G4RadioactiveDecay.cc

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//
// MODULE:              G4RadioactiveDecay.cc
//
// Author:              F Lei & P R Truscott
// Organisation:        DERA UK
// Customer:            ESA/ESTEC, NOORDWIJK
// Contract:            12115/96/JG/NL Work Order No. 3
//
// Documentation avaialable at http://www.space.dera.gov.uk/space_env/rdm.html
//   These include:
//       User Requirement Document (URD)
//       Software Specification Documents (SSD)
//       Software User Manual (SUM)
//       Technical Note (TN) on the physics and algorithms
//
//    The test and example programs are not included in the public release of 
//    G4 but they can be downloaded from
//      http://www.space.qinetiq.com/space_env/rdm.html
// 
// CHANGE HISTORY
// --------------
// 03 Oct  2012, V. Ivanchenko removed internal table for mean free path 
//                             similar to what is done for as G4Decay
// 10 July 2012, L. Desorgher
//          -In LoadDecayTable:  Add LoadedNuclei.push_back(theParentNucleus.GetParticleName());
//          also for the case where user data files are used. Correction for bug
//          1324. Changes proposed by Joa L.
//
//
// 01 May 2012, L. Desorgher
//          -Force the reading of user file to theIsotopeTable
//          -Merge the development by Fan Lei for activation computation
//
// 17 Oct 2011, L. Desorgher
//          -Add possibility for the user to load its own decay file.
//          -Set halflifethreshold negative by default to allow the tracking of all
//             excited nuclei resulting from a radioactive decay
//
// 01 June 2011, M. Kelsey -- Add directional biasing interface to allow for
//      "collimation" of decay daughters.
// 16 February 2006, V.Ivanchenko fix problem in IsApplicable connected with
//            8.0 particle design
// 18 October 2002, F. Lei
//            in the case of beta decay, added a check of the end-energy 
//            to ensure it is > 0.
//            ENSDF occationally have beta decay entries with zero energies
//
// 27 Sepetember 2001, F. Lei
//            verboselevel(0) used in constructor
//
// 01 November 2000, F.Lei
//            added " ee = e0 +1. ;" as line 763
//            tagged as "radiative_decay-V02-00-02"              
// 28 October 2000, F Lei 
//            added fast beta decay mode. Many files have been changed.
//            tagged as "radiative_decay-V02-00-01"
//
// 25 October 2000, F Lei, DERA UK
//            1) line 1185 added 'const' to work with tag "Track-V02-00-00"
//            tagged as "radiative_decay-V02-00-00"
// 14 April 2000, F Lei, DERA UK
// 0.b.4 release. Changes are:
//            1) Use PhotonEvaporation instead of DiscreteGammaDeexcitation
//            2) VR: Significant efficiency improvement
// 
// 29 February 2000, P R Truscott, DERA UK
// 0.b.3 release.
//
///////////////////////////////////////////////////////////////////////////////
//
#include "G4RadioactiveDecay.hh"
#include "G4RadioactiveDecaymessenger.hh"
 
#include "G4SystemOfUnits.hh"
#include "G4DynamicParticle.hh"
#include "G4DecayProducts.hh"
#include "G4DecayTable.hh"
#include "G4PhysicsLogVector.hh"
#include "G4ParticleChangeForRadDecay.hh"
#include "G4ITDecayChannel.hh"
#include "G4BetaMinusDecayChannel.hh"
#include "G4BetaPlusDecayChannel.hh"
#include "G4KshellECDecayChannel.hh"
#include "G4LshellECDecayChannel.hh"
#include "G4MshellECDecayChannel.hh"
#include "G4AlphaDecayChannel.hh"
#include "G4VDecayChannel.hh"
#include "G4RadioactiveDecayMode.hh"
#include "G4Ions.hh"
#include "G4IonTable.hh"
#include "G4RIsotopeTable.hh"
#include "G4BetaDecayType.hh"
#include "G4BetaDecayCorrections.hh"
#include "Randomize.hh"
#include "G4LogicalVolumeStore.hh"
#include "G4NuclearLevelManager.hh"
#include "G4NuclearLevelStore.hh"
#include "G4ThreeVector.hh"
#include "G4Electron.hh"
#include "G4Positron.hh"
#include "G4Neutron.hh"
#include "G4Gamma.hh"
#include "G4Alpha.hh"
 
#include "G4HadTmpUtil.hh"
#include "G4HadronicProcessType.hh"
#include "G4LossTableManager.hh"
#include "G4VAtomDeexcitation.hh"
 
#include <vector>
#include <sstream>
#include <algorithm>
#include <fstream>
 
using namespace CLHEP;
 
const G4double G4RadioactiveDecay::levelTolerance =2.0*keV;
const G4ThreeVector G4RadioactiveDecay::origin(0.,0.,0.);
 
G4RadioactiveDecay::G4RadioactiveDecay(const G4String& processName)
 : G4VRestDiscreteProcess(processName, fDecay), HighestValue(20.0),
   isInitialised(false), forceDecayDirection(0.,0.,0.), 
   forceDecayHalfAngle(0.*deg), verboseLevel(0)
{
#ifdef G4VERBOSE
  if (GetVerboseLevel()>1) {
    G4cout <<"G4RadioactiveDecay constructor    Name: ";
    G4cout <<processName << G4endl;   }
#endif
 
  SetProcessSubType(fRadioactiveDecay);
 
  theRadioactiveDecaymessenger = new G4RadioactiveDecaymessenger(this);
  theIsotopeTable              = new G4RIsotopeTable();
  pParticleChange              = &fParticleChangeForRadDecay;
 
  // Now register the Isotope table with G4IonTable.
  G4IonTable *theIonTable =
    (G4IonTable *)(G4ParticleTable::GetParticleTable()->GetIonTable());
  G4VIsotopeTable *aVirtualTable = theIsotopeTable;
  theIonTable->RegisterIsotopeTable(aVirtualTable);
 
  // Reset the contents of the list of nuclei for which decay scheme data
  // have been loaded.
  LoadedNuclei.clear();
 
  //
  //Reset the list of user define data file
  //
  theUserRadioactiveDataFiles.clear();
 
  //
  //
  // Apply default values.
  //
  NSourceBin  = 1;
  SBin[0]     = 0.* s;
  SBin[1]     = 1.* s;
  SProfile[0] = 1.;
  SProfile[1] = 0.;
  NDecayBin   = 1;
  DBin[0]     = 0. * s ;
  DBin[1]     = 1. * s;
  DProfile[0] = 1.;
  DProfile[1] = 0.;
  decayWindows[0] = 0;
  G4RadioactivityTable* rTable = new G4RadioactivityTable() ;
  theRadioactivityTables.push_back(rTable);
  NSplit      = 1;
  AnalogueMC  = true ;
  FBeta       = false ;
  BRBias      = true ;
  applyICM    = true ;
  applyARM    = true ;
  halflifethreshold = -1.*second;
  //
  // RDM applies to xall logical volumes as default
  isAllVolumesMode=true;
  SelectAllVolumes();
}
 
 
G4RadioactiveDecay::~G4RadioactiveDecay()
{
  delete theRadioactiveDecaymessenger;
}
 
 
G4bool
G4RadioactiveDecay::IsApplicable(const G4ParticleDefinition& aParticle)
{
  // All particles, other than G4Ions, are rejected by default
  if (((const G4Ions*)(&aParticle))->GetExcitationEnergy() > 0.) {return true;}
  if (aParticle.GetParticleName() == "GenericIon") {
    return true;
  } else if (!(aParticle.GetParticleType() == "nucleus")
             || aParticle.GetPDGLifeTime() < 0. ) {
    return false;
  }
 
  // Determine whether the nuclide falls into the correct A and Z range
 
  G4int A = ((const G4Ions*) (&aParticle))->GetAtomicMass();
  G4int Z = ((const G4Ions*) (&aParticle))->GetAtomicNumber();
  if (A > theNucleusLimits.GetAMax() || A < theNucleusLimits.GetAMin())
    {return false;}
  else if (Z > theNucleusLimits.GetZMax() || Z < theNucleusLimits.GetZMin())
    {return false;}
  return true;
}
 
 
G4bool G4RadioactiveDecay::IsLoaded(const G4ParticleDefinition &aParticle)
{
  // Check whether the radioactive decay data on the ion have already been
  // loaded
 
  return std::binary_search(LoadedNuclei.begin(),
                LoadedNuclei.end(),
                aParticle.GetParticleName());
}
 
 
void G4RadioactiveDecay::SelectAVolume(const G4String aVolume)
{
  G4LogicalVolumeStore* theLogicalVolumes;
  G4LogicalVolume *volume;
  theLogicalVolumes=G4LogicalVolumeStore::GetInstance();
  for (size_t i = 0; i < theLogicalVolumes->size(); i++){
    volume=(*theLogicalVolumes)[i];
    if (volume->GetName() == aVolume) {
      ValidVolumes.push_back(aVolume);
      std::sort(ValidVolumes.begin(), ValidVolumes.end());
      // sort need for performing binary_search
#ifdef G4VERBOSE
      if (GetVerboseLevel()>0)
    G4cout << " RDM Applies to : " << aVolume << G4endl; 
#endif
    }else if(i ==  theLogicalVolumes->size())
      {
    G4cerr << "SelectAVolume: "<<aVolume << " is not a valid logical volume name"<< G4endl; 
      }
  }
}
 
 
void G4RadioactiveDecay::DeselectAVolume(const G4String aVolume)
{
  G4LogicalVolumeStore *theLogicalVolumes;
  G4LogicalVolume *volume;
  theLogicalVolumes=G4LogicalVolumeStore::GetInstance();
  for (size_t i = 0; i < theLogicalVolumes->size(); i++){
    volume=(*theLogicalVolumes)[i];
    if (volume->GetName() == aVolume) {
      std::vector<G4String>::iterator location;
      location = std::find(ValidVolumes.begin(),ValidVolumes.end(),aVolume);
      if (location != ValidVolumes.end()) {
    ValidVolumes.erase(location);
    std::sort(ValidVolumes.begin(), ValidVolumes.end());
    isAllVolumesMode =false;
      } else {
    G4cerr << " DeselectVolume:" << aVolume << " is not in the list"<< G4endl; 
      }   
#ifdef G4VERBOSE
      if (GetVerboseLevel()>0)
    G4cout << " DeselectVolume: " << aVolume << " is removed from list"<<G4endl; 
#endif
    } else if (i ==  theLogicalVolumes->size()) {
      G4cerr << " DeselectVolume:" << aVolume
             << "is not a valid logical volume name"<< G4endl; 
    }
  }
}
 
 
void G4RadioactiveDecay::SelectAllVolumes() 
{
  G4LogicalVolumeStore *theLogicalVolumes;
  G4LogicalVolume *volume;
  theLogicalVolumes=G4LogicalVolumeStore::GetInstance();
  ValidVolumes.clear();
#ifdef G4VERBOSE
  if (GetVerboseLevel()>0)
    G4cout << " RDM Applies to all Volumes"  << G4endl;
#endif
  for (size_t i = 0; i < theLogicalVolumes->size(); i++){
    volume=(*theLogicalVolumes)[i];
    ValidVolumes.push_back(volume->GetName());    
#ifdef G4VERBOSE
    if (GetVerboseLevel()>0)
      G4cout << "         RDM Applies to Volume "  << volume->GetName() << G4endl;
#endif
  }
  std::sort(ValidVolumes.begin(), ValidVolumes.end());
  // sort needed in order to allow binary_search
  isAllVolumesMode=true;
}
 
 
void G4RadioactiveDecay::DeselectAllVolumes() 
{
  ValidVolumes.clear();
  isAllVolumesMode=false;
#ifdef G4VERBOSE
  if (GetVerboseLevel()>0)
    G4cout << " RDM removed from all volumes" << G4endl; 
#endif
}
 
 
G4bool
G4RadioactiveDecay::IsRateTableReady(const G4ParticleDefinition& aParticle)
{
  // Check whether the radioactive decay rates table for the ion has already
  // been calculated.
  G4String aParticleName = aParticle.GetParticleName();
  for (size_t i = 0; i < theDecayRateTableVector.size(); i++) {
    if (theDecayRateTableVector[i].GetIonName() == aParticleName)
      return true;
  }
  return false;
}
 
// GetDecayRateTable
// retrieve the decayratetable for the specified aParticle
 
void
G4RadioactiveDecay::GetDecayRateTable(const G4ParticleDefinition& aParticle)
{
  G4String aParticleName = aParticle.GetParticleName();
 
  for (size_t i = 0; i < theDecayRateTableVector.size(); i++) {
    if (theDecayRateTableVector[i].GetIonName() == aParticleName) {
      theDecayRateVector = theDecayRateTableVector[i].GetItsRates();
    }
  }
#ifdef G4VERBOSE
  if (GetVerboseLevel() > 0) {
    G4cout << "The DecayRate Table for "
           << aParticleName << " is selected." <<  G4endl;
  }
#endif
}
 
// GetTaoTime performs the convolution of the source time profile function
// with the decay constants in the decay chain. 
G4double G4RadioactiveDecay::GetTaoTime(const G4double t, const G4double tao)
{
  long double taotime =0.L;
  G4int nbin;
  if ( t > SBin[NSourceBin]) {
    nbin  = NSourceBin;}
  else {
    nbin = 0;
    while (t > SBin[nbin]) nbin++;
    nbin--;}
  long double lt = t ;
  long double ltao = tao;
 
  if (nbin > 0) { 
    for (G4int i = 0; i < nbin; i++) 
      {
    taotime += (long double)SProfile[i] * (std::exp(-(lt-(long double)SBin[i+1])/ltao)-std::exp(-(lt-(long double)SBin[i])/ltao));
      }
  }
  taotime +=  (long double)SProfile[nbin] * (1.L-std::exp(-(lt-(long double)SBin[nbin])/ltao));
  if (taotime < 0.)  {
    G4cout <<" Tao time =: " <<taotime << " reset to zero!"<<G4endl;
    G4cout <<" t = " << t <<" tao = " <<tao <<G4endl;
    G4cout << SBin[nbin] << " " <<SBin[0] << G4endl;
    taotime = 0.;
  }
#ifdef G4VERBOSE
  if (GetVerboseLevel()>1)
    {G4cout <<" Tao time: " <<taotime <<G4endl;}
#endif
  return (G4double)taotime ;
}
 
/*
// Other implementation tests to avoid use of  long double
G4double G4RadioactiveDecay::GetTaoTime(const G4double t, const G4double tao)
{
  long double taotime =0.L;
  G4int nbin;
  if ( t > SBin[NSourceBin]) {
    nbin  = NSourceBin;}
  else {
    nbin = 0;
    while (t > SBin[nbin]) nbin++;
    nbin--;}
  long double lt = t ;
  long double ltao = tao;
  long double factor,factor1,dt1,dt;
  if (nbin > 0) {
        for (G4int i = 0; i < nbin; i++)
          { long double s1=SBin[i];
            long double s2=SBin[i+1];
            dt1=(s2-s1)/ltao;
            if (dt1 <50.) {
                factor1=std::exp(dt1)-1.;
                if (factor1<dt1) factor1 =dt1;
                dt=(lt-s1)/ltao;
                factor=std::exp(-dt);
            }
            else {
                factor1=1.-std::exp(-dt1);
                dt=(lt-s2)/ltao;
                factor=std::exp(-dt);
            }
            G4cout<<(long double) SProfile[i] *factor*factor1<<'\t'<<std::endl;
            long double test  = (long double)SProfile[i] * (std::exp(-(lt-(long double)SBin[i+1])/ltao)-std::exp(-(lt-(long double)SBin[i])/ltao));
            G4cout<<test<<std::endl;
            taotime += (long double) SProfile[i] *factor*factor1;
       }
   }
  long double s=SBin[nbin];
  dt1=(lt-s)/ltao;
  factor=1.-std::exp(-dt1);
  taotime += (long double)  SProfile[nbin] *factor;
 if (taotime < 0.)  {
    G4cout <<" Tao time =: " <<taotime << " reset to zero!"<<G4endl;
    G4cout <<" t = " << t <<" tao = " <<tao <<G4endl;
    G4cout << SBin[nbin] << " " <<SBin[0] << G4endl;
    taotime = 0.;
  }
#ifdef G4VERBOSE
  if (GetVerboseLevel()>1)
    {G4cout <<" Tao time: " <<taotime <<G4endl;}
#endif
  return (G4double)taotime ;
}
 
 
 
G4double G4RadioactiveDecay::GetTaoTime(const G4double t, const G4double tao)
{
  G4double taotime =0.;
  G4int nbin;
  if ( t > SBin[NSourceBin]) {
    nbin  = NSourceBin;}
  else {
    nbin = 0;
    while (t > SBin[nbin]) nbin++;
    nbin--;}
  G4double lt = t ;
  G4double ltao = tao;
  G4double factor,factor1,dt1,dt;
 
  if (nbin > 0) {
    for (G4int i = 0; i < nbin; i++)
      { dt1=(SBin[i+1]-SBin[i])/ltao;
        if (dt1 <50.) {
            factor1=std::exp(dt1)-1.;
            if (factor1<dt1) factor1 =dt1;
            dt=(lt-SBin[i])/ltao;
            factor=std::exp(-(lt-SBin[i])/ltao);
            G4cout<<factor<<'\t'<<factor1<<std::endl;
        }
        else {
            factor1=1.-std::exp(-dt1);
            factor=std::exp(-(lt-SBin[i+1])/ltao);
        }
        G4cout<<factor<<'\t'<<factor1<<std::endl;
        taotime += SProfile[i] *factor*factor1;
        G4cout<<taotime<<std::endl;
      }
  }
  dt1=(lt-SBin[nbin])/ltao;
  factor=1.-std::exp(-dt1);
  if (factor<(dt1-0.5*dt1*dt1)) factor =dt1-0.5*dt1*dt1;
 
 
  taotime +=  SProfile[nbin] *factor;
  G4cout<<factor<<'\t'<<taotime<<std::endl;
  if (taotime < 0.)  {
    G4cout <<" Tao time =: " <<taotime << " reset to zero!"<<G4endl;
    G4cout <<" t = " << t <<" tao = " <<tao <<G4endl;
    G4cout << SBin[nbin] << " " <<SBin[0] << G4endl;
    taotime = 0.;
  }
 
#ifdef G4VERBOSE
  if (GetVerboseLevel()>1)
    {G4cout <<" Tao time: " <<taotime <<G4endl;}
#endif
  return (G4double)taotime ;
}
*/
////////////////////////////////////////////////////////////////////////////////
//                                                                            //
//  GetDecayTime                                                              //
//    Randomly select a decay time for the decay process, following the       //
//    supplied decay time bias scheme.                                        //
//                                                                            //
////////////////////////////////////////////////////////////////////////////////
 
G4double G4RadioactiveDecay::GetDecayTime()
{
  G4double decaytime = 0.;
  G4double rand = G4UniformRand();
  G4int i = 0;
  while ( DProfile[i] < rand) i++;
  rand = G4UniformRand();
  decaytime = DBin[i] + rand*(DBin[i+1]-DBin[i]);
#ifdef G4VERBOSE
  if (GetVerboseLevel()>1)
    {G4cout <<" Decay time: " <<decaytime/s <<"[s]" <<G4endl;}
#endif
  return  decaytime;        
}
 
 
G4int G4RadioactiveDecay::GetDecayTimeBin(const G4double aDecayTime)
{
  G4int i = 0;
  while ( aDecayTime > DBin[i] ) i++;
  return  i;
}
 
////////////////////////////////////////////////////////////////////////////////
//                                                                            //
//  GetMeanLifeTime (required by the base class)                              //
//                                                                            //
////////////////////////////////////////////////////////////////////////////////
 
G4double G4RadioactiveDecay::GetMeanLifeTime(const G4Track& theTrack,
                         G4ForceCondition* )
{
  // For varience reduction implementation the time is set to 0 so as to 
  // force the particle to decay immediately.
  // in analogueMC mode it return the particles meanlife.
  // 
  G4double meanlife = 0.;
  if (AnalogueMC) {
    const G4DynamicParticle* theParticle = theTrack.GetDynamicParticle();
    G4ParticleDefinition* theParticleDef = theParticle->GetDefinition();
    G4double theLife = theParticleDef->GetPDGLifeTime();
 
#ifdef G4VERBOSE
    if (GetVerboseLevel()>2)
      {
    G4cout <<"G4RadioactiveDecay::GetMeanLifeTime() " <<G4endl;
    G4cout <<"KineticEnergy:" <<theParticle->GetKineticEnergy()/GeV <<"[GeV]";
    G4cout <<"Mass:" <<theParticle->GetMass()/GeV <<"[GeV]"; 
    G4cout <<"Life time: " <<theLife/ns <<"[ns]" << G4endl;
      }
#endif
    if (theParticleDef->GetPDGStable()) {meanlife = DBL_MAX;}
    else if (theLife < 0.0) {meanlife = DBL_MAX;}
    else {meanlife = theLife;}
    // set the meanlife to zero for excited istopes which is not in the RDM database
    if (((const G4Ions*)(theParticleDef))->GetExcitationEnergy() > 0. && meanlife == DBL_MAX) {meanlife = 0.;}
  }
#ifdef G4VERBOSE
  if (GetVerboseLevel()>1)
    {G4cout <<"mean life time: " <<meanlife/s <<"[s]" <<G4endl;}
#endif
 
  return  meanlife;
}
 
////////////////////////////////////////////////////////////////////////
//                                                                    //
//  GetMeanFreePath for decay in flight                               //
//                                                                    //
////////////////////////////////////////////////////////////////////////
 
G4double G4RadioactiveDecay::GetMeanFreePath (const G4Track& aTrack,
                          G4double, G4ForceCondition*)
{
  // get particle
  const G4DynamicParticle* aParticle = aTrack.GetDynamicParticle();
 
  // returns the mean free path in GEANT4 internal units
  G4double pathlength;
  G4ParticleDefinition* aParticleDef = aParticle->GetDefinition();
  G4double aCtau = c_light * aParticleDef->GetPDGLifeTime();
  G4double aMass = aParticle->GetMass();
 
#ifdef G4VERBOSE
  if (GetVerboseLevel()>2) {
    G4cout << "G4RadioactiveDecay::GetMeanFreePath() "<< G4endl;
    G4cout << "KineticEnergy:" << aParticle->GetKineticEnergy()/GeV <<"[GeV]";
    G4cout << "Mass:" << aMass/GeV <<"[GeV]";
    G4cout << "c*Tau:" << aCtau/m <<"[m]" <<G4endl;
  }
#endif
 
  // check if the particle is stable?
  if (aParticleDef->GetPDGStable()) {
    pathlength = DBL_MAX;
 
  } else if (aCtau < 0.0) {
    pathlength =  DBL_MAX;
 
    //check if the particle has very short life time ?
  } else if (aCtau < DBL_MIN) {
    pathlength =  DBL_MIN;
 
    //check if zero mass
  } else if (aMass <  DBL_MIN)  {
    pathlength =  DBL_MAX;
#ifdef G4VERBOSE
    if (GetVerboseLevel()>1) {
      G4cerr << " Zero Mass particle " << G4endl;
    }
#endif
  } else {
    //calculate the mean free path
    // by using normalized kinetic energy (= Ekin/mass)
    G4double rKineticEnergy = aParticle->GetKineticEnergy()/aMass;
    if ( rKineticEnergy > HighestValue) {
      // beta >> 1
      pathlength = ( rKineticEnergy + 1.0)* aCtau;
    } else if ( rKineticEnergy < DBL_MIN ) {
      // too slow particle
#ifdef G4VERBOSE
      if (GetVerboseLevel()>2) {
    G4cout << "G4Decay::GetMeanFreePath()   !!particle stops!!";
    G4cout << aParticleDef->GetParticleName() << G4endl;
    G4cout << "KineticEnergy:" << aParticle->GetKineticEnergy()/GeV 
           <<"[GeV]";
      }
#endif
      pathlength = DBL_MIN;
    } else {
      // beta << 1
      pathlength = aCtau*(aParticle->GetTotalMomentum())/aMass;
    }
  }
#ifdef G4VERBOSE
  if (GetVerboseLevel()>1) {
    G4cout << "mean free path: "<< pathlength/m << "[m]" << G4endl;
  }
#endif
  return  pathlength;
}
 
////////////////////////////////////////////////////////////////////////
//                                                                    //
//  BuildPhysicsTable - initialisation of atomic de-excitation        //
//                                                                    //
////////////////////////////////////////////////////////////////////////
 
void G4RadioactiveDecay::BuildPhysicsTable(const G4ParticleDefinition&)
{
  if(!isInitialised) {
    isInitialised = true;
    G4VAtomDeexcitation* p = G4LossTableManager::Instance()->AtomDeexcitation();
    if(p) { p->InitialiseAtomicDeexcitation(); }
  }
}
 
////////////////////////////////////////////////////////////////////////////////
//                                                                            //
//  LoadDecayTable loads the decay scheme from the RadioactiveDecay database  // 
//  for the parent nucleus.                                                   //
//                                                                            //
////////////////////////////////////////////////////////////////////////////////
 
G4DecayTable*
G4RadioactiveDecay::LoadDecayTable(G4ParticleDefinition& theParentNucleus)
{
  // Create and initialise variables used in the method.
  G4DecayTable* theDecayTable = new G4DecayTable();
 
  // Generate input data file name using Z and A of the parent nucleus
  // file containing radioactive decay data.
  G4int A    = ((const G4Ions*)(&theParentNucleus))->GetAtomicMass();
  G4int Z    = ((const G4Ions*)(&theParentNucleus))->GetAtomicNumber();
  G4double E = ((const G4Ions*)(&theParentNucleus))->GetExcitationEnergy();
 
  //Check if data have been provided by the user
  G4String file= theUserRadioactiveDataFiles[1000*A+Z];
 
  if (file =="") {
    if (!getenv("G4RADIOACTIVEDATA") ) {
      G4cout << "Please setenv G4RADIOACTIVEDATA to point to the radioactive decay data files."
             << G4endl;
      throw G4HadronicException(__FILE__, __LINE__,
                  "Please setenv G4RADIOACTIVEDATA to point to the radioactive decay data files.");
    }
    G4String dirName = getenv("G4RADIOACTIVEDATA");
 
    std::ostringstream os;
    os <<dirName <<"/z" <<Z <<".a" <<A <<'\0';
    file = os.str();
  }
 
  LoadedNuclei.push_back(theParentNucleus.GetParticleName());
  std::sort( LoadedNuclei.begin(), LoadedNuclei.end() );
  // sort needed to allow binary_search
 
  std::ifstream DecaySchemeFile(file);
 
  G4bool found(false);
  if (DecaySchemeFile) { 
    // Initialise variables used for reading in radioactive decay data.
    G4int nMode = 7;
    G4bool modeFirstRecord[7];
    G4double modeTotalBR[7] = {0.0};
    G4double modeSumBR[7];
    for (G4int i = 0; i < nMode; i++) {
      modeFirstRecord[i] = true;
      modeSumBR[i] = 0.0;
    }
 
    G4bool complete(false);
    char inputChars[100]={' '};
    G4String inputLine;
    G4String recordType("");
    G4RadioactiveDecayMode theDecayMode;
    G4double a(0.0);
    G4double b(0.0);
    G4double c(0.0);
    G4BetaDecayType betaType(allowed);
    G4double e0;
 
    // Loop through each data file record until you identify the decay
    // data relating to the nuclide of concern.
 
    while (!complete && !DecaySchemeFile.getline(inputChars, 100).eof()) {
      inputLine = inputChars;
      inputLine = inputLine.strip(1);
      if (inputChars[0] != '#' && inputLine.length() != 0) {
    std::istringstream tmpStream(inputLine);
 
    if (inputChars[0] == 'P') {
          // Nucleus is a parent type.  Check excitation level to see if it
          // matches that of theParentNucleus
      tmpStream >> recordType >> a >> b;
      if (found) {complete = true;}
      else {found = (std::abs(a*keV - E) < levelTolerance);}
 
    } else if (found) {
      // The right part of the radioactive decay data file has been found.  Search
      // through it to determine the mode of decay of the subsequent records.
      if (inputChars[0] == 'W') {
#ifdef G4VERBOSE
        if (GetVerboseLevel() > 0) {
          // a comment line identified and print out the message
          //
          G4cout << " Warning in G4RadioactiveDecay::LoadDecayTable " << G4endl;
          G4cout << "   In data file " << file << G4endl;
          G4cout << "   " << inputLine << G4endl;
        }
#endif
      } else {
        tmpStream >> theDecayMode >> a >> b >> c >> betaType;
 
            // Allowed transitions are the default. Forbidden transitions are
            // indicated in the last column.
            if (inputLine.length() < 80) betaType = allowed;
            a /= 1000.;
            c /= 1000.;
 
            switch (theDecayMode) {
 
              case IT:   // Isomeric transition
              {
                G4ITDecayChannel* anITChannel =
                  new G4ITDecayChannel(GetVerboseLevel(),
                                       (const G4Ions*)& theParentNucleus, b);
                anITChannel->SetICM(applyICM);
                anITChannel->SetARM(applyARM);
                anITChannel->SetHLThreshold(halflifethreshold);
                theDecayTable->Insert(anITChannel);
              }
              break;
 
              case BetaMinus:
              {
                if (modeFirstRecord[1]) {
                  modeFirstRecord[1] = false;
                  modeTotalBR[1] = b;
                } else {
                  if (c > 0.) {
                    e0 = c*MeV/0.511;
                    G4BetaDecayCorrections corrections(Z+1, A);
 
                    // array to store function shape
                    G4int npti = 100;               
                    G4double* pdf = new G4double[npti];
 
                    G4double e;   // Total electron energy in units of electron mass
                    G4double p;   // Electron momentum in units of electron mass 
                    G4double f;   // Spectral shape function value
                    for (G4int ptn = 0; ptn < npti; ptn++) {
                      // Calculate simple phase space spectrum
                      e = 1. + e0*(ptn+0.5)/100.;
                      p = std::sqrt(e*e - 1.);
                      f = p*e*(e0-e+1)*(e0-e+1);
 
                      // Apply Fermi factor to get allowed shape
                      f *= corrections.FermiFunction(e);
 
                      // Apply shape factor for forbidden transitions
                      f *= corrections.ShapeFactor(betaType, p, e0-e+1.);
                      pdf[ptn] = f;
                    }
 
                    RandGeneral* aRandomEnergy = new RandGeneral( pdf, npti);  
                    G4BetaMinusDecayChannel *aBetaMinusChannel = new
                    G4BetaMinusDecayChannel(GetVerboseLevel(), &theParentNucleus,
                                            b, c*MeV, a*MeV, 0, FBeta, aRandomEnergy);
                    aBetaMinusChannel->SetICM(applyICM);
                    aBetaMinusChannel->SetARM(applyARM);
                    aBetaMinusChannel->SetHLThreshold(halflifethreshold);
                    theDecayTable->Insert(aBetaMinusChannel);
                    modeSumBR[1] += b;
                    delete[] pdf;
                  } // c > 0
                } // if not first record
              }
              break;
 
              case BetaPlus:
              {
                if (modeFirstRecord[2]) {
                  modeFirstRecord[2] = false;
                  modeTotalBR[2] = b;
                } else {
                  e0 = c*MeV/0.511 - 2.;
                  // Need to test e0 for nuclei which have Q < 2Me in their
                  // data files (e.g. z67.a162)
                  if (e0 > 0.) {
                    G4BetaDecayCorrections corrections(1-Z, A);
 
                    // array to store function shape
                    G4int npti = 100;               
                    G4double* pdf = new G4double[npti];
 
                    G4double e;   // Total positron energy in units of electron mass
                    G4double p;   // Positron momentum in units of electron mass
                    G4double f;   // Spectral shape function value
            for (G4int ptn = 0; ptn < npti; ptn++) {
                      // Calculate simple phase space spectrum
                      e = 1. + e0*(ptn+0.5)/100.;
                      p = std::sqrt(e*e - 1.);
                      f = p*e*(e0-e+1)*(e0-e+1);
 
                      // Apply Fermi factor to get allowed shape
                      f *= corrections.FermiFunction(e);
 
                      // Apply shape factor for forbidden transitions
                      f *= corrections.ShapeFactor(betaType, p, e0-e+1.);
                      pdf[ptn] = f;
            }
            RandGeneral* aRandomEnergy = new RandGeneral( pdf, npti);  
            G4BetaPlusDecayChannel *aBetaPlusChannel = new 
            G4BetaPlusDecayChannel(GetVerboseLevel(), &theParentNucleus,
                                           b, c*MeV, a*MeV, 0, FBeta, aRandomEnergy);
            aBetaPlusChannel->SetICM(applyICM);
            aBetaPlusChannel->SetARM(applyARM);
            aBetaPlusChannel->SetHLThreshold(halflifethreshold);
            theDecayTable->Insert(aBetaPlusChannel);
            modeSumBR[2] += b;
                    delete[] pdf;
                  } // if e0 > 0
                } // if not first record
              }
              break;
 
              case KshellEC:  // K-shell electron capture
 
                if (modeFirstRecord[3]) {
                  modeFirstRecord[3] = false;
                  modeTotalBR[3] = b;
                } else {
                  G4KshellECDecayChannel* aKECChannel =
                    new G4KshellECDecayChannel(GetVerboseLevel(),
                                               &theParentNucleus,
                                               b, c*MeV, a*MeV);
                  aKECChannel->SetICM(applyICM);
                  aKECChannel->SetARM(applyARM);
                  aKECChannel->SetHLThreshold(halflifethreshold);
                  theDecayTable->Insert(aKECChannel);
                  modeSumBR[3] += b;
                }
                break;
 
          case LshellEC:  // L-shell electron capture
 
                if (modeFirstRecord[4]) {
                  modeFirstRecord[4] = false;
                  modeTotalBR[4] = b;
                } else {
          G4LshellECDecayChannel *aLECChannel = new
            G4LshellECDecayChannel (GetVerboseLevel(), &theParentNucleus,
                        b, c*MeV, a*MeV);
          aLECChannel->SetICM(applyICM);
          aLECChannel->SetARM(applyARM);
          aLECChannel->SetHLThreshold(halflifethreshold);
          theDecayTable->Insert(aLECChannel);
          modeSumBR[4] += b;
        }
                break;
 
              case MshellEC:  // M-shell electron capture
                              // In this implementation it is added to L-shell case
                if (modeFirstRecord[5]) {
                  modeFirstRecord[5] = false;
                  modeTotalBR[5] = b;
                } else {
                  G4MshellECDecayChannel* aMECChannel =
                    new G4MshellECDecayChannel(GetVerboseLevel(),
                                               &theParentNucleus,
                                               b, c*MeV, a*MeV);
                  aMECChannel->SetICM(applyICM);
                  aMECChannel->SetARM(applyARM);
                  aMECChannel->SetHLThreshold(halflifethreshold);
                  theDecayTable->Insert(aMECChannel);
                  modeSumBR[5] += b;
                }
                break;
 
              case Alpha:
                  //G4cout<<"Alpha channel"<<a<<'\t'<<b<<'\t'<<c<<std::endl;
 
                  if (modeFirstRecord[6]) {
                  modeFirstRecord[6] = false;
                  modeTotalBR[6] = b;
                } else {
                  G4AlphaDecayChannel* anAlphaChannel =
                     new G4AlphaDecayChannel(GetVerboseLevel(),
                                             &theParentNucleus,
                                             b, c*MeV, a*MeV);
                  anAlphaChannel->SetICM(applyICM);
                  anAlphaChannel->SetARM(applyARM);
                  anAlphaChannel->SetHLThreshold(halflifethreshold);
                  theDecayTable->Insert(anAlphaChannel);
                  modeSumBR[6] += b;
                }
                break;
              case SpFission:
                  //Still needed to be implemented
                  //G4cout<<"Sp fission channel"<<a<<'\t'<<b<<'\t'<<c<<std::endl;
                  break;
              case ERROR:
 
              default:
                G4Exception("G4RadioactiveDecay::LoadDecayTable()", "HAD_RDM_000",
                            FatalException, "Selected decay mode does not exist");
            }  // switch
      }  // if char == W
        }  // if char == P 
      }  // if char != #
    }  // While
 
    // Go through the decay table and make sure that the branching ratios are
    // correctly normalised.
 
    G4VDecayChannel* theChannel = 0;
    G4NuclearDecayChannel* theNuclearDecayChannel = 0;
    G4String mode = "";
 
    G4double theBR = 0.0;
    for (G4int i = 0; i < theDecayTable->entries(); i++) {
      theChannel = theDecayTable->GetDecayChannel(i);
      theNuclearDecayChannel = static_cast<G4NuclearDecayChannel*>(theChannel);
      theDecayMode = theNuclearDecayChannel->GetDecayMode();
 
      if (theDecayMode != IT) {
    theBR = theChannel->GetBR();
    theChannel->SetBR(theBR*modeTotalBR[theDecayMode]/modeSumBR[theDecayMode]);
      }
    } 
  }   // if (DecaySchemeFile)   
  DecaySchemeFile.close();
 
        
  if (!found && E > 0.) {
    // cases where IT cascade for exited isotopes without entry in RDM database
    // Decay mode is isomeric transition.
    //
    G4ITDecayChannel *anITChannel = new G4ITDecayChannel
      (GetVerboseLevel(), (const G4Ions*) &theParentNucleus, 1);
    anITChannel->SetICM(applyICM);
    anITChannel->SetARM(applyARM);
    anITChannel->SetHLThreshold(halflifethreshold);
    theDecayTable->Insert(anITChannel);
  } 
  if (!theDecayTable) {
    //
    // There is no radioactive decay data for this nucleus.  Return a null
    // decay table.
    //
    G4cerr <<"G4RadoactiveDecay::LoadDecayTable() : cannot find ion radioactive decay file " <<G4endl;
    theDecayTable = 0;
    return theDecayTable;
  } 
  if (theDecayTable && GetVerboseLevel()>1)
    {
      G4cout <<"G4RadioactiveDecay::LoadDecayTable()" << G4endl;
      G4cout << "  No. of  entries: "<< theDecayTable->entries() <<G4endl;
      theDecayTable ->DumpInfo();
    }
 
  return theDecayTable;
}
////////////////////////////////////////////////////////////////////
//
void G4RadioactiveDecay::AddUserDecayDataFile(G4int Z, G4int A,G4String filename)
{ if (Z<1 || A<2) {
    G4cout<<"Z and A not valid!"<<G4endl;
  }
 
  std::ifstream DecaySchemeFile(filename);
  if (DecaySchemeFile){
    G4int ID_ion=A*1000+Z;
    theUserRadioactiveDataFiles[ID_ion]=filename;
    theIsotopeTable->AddUserDecayDataFile(Z,A,filename);
  }
  else {
    G4cout<<"The file "<<filename<<" does not exist!"<<G4endl;
  }
}
////////////////////////////////////////////////////////////////////////
//
 
 
void
G4RadioactiveDecay::SetDecayRate(G4int theZ, G4int theA, G4double theE, 
                                 G4int theG, std::vector<G4double> theRates, 
                                 std::vector<G4double> theTaos)
{ 
  //fill the decay rate vector 
  theDecayRate.SetZ(theZ);
  theDecayRate.SetA(theA);
  theDecayRate.SetE(theE);
  theDecayRate.SetGeneration(theG);
  theDecayRate.SetDecayRateC(theRates);
  theDecayRate.SetTaos(theTaos);
}
 
//////////////////////////////////////////////////////////////////////////
// 
void
G4RadioactiveDecay::AddDecayRateTable(const G4ParticleDefinition& theParentNucleus)
{
  // 1) To calculate all the coefficiecies required to derive the
  //    radioactivities for all progeny of theParentNucleus
  //
  // 2) Add the coefficiencies to the decay rate table vector 
  //
 
  //
  // Create and initialise variables used in the method.
  //
  theDecayRateVector.clear();
 
  G4int nGeneration = 0;
  std::vector<G4double> rates;
  std::vector<G4double> taos;
 
  // start rate is -1.
  // Eq.4.26 of the Technical Note
  rates.push_back(-1.);
  //
  //
  G4int A = ((const G4Ions*)(&theParentNucleus))->GetAtomicMass();
  G4int Z = ((const G4Ions*)(&theParentNucleus))->GetAtomicNumber();
  G4double E = ((const G4Ions*)(&theParentNucleus))->GetExcitationEnergy();
  G4double tao = theParentNucleus.GetPDGLifeTime();
  if (tao < 0.) tao = 1e-100;
  taos.push_back(tao);
  G4int nEntry = 0;
 
  //fill the decay rate with the intial isotope data
  SetDecayRate(Z,A,E,nGeneration,rates,taos);
 
  // store the decay rate in decay rate vector
  theDecayRateVector.push_back(theDecayRate);
  nEntry++;
 
  // now start treating the sencondary generations..
 
  G4bool stable = false;
  G4int i;
  G4int j;
  G4VDecayChannel* theChannel = 0;
  G4NuclearDecayChannel* theNuclearDecayChannel = 0;
  G4ITDecayChannel* theITChannel = 0;
  G4BetaMinusDecayChannel *theBetaMinusChannel = 0;
  G4BetaPlusDecayChannel *theBetaPlusChannel = 0;
  G4AlphaDecayChannel *theAlphaChannel = 0;
  G4RadioactiveDecayMode theDecayMode;
  G4double theBR = 0.0;
  G4int AP = 0;
  G4int ZP = 0;
  G4int AD = 0;
  G4int ZD = 0;
  G4double EP = 0.;
  std::vector<G4double> TP;
  std::vector<G4double> RP;
  G4ParticleDefinition *theDaughterNucleus;
  G4double daughterExcitation;
  G4ParticleDefinition *aParentNucleus;
  G4IonTable* theIonTable;
  G4DecayTable *aTempDecayTable;
  G4double theRate;
  G4double TaoPlus;
  G4int nS = 0;
  G4int nT = nEntry;
  G4double brs[7];
  //
  theIonTable =
    (G4IonTable*)(G4ParticleTable::GetParticleTable()->GetIonTable());
 
  while (!stable) {
    nGeneration++;
    for (j = nS; j< nT; j++) {
      ZP = theDecayRateVector[j].GetZ();
      AP = theDecayRateVector[j].GetA();
      EP = theDecayRateVector[j].GetE();
      RP = theDecayRateVector[j].GetDecayRateC();
      TP = theDecayRateVector[j].GetTaos();      
      if (GetVerboseLevel()>0){
    G4cout <<"G4RadioactiveDecay::AddDecayRateTable : "
           << " daughters of ("<< ZP <<", "<<AP<<", "
           << EP <<") "
           << " are being calculated. "   
           <<" generation = "
           << nGeneration << G4endl;
      }
      aParentNucleus = theIonTable->GetIon(ZP,AP,EP);
      if (!IsLoaded(*aParentNucleus)){
    aParentNucleus->SetDecayTable(LoadDecayTable(*aParentNucleus));
      }
    
      G4DecayTable* theDecayTable = new G4DecayTable();
      aTempDecayTable = aParentNucleus->GetDecayTable();
      for (i=0; i< 7; i++) brs[i] = 0.0;
 
      //
      // Go through the decay table and to combine the same decay channels
      //
      for (i=0; i<aTempDecayTable->entries(); i++) {
    theChannel             = aTempDecayTable->GetDecayChannel(i);
    theNuclearDecayChannel = static_cast<G4NuclearDecayChannel *>(theChannel);
    theDecayMode           = theNuclearDecayChannel->GetDecayMode();
    daughterExcitation = theNuclearDecayChannel->GetDaughterExcitation ();
    theDaughterNucleus = theNuclearDecayChannel->GetDaughterNucleus () ;
    AD = ((const G4Ions*)(theDaughterNucleus))->GetAtomicMass();
    ZD = ((const G4Ions*)(theDaughterNucleus))->GetAtomicNumber();  
    G4NuclearLevelManager* levelManager = 
           G4NuclearLevelStore::GetInstance()->GetManager(ZD, AD);
    if (levelManager->NumberOfLevels() ) {
      const G4NuclearLevel* level =
              levelManager->NearestLevel (daughterExcitation);
 
      if (std::abs(daughterExcitation - level->Energy()) < levelTolerance) {
        // Level half-life is in ns and the threshold is set to 1 micros by default, user can set it via the UI command
        if (level->HalfLife()*ns >= halflifethreshold ){    
          // save the metastable nucleus 
          theDecayTable->Insert(theChannel);
        } 
        else{
          brs[theDecayMode] += theChannel->GetBR();
        }
      }
      else {
        brs[theDecayMode] += theChannel->GetBR();
      }
    }
    else{
      brs[theDecayMode] += theChannel->GetBR();
    }
      }     
      brs[2] = brs[2]+brs[3]+brs[4]+brs[5];
      brs[3] = brs[4] =brs[5] =  0.0;
      for (i= 0; i<7; i++){
    if (brs[i] > 0.) {
      switch ( i ) {
      case 0:
        //
        //
        // Decay mode is isomeric transition.
        //
 
        theITChannel =  new G4ITDecayChannel
          (0, (const G4Ions*) aParentNucleus, brs[0]);
 
        theDecayTable->Insert(theITChannel);
        break;
 
      case 1:
        //
        //
        // Decay mode is beta-.
        //
        theBetaMinusChannel = new G4BetaMinusDecayChannel (0, aParentNucleus,
                                   brs[1], 0.*MeV, 0.*MeV, 1, false, 0);
        theDecayTable->Insert(theBetaMinusChannel);
 
        break;
 
      case 2:
        //
        //
        // Decay mode is beta+ + EC.
        //
        theBetaPlusChannel = new G4BetaPlusDecayChannel (GetVerboseLevel(), aParentNucleus,
                                 brs[2], 0.*MeV, 0.*MeV, 1, false, 0);
        theDecayTable->Insert(theBetaPlusChannel);
        break;            
 
      case 6:
        //
        //
        // Decay mode is alpha.
        //
        theAlphaChannel = new G4AlphaDecayChannel(GetVerboseLevel(),
                                                      aParentNucleus,
                              brs[6], 0.*MeV, 0.*MeV);
        theDecayTable->Insert(theAlphaChannel);
        break;
 
      default:
        break;
      }
    }
      }
      // 
      // loop over all branches in theDecayTable
      //
      for (i = 0; i < theDecayTable->entries(); i++){
    theChannel = theDecayTable->GetDecayChannel(i);
    theNuclearDecayChannel = static_cast<G4NuclearDecayChannel*>(theChannel);
    theBR = theChannel->GetBR();
    theDaughterNucleus = theNuclearDecayChannel->GetDaughterNucleus();
    //  first check if the decay of the original nucleus is an IT channel, if true create a new groud-level nucleus
    if (theNuclearDecayChannel->GetDecayMode() == IT && nGeneration == 1) {
      A = ((const G4Ions*)(theDaughterNucleus))->GetAtomicMass();
      Z = ((const G4Ions*)(theDaughterNucleus))->GetAtomicNumber();
      theDaughterNucleus=theIonTable->GetIon(Z,A,0.);
        }
        if (IsApplicable(*theDaughterNucleus) &&
            theBR && 
            aParentNucleus != theDaughterNucleus) { 
      // need to make sure daugher has decaytable
      if (!IsLoaded(*theDaughterNucleus)){
        theDaughterNucleus->SetDecayTable(LoadDecayTable(*theDaughterNucleus));
      }
      if (theDaughterNucleus->GetDecayTable()->entries() ) {
        //
        A = ((const G4Ions*)(theDaughterNucleus))->GetAtomicMass();
        Z = ((const G4Ions*)(theDaughterNucleus))->GetAtomicNumber();
        E = ((const G4Ions*)(theDaughterNucleus))->GetExcitationEnergy();
 
        TaoPlus = theDaughterNucleus->GetPDGLifeTime();
        //      cout << TaoPlus <<G4endl;
 
        if (TaoPlus <= 0.)  TaoPlus = 1e-100;
 
 
 
        // first set the taos, one simply need to add to the parent ones
        taos.clear();
        taos = TP;
        size_t k;
        //check that TaoPlus differs from other taos from at least 1.e5 relative difference
        //for (k = 0; k < TP.size(); k++){
        //  if (std::abs((TaoPlus-TP[k])/TP[k])<1.e-5 ) TaoPlus=1.00001*TP[k];
        //}
        taos.push_back(TaoPlus);
        // now calculate the coefficiencies
        //
        // they are in two parts, first the less than n ones
        // Eq 4.24 of the TN
        rates.clear();
        long double ta1,ta2;
        ta2 = (long double)TaoPlus;
        for (k = 0; k < RP.size(); k++){
          ta1 = (long double)TP[k];
          if (ta1 == ta2) {
        theRate = 1.e100;
          }else{
        theRate = ta1/(ta1-ta2);}
          theRate = theRate * theBR * RP[k];
          rates.push_back(theRate);
        }
        //
        // the sencond part: the n:n coefficiency
        // Eq 4.25 of the TN.  Note Yn+1 is zero apart from Y1 which is -1 as treated at line 1013
        // 
        theRate = 0.;
        long double aRate, aRate1;
        aRate1 = 0.L;
        for (k = 0; k < RP.size(); k++){
          ta1 = (long double)TP[k];
          if (ta1 == ta2 ) {
        aRate = 1.e100;
          }else {
        aRate = ta2/(ta1-ta2);}
          aRate = aRate * (long double)(theBR * RP[k]);
          aRate1 += aRate;
        }
        theRate = -aRate1;
        rates.push_back(theRate);         
        SetDecayRate (Z,A,E,nGeneration,rates,taos);
        theDecayRateVector.push_back(theDecayRate);
        nEntry++;
      }
    } // end of testing daughter nucleus
      } // end of i loop( the branches) 
      //      delete theDecayTable;
 
    } //end of for j loop
    nS = nT;
    nT = nEntry;
    if (nS == nT) stable = true;
  }
 
  //end of while loop
  // the calculation completed here
 
 
  // fill the first part of the decay rate table
  // which is the name of the original particle (isotope) 
  //
  theDecayRateTable.SetIonName(theParentNucleus.GetParticleName()); 
  //
  //
  // now fill the decay table with the newly completed decay rate vector
  //
 
  theDecayRateTable.SetItsRates(theDecayRateVector);
 
  //
  // finally add the decayratetable to the tablevector
  //
  theDecayRateTableVector.push_back(theDecayRateTable);
}
 
////////////////////////////////////////////////////////////////////////////////
//                                                                            //
//  SetSourceTimeProfile                                                      //
//     read in the source time profile function (histogram)                   //
//                                                                            //
////////////////////////////////////////////////////////////////////////////////
 
void G4RadioactiveDecay::SetSourceTimeProfile(G4String filename)
{
  std::ifstream infile ( filename, std::ios::in );
  if (!infile) {
    G4ExceptionDescription ed;
    ed << " Could not open file " << filename << G4endl; 
    G4Exception("G4RadioactiveDecay::SetSourceTimeProfile()", "HAD_RDM_001",
                FatalException, ed);
  }
 
  G4double bin, flux;
  NSourceBin = -1;
  while (infile >> bin >> flux ) {
    NSourceBin++;
    if (NSourceBin > 99) {
      G4Exception("G4RadioactiveDecay::SetSourceTimeProfile()", "HAD_RDM_002",
                  FatalException, "Input source time file too big (>100 rows)");
 
    } else {
      SBin[NSourceBin] = bin * s;
      SProfile[NSourceBin] = flux;
    }
  }
  SetAnalogueMonteCarlo(0);
  infile.close();
 
#ifdef G4VERBOSE
  if (GetVerboseLevel()>1)
    {G4cout <<" Source Timeprofile Nbin = " << NSourceBin <<G4endl;}
#endif
}
 
////////////////////////////////////////////////////////////////////////////////
//                                                                            //
//  SetDecayBiasProfile                                                       //
//    read in the decay bias scheme function (histogram)                      //
//                                                                            //
////////////////////////////////////////////////////////////////////////////////
 
void G4RadioactiveDecay::SetDecayBias(G4String filename)
{
  
  std::ifstream infile(filename, std::ios::in);
  if (!infile) G4Exception("G4RadioactiveDecay::SetDecayBias()", "HAD_RDM_003",
                           FatalException, "Unable to open bias data file" );
 
  G4double bin, flux;
  G4int dWindows = 0;
  G4int i ;
 
  theRadioactivityTables.clear();
 
  NDecayBin = -1;
  while (infile >> bin >> flux ) {
    NDecayBin++;
    if (NDecayBin > 99) {
      G4Exception("G4RadioactiveDecay::SetDecayBias()", "HAD_RDM_004",
                  FatalException, "Input bias file too big (>100 rows)" );
    } else {
      DBin[NDecayBin] = bin * s;
      DProfile[NDecayBin] = flux;
      if (flux > 0.) {
        decayWindows[NDecayBin] = dWindows;
        dWindows++;
        G4RadioactivityTable *rTable = new G4RadioactivityTable() ;
        theRadioactivityTables.push_back(rTable);
      }
    }
  }
  for ( i = 1; i<= NDecayBin; i++) DProfile[i] += DProfile[i-1];
  for ( i = 0; i<= NDecayBin; i++) DProfile[i] /= DProfile[NDecayBin];
  // converted to accumulated probabilities
 
  SetAnalogueMonteCarlo(0);
  infile.close();
 
#ifdef G4VERBOSE
  if (GetVerboseLevel()>1)
    {G4cout <<" Decay Bias Profile  Nbin = " << NDecayBin <<G4endl;}
#endif
}
 
////////////////////////////////////////////////////////////////////////////////
//                                                                            //
//  DecayIt                                                                   //
//                                                                            //
////////////////////////////////////////////////////////////////////////////////
 
G4VParticleChange*
G4RadioactiveDecay::DecayIt(const G4Track& theTrack, const G4Step&)
{
  // Initialize the G4ParticleChange object. Get the particle details and the
  // decay table.
 
  fParticleChangeForRadDecay.Initialize(theTrack);
  const G4DynamicParticle* theParticle = theTrack.GetDynamicParticle();
  G4ParticleDefinition *theParticleDef = theParticle->GetDefinition();
 
  // First check whether RDM applies to the current logical volume
  if (!isAllVolumesMode){
   if (!std::binary_search(ValidVolumes.begin(), ValidVolumes.end(),
              theTrack.GetVolume()->GetLogicalVolume()->GetName())) {
#ifdef G4VERBOSE
    if (GetVerboseLevel()>0) {
      G4cout <<"G4RadioactiveDecay::DecayIt : "
             << theTrack.GetVolume()->GetLogicalVolume()->GetName()
             << " is not selected for the RDM"<< G4endl;
      G4cout << " There are " << ValidVolumes.size() << " volumes" << G4endl;
      G4cout << " The Valid volumes are " << G4endl;
      for (size_t i = 0; i< ValidVolumes.size(); i++) G4cout << ValidVolumes[i] << G4endl;
    }
#endif
    fParticleChangeForRadDecay.SetNumberOfSecondaries(0);
 
    // Kill the parent particle.
 
    fParticleChangeForRadDecay.ProposeTrackStatus( fStopAndKill ) ;
    fParticleChangeForRadDecay.ProposeLocalEnergyDeposit(0.0);
    ClearNumberOfInteractionLengthLeft();
    return &fParticleChangeForRadDecay;
   }
  }
 
  // now check is the particle is valid for RDM
 
  if (!(IsApplicable(*theParticleDef))) { 
    //
    // The particle is not a Ion or outside the nucleuslimits for decay
    //
#ifdef G4VERBOSE
    if (GetVerboseLevel()>0) {
      G4cerr <<"G4RadioactiveDecay::DecayIt : "
         <<theParticleDef->GetParticleName() 
         << " is not a valid nucleus for the RDM"<< G4endl;
    }
#endif
    fParticleChangeForRadDecay.SetNumberOfSecondaries(0);
 
    //
    // Kill the parent particle.
    //
    fParticleChangeForRadDecay.ProposeTrackStatus( fStopAndKill ) ;
    fParticleChangeForRadDecay.ProposeLocalEnergyDeposit(0.0);
    ClearNumberOfInteractionLengthLeft();
    return &fParticleChangeForRadDecay;
  }
 
  if (!IsLoaded(*theParticleDef))
    theParticleDef->SetDecayTable(LoadDecayTable(*theParticleDef));
 
  G4DecayTable* theDecayTable = theParticleDef->GetDecayTable();
 
  if (theDecayTable == 0 || theDecayTable->entries() == 0) {
      // There are no data in the decay table.  Set the particle change parameters
      // to indicate this.
#ifdef G4VERBOSE
      if (GetVerboseLevel()>0)
    {
      G4cerr <<"G4RadioactiveDecay::DecayIt : decay table not defined  for ";
      G4cerr <<theParticleDef->GetParticleName() <<G4endl;
    }
#endif
      fParticleChangeForRadDecay.SetNumberOfSecondaries(0);
 
      // Kill the parent particle.
      fParticleChangeForRadDecay.ProposeTrackStatus( fStopAndKill ) ;
      fParticleChangeForRadDecay.ProposeLocalEnergyDeposit(0.0);
      ClearNumberOfInteractionLengthLeft();
      return &fParticleChangeForRadDecay;
 
  } else { 
    // Data found.  Try to decay nucleus
    G4double energyDeposit = 0.0;
    G4double finalGlobalTime = theTrack.GetGlobalTime();
    G4double finalLocalTime = theTrack.GetLocalTime();
    G4int index;
    G4ThreeVector currentPosition;
    currentPosition = theTrack.GetPosition();
 
    // Check whether use Analogue or VR implementation
    if (AnalogueMC) {
#ifdef G4VERBOSE
      if (GetVerboseLevel() > 0)
        G4cout <<"DecayIt:  Analogue MC version " << G4endl;
#endif
 
      G4DecayProducts* products = DoDecay(*theParticleDef);
 
      // Check if the product is the same as input and kill the track if
      // necessary to prevent infinite loop (11/05/10, F.Lei)
      if ( products->entries() == 1) {
        fParticleChangeForRadDecay.SetNumberOfSecondaries(0);
        fParticleChangeForRadDecay.ProposeTrackStatus( fStopAndKill ) ;
        fParticleChangeForRadDecay.ProposeLocalEnergyDeposit(0.0);
        ClearNumberOfInteractionLengthLeft();
        return &fParticleChangeForRadDecay;
      }
 
      // Get parent particle information and boost the decay products to the
      // laboratory frame based on this information.
      G4double ParentEnergy = theParticle->GetTotalEnergy();
      G4ThreeVector ParentDirection(theParticle->GetMomentumDirection());
 
      if (theTrack.GetTrackStatus() == fStopButAlive) {
        // The particle is decayed at rest.
        // since the time is still for rest particle in G4 we need to add the
        // additional time lapsed between the particle come to rest and the
        // actual decay.  This time is simply sampled with the mean-life of
        // the particle.  But we need to protect the case PDGTime < 0.
        // (F.Lei 11/05/10)
        G4double temptime = -std::log( G4UniformRand())
                            *theParticleDef->GetPDGLifeTime();
        if (temptime < 0.) temptime = 0.; 
        finalGlobalTime += temptime;
        finalLocalTime += temptime;
        energyDeposit += theParticle->GetKineticEnergy();
      } else {
        // The particle is decayed in flight (PostStep case).
        products->Boost( ParentEnergy, ParentDirection);
      }
 
      // Add products in theParticleChangeForRadDecay.
      G4int numberOfSecondaries = products->entries();
      fParticleChangeForRadDecay.SetNumberOfSecondaries(numberOfSecondaries);
#ifdef G4VERBOSE
      if (GetVerboseLevel()>1) {
        G4cout <<"G4RadioactiveDecay::DecayIt : Decay vertex :";
        G4cout <<" Time: " <<finalGlobalTime/ns <<"[ns]";
        G4cout <<" X:" <<(theTrack.GetPosition()).x() /cm <<"[cm]";
        G4cout <<" Y:" <<(theTrack.GetPosition()).y() /cm <<"[cm]";
        G4cout <<" Z:" <<(theTrack.GetPosition()).z() /cm <<"[cm]";
        G4cout << G4endl;
        G4cout <<"G4Decay::DecayIt  : decay products in Lab. Frame" <<G4endl;
        products->DumpInfo();
      }
#endif
      for (index=0; index < numberOfSecondaries; index++) {
        G4Track* secondary = new G4Track(products->PopProducts(),
                                         finalGlobalTime, currentPosition);
        secondary->SetGoodForTrackingFlag();
        secondary->SetTouchableHandle(theTrack.GetTouchableHandle());
        fParticleChangeForRadDecay.AddSecondary(secondary);
      }
      delete products;
      // end of analogue MC algorithm
 
    } else {
      // Variance Reduction Method
#ifdef G4VERBOSE
      if (GetVerboseLevel()>0)
        G4cout << "DecayIt: Variance Reduction version " << G4endl;
#endif
      if (!IsRateTableReady(*theParticleDef)) {
        // if the decayrates are not ready, calculate them and 
        // add to the rate table vector 
        AddDecayRateTable(*theParticleDef);
      }
      //retrieve the rates 
      GetDecayRateTable(*theParticleDef);
 
      // declare some of the variables required in the implementation
      G4ParticleDefinition* parentNucleus;
      G4IonTable* theIonTable;
      G4int PZ;
      G4int PA;
      G4double PE;
      std::vector<G4double> PT;
      std::vector<G4double> PR;
      G4double taotime;
      long double decayRate;
 
      size_t i;
      size_t j;
      G4int numberOfSecondaries;
      G4int totalNumberOfSecondaries = 0;
      G4double currentTime = 0.;
      G4int ndecaych;
      G4DynamicParticle* asecondaryparticle;
      std::vector<G4DynamicParticle*> secondaryparticles;
      std::vector<G4double> pw;
      std::vector<G4double> ptime;
      pw.clear();
      ptime.clear();
 
      //now apply the nucleus splitting
      for (G4int n = 0; n < NSplit; n++) {
        // Get the decay time following the decay probability function 
        // suppllied by user  
        G4double theDecayTime = GetDecayTime();
        G4int nbin = GetDecayTimeBin(theDecayTime);
        
        // calculate the first part of the weight function  
        G4double weight1 = 1.; 
        if (nbin == 1) {
          weight1 = 1./DProfile[nbin-1] 
                    *(DBin[nbin]-DBin[nbin-1])/NSplit;
        } else if (nbin > 1) {
          weight1 = 1./(DProfile[nbin]-DProfile[nbin-2])
                    *(DBin[nbin]-DBin[nbin-1])/NSplit;
        }
 
        // it should be calculated in seconds
        weight1 /= s ;
        
        // loop over all the possible secondaries of the nucleus
        // the first one is itself.
        for (i = 0; i < theDecayRateVector.size(); i++) {
          PZ = theDecayRateVector[i].GetZ();
          PA = theDecayRateVector[i].GetA();
          PE = theDecayRateVector[i].GetE();
          PT = theDecayRateVector[i].GetTaos();
          PR = theDecayRateVector[i].GetDecayRateC();
 
          // Calculate the decay rate of the isotope
          // decayRate is the radioactivity of isotope (PZ,PA,PE) at the 
          // time 'theDecayTime'
          // it will be used to calculate the statistical weight of the 
          // decay products of this isotope
 
          //  G4cout <<"PA= "<< PA << " PZ= " << PZ << " PE= "<< PE  <<G4endl;
          decayRate = 0.L;
          for (j = 0; j < PT.size(); j++) {
            taotime = GetTaoTime(theDecayTime,PT[j]);
            decayRate -= PR[j] * (long double)taotime;
            // Eq.4.23 of of the TN
            // note the negative here is required as the rate in the
            // equation is defined to be negative, 
            // i.e. decay away, but we need positive value here.
 
            // G4cout << j << "\t"<< PT[j]/s <<"\t"<<PR[j]<< "\t"
            //        << decayRate << G4endl;       
          }
 
          // add the isotope to the radioactivity tables
          //  G4cout <<theDecayTime/s <<"\t"<<nbin<<G4endl;
          //  G4cout << theTrack.GetWeight() <<"\t"<<weight1<<"\t"<<decayRate<< G4endl;
          theRadioactivityTables[decayWindows[nbin-1]]->AddIsotope(PZ,PA,PE,weight1*decayRate,theTrack.GetWeight());
 
          // Now calculate the statistical weight
          // One needs to fold the source bias function with the decaytime
          // also need to include the track weight! (F.Lei, 28/10/10)
          G4double weight = weight1*decayRate*theTrack.GetWeight();
 
 
 
          // decay the isotope 
          theIonTable = (G4IonTable *)(G4ParticleTable::GetParticleTable()->GetIonTable());
          parentNucleus = theIonTable->GetIon(PZ,PA,PE);
 
          // Create a temprary products buffer.
          // Its contents to be transfered to the products at the end of the loop
          G4DecayProducts* tempprods = 0;
 
          // Decide whether to apply branching ratio bias or not         
          if (BRBias) {
            G4DecayTable* decayTable = parentNucleus->GetDecayTable();
            ndecaych = G4int(decayTable->entries()*G4UniformRand());
            G4VDecayChannel* theDecayChannel = decayTable->GetDecayChannel(ndecaych);
            if (theDecayChannel == 0) {
              // Decay channel not found.
#ifdef G4VERBOSE
              if (GetVerboseLevel()>0) {
                G4cerr << " G4RadioactiveDecay::DoIt : cannot determine decay channel ";
                G4cerr << " for this nucleus; decay as if no biasing active ";
                G4cerr << G4endl;
                decayTable ->DumpInfo();
              }
#endif
              tempprods = DoDecay(*parentNucleus);  // DHW 6 Dec 2010 - do decay as if no biasing
                                                    //           to avoid deref of temppprods = 0
            } else {
              // A decay channel has been identified, so execute the DecayIt.
              G4double tempmass = parentNucleus->GetPDGMass();
              tempprods = theDecayChannel->DecayIt(tempmass);
              weight *= (theDecayChannel->GetBR())*(decayTable->entries());
            }
          } else {
            tempprods = DoDecay(*parentNucleus);
          }
 
          // save the secondaries for buffers
          numberOfSecondaries = tempprods->entries();
          currentTime = finalGlobalTime + theDecayTime;
          for (index = 0; index < numberOfSecondaries; index++) {
            asecondaryparticle = tempprods->PopProducts();
            if (asecondaryparticle->GetDefinition()->GetBaryonNumber() < 5) {
              pw.push_back(weight);
              ptime.push_back(currentTime);
              secondaryparticles.push_back(asecondaryparticle);
            }
          }
          delete tempprods;
 
        } // end of i loop
      } // end of n loop 
 
      // now deal with the secondaries in the two stl containers
      // and submmit them back to the tracking manager
      totalNumberOfSecondaries = pw.size();
      fParticleChangeForRadDecay.SetNumberOfSecondaries(totalNumberOfSecondaries);
      for (index=0; index < totalNumberOfSecondaries; index++) { 
        G4Track* secondary = new G4Track(secondaryparticles[index],
                                         ptime[index], currentPosition);
        secondary->SetGoodForTrackingFlag();       
        secondary->SetTouchableHandle(theTrack.GetTouchableHandle());
        secondary->SetWeight(pw[index]);       
        fParticleChangeForRadDecay.AddSecondary(secondary); 
      }
      // make sure the original track is set to stop and its kinematic energy collected
      // 
      //theTrack.SetTrackStatus(fStopButAlive);
      //energyDeposit += theParticle->GetKineticEnergy();
 
    } // End of Variance Reduction 
 
    // Kill the parent particle
    fParticleChangeForRadDecay.ProposeTrackStatus(fStopAndKill) ;
    fParticleChangeForRadDecay.ProposeLocalEnergyDeposit(energyDeposit); 
    fParticleChangeForRadDecay.ProposeLocalTime(finalLocalTime);
    // Reset NumberOfInteractionLengthLeft.
    ClearNumberOfInteractionLengthLeft();
 
    return &fParticleChangeForRadDecay ;
  }
} 
 
 
G4DecayProducts*
G4RadioactiveDecay::DoDecay(G4ParticleDefinition& theParticleDef)
{
  G4DecayProducts* products = 0;
 
  // follow the decaytable and generate the secondaries...
#ifdef G4VERBOSE
  if (GetVerboseLevel()>0) G4cout<<"Begin of DoDecay..."<<G4endl;
#endif
 
  G4DecayTable* theDecayTable = theParticleDef.GetDecayTable();
 
  // Choose a decay channel.
#ifdef G4VERBOSE
  if (GetVerboseLevel()>0) G4cout <<"Selecte a channel..."<<G4endl;
#endif
 
  G4VDecayChannel* theDecayChannel = theDecayTable->SelectADecayChannel();
  if (theDecayChannel == 0) {
    // Decay channel not found.
    G4cerr <<"G4RadioactiveDecay::DoIt : can not determine decay channel";
    G4cerr <<G4endl;
    theDecayTable ->DumpInfo();
  } else {
    // A decay channel has been identified, so execute the DecayIt.
#ifdef G4VERBOSE
    if (GetVerboseLevel()>1) {
      G4cerr <<"G4RadioactiveDecay::DoIt : selected decay channel  addr:";
      G4cerr <<theDecayChannel <<G4endl;
    }
#endif
    G4double tempmass = theParticleDef.GetPDGMass();
    products = theDecayChannel->DecayIt(tempmass);
    // Apply directional bias if requested by user
    CollimateDecay(products);
  }
 
  return products;
}
 
 
// Apply directional bias for "visible" daughters (e+-, gamma, n, alpha)
 
void G4RadioactiveDecay::CollimateDecay(G4DecayProducts* products) {
  if (origin == forceDecayDirection) return;    // No collimation requested
  if (180.*deg == forceDecayHalfAngle) return;
  if (0 == products || 0 == products->entries()) return;
 
#ifdef G4VERBOSE
  if (GetVerboseLevel()>0) G4cout<<"Begin of CollimateDecay..."<<G4endl;
#endif
 
  // Particles suitable for directional biasing (for if-blocks below)
  static const G4ParticleDefinition* electron = G4Electron::Definition();
  static const G4ParticleDefinition* positron = G4Positron::Definition();
  static const G4ParticleDefinition* neutron  = G4Neutron::Definition();
  static const G4ParticleDefinition* gamma    = G4Gamma::Definition();
  static const G4ParticleDefinition* alpha    = G4Alpha::Definition();
 
  G4ThreeVector newDirection;       // Re-use to avoid memory churn
  for (G4int i=0; i<products->entries(); i++) {
    G4DynamicParticle* daughter = (*products)[i];
    const G4ParticleDefinition* daughterType = daughter->GetParticleDefinition();
 
    if (daughterType == electron || daughterType == positron ||
    daughterType == neutron || daughterType == gamma ||
    daughterType == alpha) CollimateDecayProduct(daughter);
  }
}
 
void G4RadioactiveDecay::CollimateDecayProduct(G4DynamicParticle* daughter) {
#ifdef G4VERBOSE
  if (GetVerboseLevel() > 1) {
    G4cout << "CollimateDecayProduct for daughter "
       << daughter->GetParticleDefinition()->GetParticleName() << G4endl;
  }
#endif
 
  G4ThreeVector collimate = ChooseCollimationDirection();
  if (origin != collimate) daughter->SetMomentumDirection(collimate);
}
 
 
// Choose random direction within collimation cone
 
G4ThreeVector G4RadioactiveDecay::ChooseCollimationDirection() const {
  if (origin == forceDecayDirection) return origin; // Don't do collimation
  if (forceDecayHalfAngle == 180.*deg) return origin;
 
  G4ThreeVector dir = forceDecayDirection;
 
  // Return direction offset by random throw
  if (forceDecayHalfAngle > 0.) {
    // Generate uniform direction around central axis
    G4double phi = 2.*pi*G4UniformRand();
    G4double cosMin = std::cos(forceDecayHalfAngle);
    G4double cosTheta = (1.-cosMin)*G4UniformRand() + cosMin;   // [cosMin,1.)
    
    dir.setPhi(dir.phi()+phi);
    dir.setTheta(dir.theta()+std::acos(cosTheta));
  }
 
#ifdef G4VERBOSE
  if (GetVerboseLevel()>1)
    G4cout << " ChooseCollimationDirection returns " << dir << G4endl;
#endif
 
  return dir;
}