEnergy(secondaryParticleKineticEnergy / MeV);
	}
	if(secondaryParticleName == "deuteron") {
	    analysis->hydrogenEnergy((secondaryParticleKineticEnergy/2) / MeV);
	}
	if(secondaryParticleName == "triton") {
	    analysis->hydrogenEnergy((secondaryParticleKineticEnergy/3) / MeV);
	}
	if(secondaryParticleName == "alpha") {
	    analysis->heliumEnergy((secondaryParticleKineticEnergy/4) / MeV);
	}
	if(secondaryParticleName == "He3"){
	    analysis->heliumEnergy((secondaryParticleKineticEnergy/3) / MeV);		
	}
#endif

	aStep->GetTrack()->SetTrackStatus(fKillTrackAndSecondaries);
    }

    // Electromagnetic and hadronic processes of primary particles in the phantom
    //setting phantomPhys correctly will break something here fixme
    if ((aStep -> GetTrack() -> GetTrackID() == 1) &&
	    (aStep -> GetTrack() -> GetVolume() -> GetName() == "PhantomPhys") &&
	    (aStep -> GetPostStepPoint() -> GetProcessDefinedStep() != NULL))
    {
	G4String process = aStep -> GetPostStepPoint() -> 
	    GetProcessDefinedStep() -> GetProcessName();

	if ((process == "Transportation") || (process == "StepLimiter")) {;}
	else 
	{
	    if ((process == "msc") || (process == "hLowEIoni") || (process == "hIoni")) 
	    { 
		runAction -> AddEMProcess();
	    } 
	    else  
	    {
		runAction -> AddHadronicProcess();

		if ( (process != "LElastic") && (process != "ProtonInelastic") && (process != "hElastic") )
		    G4cout << "Warning! Unknown proton process: "<< process << G4endl;
	    }
	}         
    }

    // Retrieve information about the secondary particles originated in the phantom

    G4SteppingManager*  steppingManager = fpSteppingManager;

    // check if it is alive
    //if(theTrack-> GetTrackStatus() == fAlive) { return; }

    // Retrieve the secondary particles
    G4TrackVector* fSecondary = steppingManager -> GetfSecondary();

    for(size_t lp1=0;lp1<(*fSecondary).size(); lp1++)
    { 
	G4String volumeName = (*fSecondary)[lp1] -> GetVolume() -> GetName(); 

	if (volumeName == "phantomPhys")
	{
#ifdef G4ANALYSIS_USE_ROOT   
	    G4String secondaryParticleName =  (*fSecondary)[lp1]->GetDefinition() -> GetParticleName();  
	    G4double secondaryParticleKineticEnergy =  (*fSecondary)[lp1] -> GetKineticEnergy();     

	    HadrontherapyAnalysisManager* analysis =  HadrontherapyAnalysisManager::GetInstance();   

	    if (secondaryParticleName == "e-")
		analysis -> electronEnergyDistribution(secondaryParticleKineticEnergy/MeV);

	    if (secondaryParticleName == "gamma")
		analysis -> gammaEnergyDistribution(secondaryParticleKineticEnergy/MeV);

	    if (secondaryParticleName == "deuteron")
		analysis -> deuteronEnergyDistribution(secondaryParticleKineticEnergy/MeV);

	    if (secondaryParticleName == "triton")
		analysis -> tritonEnergyDistribution(secondaryParticleKineticEnergy/MeV);

	    if (secondaryParticleName == "alpha")
		analysis -> alphaEnergyDistribution(secondaryParticleKineticEnergy/MeV);

	    G4double z = (*fSecondary)[lp1]-> GetDynamicParticle() -> GetDefinition() -> GetPDGCharge();
	    if (z > 0.)
	    {      
		G4int a = (*fSecondary)[lp1]-> GetDynamicParticle() -> GetDefinition() -> GetBaryonNumber();
		G4int electronOccupancy = (*fSecondary)[lp1] ->  GetDynamicParticle() -> GetTotalOccupancy(); 

		// If a generic ion is originated in the detector, its baryonic number, PDG charge, 
		// total number of electrons in the orbitals are stored in a ntuple 
		analysis -> genericIonInformation(a, z, electronOccupancy, secondaryParticleKineticEnergy/MeV);
	    }
#endif
	}
    }
}