---

ReactorDetector.cpp

Go to the documentation of this file.

#include <math.h>
#include <iostream.h>
#include <string.h>
#include "ReactorEvent.hh"
#include "ReactorFortran.hh"
#include "ReactorConstants.hh"
#include "DetectorDefaults.hh"
#include "ReactorXC.hh"
#include "ReactorDetector.hh"
#include "ReactorScint.hh"
#include "MyTlSource.hh"
#include "MyBiSource.hh"
//
// constructor
//
ReactorDetector::ReactorDetector(){
  //
  // initialize PMT arrays
  //
  Xpmt = new double[0];
  Ypmt = new double[0];
  Zpmt = new double[0];
  PMTOutputArray = new PMToutput*[0];
  PMTdata = new PMT[0];
  PMTelectron = new PMT[0];
  PMTpositron = new PMT[0];
  PMTneutron = new PMT[0];
  PMTthallium = new PMT[0];
  PMTbismuth = new PMT[0];
  PMTcalifornium = new PMT[0];
  PMTmuon = new PMT[0];
  //
  // Set parameters
  //
  SetNominalParameters();
  SetPMT();
  SetNeutronPropStuff();
  //
  // initialize gamma arrays
  //
  Ngamma = 0;
  Rgamma = new double[Ngamma];
  Egamma = new double[Ngamma];
  Tgamma = new double[Ngamma];
  Ogamma = new std::string[Ngamma];
  //
  // initialize PMT charge spectrum
  //
  float Qlo = 0.001;
  float Qhi = 10.0;
  funlxp_(QSpectrum,Qspace,Qlo,Qhi);

  Nneutron = 0;
  Absorber = new double[Nneutron];
  NeutronSteps = new double[Nneutron];

  pmtRadCount = 0;
  MergeTime = 0;
}
//
// destructor
//
ReactorDetector::~ReactorDetector(){
  delete[] Xpmt;
  delete[] Ypmt;
  delete[] Zpmt;
  delete[] PMTOutputArray;
  delete[] PMTdata;
  delete[] PMTelectron;
  delete[] PMTpositron;
  delete[] PMTneutron;
  delete[] PMTthallium;
  delete[] PMTbismuth;
  delete[] PMTcalifornium;
  delete[] PMTmuon;
  delete[] Rgamma;
  delete[] Egamma;
  delete[] Tgamma;
  delete[] Ogamma;
  delete[] Absorber;
  delete[] NeutronSteps;
}
//
// copy constructor
//
ReactorDetector::ReactorDetector(const ReactorDetector& Detector){

  R0=Detector.R0;
  R1=Detector.R1;
  R2=Detector.R2;
  GdConcentration=Detector.GdConcentration;
  refracGd=Detector.refracGd;
  refracSc=Detector.refracSc;
  mfpGd=Detector.mfpGd;
  mfpSc=Detector.mfpSc;
  MeanNeuDispl = Detector.MeanNeuDispl;
  FastNeutronOption = Detector.FastNeutronOption;
  PMTDebugOption = Detector.PMTDebugOption;
  MergeTime = Detector.MergeTime;
  Temperature = Detector.Temperature;
  tGd=Detector.tGd;
  tSc=Detector.tSc;
  GdCaptureFraction=Detector.GdCaptureFraction;
  GammasPerGd=Detector.GammasPerGd;
  attenlGd=Detector.attenlGd;
  attenlSc=Detector.attenlSc;
  PhotonsPerMeV=Detector.PhotonsPerMeV;
  PMTcoverage=Detector.PMTcoverage;
  PMTdiameter=Detector.PMTdiameter;
  PMTqe=Detector.PMTqe;
  ScintDecayTime=Detector.ScintDecayTime;
  for(int i=0;i<4;i++){
    a[i] = Detector.a[i];
    z[i] = Detector.z[i];
    nn[i] = Detector.nn[i];
  }

  Npmt = Detector.Npmt;
  Ncosbins = Detector.Ncosbins;
  Nphibins = Detector.Nphibins;

  Xpmt = new double[Npmt];
  Ypmt = new double[Npmt];
  Zpmt = new double[Npmt];
  PMTOutputArray = new PMToutput*[Npmt];

  double* pold = Detector.Xpmt+Npmt;
  double* pnew = Xpmt+Npmt;
  while(pnew>Ypmt)*--pnew=*--pold;

  pold = Detector.Ypmt+Npmt;
  pnew = Ypmt+Npmt;
  while(pnew>Ypmt)*--pnew=*--pold;

  pold = Detector.Zpmt+Npmt;
  pnew = Zpmt+Npmt;
  while(pnew>Zpmt)*--pnew=*--pold;

  PHelectron = Detector.PHelectron;
  PHpositron = Detector.PHpositron;
  PHneutron = Detector.PHneutron;
  PHthallium = Detector.PHthallium;
  PHbismuth = Detector.PHbismuth;
  PHcalifornium = Detector.PHcalifornium;
  PHmuon = Detector.PHmuon;

  PHeleReco = Detector.PHeleReco;
  PHposReco = Detector.PHposReco;
  PHneuReco = Detector.PHneuReco;
  PHthaReco = Detector.PHthaReco;
  PHbisReco = Detector.PHbisReco;
  PHcalReco = Detector.PHcalReco;
  PHmuoReco = Detector.PHmuoReco;

  TimePositron = Detector.TimePositron;
  TimeNeutron = Detector.TimeNeutron;

  for(int i=0;i<3;i++){
    DipolePositron[i] = Detector.DipolePositron[i];
    DipoleNeutron[i] = Detector.DipoleNeutron[i];
  }

  HitPmtsPos = Detector.HitPmtsPos;
  HitPmtsNeu = Detector.HitPmtsNeu;
  HitPmtsTha = Detector.HitPmtsTha;
  HitPmtsBis = Detector.HitPmtsBis;
  HitPmtsCal = Detector.HitPmtsCal;
  HitPmtsMuo = Detector.HitPmtsMuo;
  HitPmtsEle = Detector.HitPmtsEle;

  for(int i=0;i<7;i++){
    MeanNpe[i]=Detector.MeanNpe[i];
    MeanAtten[i] = Detector.MeanAtten[i];
    MeanSfactor[i] = Detector.MeanSfactor[i];
  }

  Nneutron = Detector.Nneutron;
  Absorber = new double[Nneutron];
  pold = Detector.Absorber+Nneutron;
  pnew = Absorber+Nneutron;
  while(pnew>Absorber)*--pnew=*--pold;

  NeutronSteps = new double[Nneutron];
  pold = Detector.NeutronSteps+Nneutron;
  pnew = NeutronSteps+Nneutron;
  while(pnew>NeutronSteps)*--pnew=*--pold;

  Ngamma = Detector.Ngamma;
  Rgamma = new double[Ngamma];
  pold = Detector.Rgamma+3*Ngamma;
  pnew = Rgamma+3*Ngamma;
  while(pnew>Rgamma)*--pnew=*--pold;

  Egamma = new double[Ngamma];
  pold = Detector.Egamma+Ngamma;
  pnew = Egamma+Ngamma;
  while(pnew>Egamma)*--pnew=*--pold;

  Tgamma = new double[Ngamma];
  pold = Detector.Tgamma+Ngamma;
  pnew = Tgamma+Ngamma;
  while(pnew>Tgamma)*--pnew=*--pold;

  Ogamma = new std::string[Ngamma];
  std::string* rold = Detector.Ogamma+Ngamma;
  std::string* rnew = Ogamma+Ngamma;
  while(rnew>Ogamma)*--rnew=*--rold;

  PMTsize = Detector.PMTsize;
  PMTlen = Detector.PMTlen;
  PMTdata = new PMT[PMTsize];
  PMT* qold = Detector.PMTdata+PMTsize;
  PMT* qnew = PMTdata+PMTsize;
  while(qnew>PMTdata)*--qnew=*--qold;

  PMTelectron = new PMT[Npmt];
  qold = Detector.PMTelectron+Npmt;
  qnew = PMTelectron+Npmt;
  while(qnew>PMTelectron)*--qnew=*--qold;

  PMTpositron = new PMT[Npmt];
  qold = Detector.PMTpositron+Npmt;
  qnew = PMTpositron+Npmt;
  while(qnew>PMTpositron)*--qnew=*--qold;

  PMTneutron = new PMT[Npmt];
  qold = Detector.PMTneutron+Npmt;
  qnew = PMTneutron+Npmt;
  while(qnew>PMTneutron)*--qnew=*--qold;

  PMTthallium = new PMT[Npmt];
  qold = Detector.PMTthallium+Npmt;
  qnew = PMTthallium+Npmt;
  while(qnew>PMTthallium)*--qnew=*--qold;

  PMTbismuth = new PMT[Npmt];
  qold = Detector.PMTbismuth+Npmt;
  qnew = PMTbismuth+Npmt;
  while(qnew>PMTbismuth)*--qnew=*--qold;

  PMTcalifornium = new PMT[Npmt];
  qold = Detector.PMTcalifornium+Npmt;
  qnew = PMTcalifornium+Npmt;
  while(qnew>PMTcalifornium)*--qnew=*--qold;

  PMTmuon = new PMT[Npmt];
  qold = Detector.PMTmuon+Npmt;
  qnew = PMTmuon+Npmt;
  while(qnew>PMTmuon)*--qnew=*--qold;
}    
//
// = operator
//
ReactorDetector& ReactorDetector::operator=(const ReactorDetector& rhs){

  if(this == &rhs)return *this;

  R0=rhs.R0;
  R1=rhs.R1;
  R2=rhs.R2;
  GdConcentration=rhs.GdConcentration;
  refracGd=rhs.refracGd;
  refracSc=rhs.refracSc;
  mfpGd=rhs.mfpGd;
  mfpSc=rhs.mfpSc;
  MeanNeuDispl = rhs.MeanNeuDispl;
  FastNeutronOption = rhs.FastNeutronOption;
  PMTDebugOption = rhs.PMTDebugOption;
  MergeTime = rhs.MergeTime;
  Temperature = rhs.Temperature;
  tGd=rhs.tGd;
  tSc=rhs.tSc;
  GdCaptureFraction=rhs.GdCaptureFraction;
  GammasPerGd=rhs.GammasPerGd;
  attenlGd=rhs.attenlGd;
  attenlSc=rhs.attenlSc;
  PhotonsPerMeV=rhs.PhotonsPerMeV;
  PMTcoverage=rhs.PMTcoverage;
  PMTdiameter=rhs.PMTdiameter;
  PMTqe=rhs.PMTqe;
  ScintDecayTime=rhs.ScintDecayTime;
  for(int i=0;i<4;i++){
    a[i] = rhs.a[i];
    z[i] = rhs.z[i];
    nn[i] = rhs.nn[i];
  }

  Npmt = rhs.Npmt;
  Ncosbins = rhs.Ncosbins;
  Nphibins = rhs.Nphibins;

  delete[] Xpmt;
  delete[] Ypmt;
  delete[] Zpmt;
  delete[] PMTOutputArray;

  Xpmt = new double[Npmt];
  Ypmt = new double[Npmt];  
  Zpmt = new double[Npmt];
  PMTOutputArray = new PMToutput*[Npmt];

  double* pold = rhs.Xpmt+Npmt;
  double* pnew = Xpmt+Npmt;
  while(pnew>Ypmt)*--pnew=*--pold;

  pold = rhs.Ypmt+Npmt;
  pnew = Ypmt+Npmt;
  while(pnew>Ypmt)*--pnew=*--pold;

  pold = rhs.Zpmt+Npmt;
  pnew = Zpmt+Npmt;
  while(pnew>Zpmt)*--pnew=*--pold;

  PHelectron = rhs.PHelectron;
  PHpositron = rhs.PHpositron;
  PHneutron = rhs.PHneutron;
  PHthallium = rhs.PHthallium;
  PHbismuth = rhs.PHbismuth;
  PHcalifornium = rhs.PHcalifornium;
  PHmuon = rhs.PHmuon;

  PHeleReco = rhs.PHeleReco;
  PHposReco = rhs.PHposReco;
  PHneuReco = rhs.PHneuReco;
  PHthaReco = rhs.PHthaReco;
  PHbisReco = rhs.PHbisReco;
  PHcalReco = rhs.PHcalReco;
  PHmuoReco = rhs.PHmuoReco;

  TimePositron = rhs.TimePositron;
  TimeNeutron = rhs.TimeNeutron;

  for(int i=0;i<3;i++){
    DipolePositron[i] = rhs.DipolePositron[i];
    DipoleNeutron[i] = rhs.DipoleNeutron[i];
  }

  HitPmtsPos = rhs.HitPmtsPos;
  HitPmtsNeu = rhs.HitPmtsNeu;
  HitPmtsTha = rhs.HitPmtsTha;
  HitPmtsBis = rhs.HitPmtsBis;
  HitPmtsCal = rhs.HitPmtsCal;
  HitPmtsMuo = rhs.HitPmtsMuo;
  HitPmtsEle = rhs.HitPmtsEle;  

  for (int i=0;i<7;i++){
    MeanNpe[i] = rhs.MeanNpe[i];
    MeanAtten[i] = rhs.MeanAtten[i];
    MeanSfactor[i] = rhs.MeanSfactor[i];
  }

  Nneutron = rhs.Nneutron;

  delete[] Absorber;
  Absorber = new double[Nneutron];
  pold = rhs.Absorber+Nneutron;
  pnew = Absorber+Nneutron;
  while(pnew>Absorber)*--pnew=*--pold;

  delete[] NeutronSteps;
  NeutronSteps = new double[Nneutron];
  pold = rhs.NeutronSteps+Nneutron;
  pnew = NeutronSteps+Nneutron;
  while(pnew>NeutronSteps)*--pnew=*--pold;

  Ngamma = rhs.Ngamma;

  delete[] Rgamma;
  Rgamma = new double[Ngamma];
  pold = rhs.Rgamma+3*Ngamma;
  pnew = Rgamma+3*Ngamma;
  while(pnew>Rgamma)*--pnew=*--pold;

  delete[] Egamma;
  Egamma = new double[Ngamma];
  pold = rhs.Egamma+Ngamma;
  pnew = Egamma+Ngamma;
  while(pnew>Egamma)*--pnew=*--pold;

  delete[] Tgamma;
  Tgamma = new double[Ngamma];
  pold = rhs.Tgamma+Ngamma;
  pnew = Tgamma+Ngamma;
  while(pnew>Tgamma)*--pnew=*--pold;

  delete[] Ogamma;
  Ogamma = new std::string[Ngamma];
  std::string* rold = rhs.Ogamma+Ngamma;
  std::string* rnew = Ogamma+Ngamma;
  while(rnew>Ogamma)*--rnew=*--rold;

  PMTsize = rhs.PMTsize;
  PMTlen = rhs.PMTlen;
  delete[] PMTdata;
  PMTdata = new PMT[PMTsize];
  PMT* qold = rhs.PMTdata+PMTsize;
  PMT* qnew = PMTdata+PMTsize;
  while(qnew>PMTdata)*--qnew=*--qold;

  delete[] PMTelectron;
  PMTelectron = new PMT[Npmt];
  qold = rhs.PMTelectron+Npmt;
  qnew = PMTelectron+Npmt;
  while(qnew>PMTelectron)*--qnew=*--qold;

  delete[] PMTpositron;
  PMTpositron = new PMT[Npmt];
  qold = rhs.PMTpositron+Npmt;
  qnew = PMTpositron+Npmt;
  while(qnew>PMTpositron)*--qnew=*--qold;

  delete[] PMTneutron;
  PMTneutron = new PMT[Npmt];
  qold = rhs.PMTneutron+Npmt;
  qnew = PMTneutron+Npmt;
  while(qnew>PMTneutron)*--qnew=*--qold;

  delete[] PMTthallium;
  PMTthallium = new PMT[Npmt];
  qold = rhs.PMTthallium+Npmt;
  qnew = PMTthallium+Npmt;
  while(qnew>PMTthallium)*--qnew=*--qold;

  delete[] PMTbismuth;
  PMTbismuth = new PMT[Npmt];
  qold = rhs.PMTbismuth+Npmt;
  qnew = PMTbismuth+Npmt;
  while(qnew>PMTbismuth)*--qnew=*--qold;

  delete[] PMTcalifornium;
  PMTcalifornium = new PMT[Npmt];
  qold = rhs.PMTcalifornium+Npmt;
  qnew = PMTcalifornium+Npmt;
  while(qnew>PMTcalifornium)*--qnew=*--qold;

  delete[] PMTmuon;
  PMTmuon = new PMT[Npmt];
  qold = rhs.PMTmuon+Npmt;
  qnew = PMTmuon+Npmt;
  while(qnew>PMTmuon)*--qnew=*--qold;

  return *this;

}
//
// PMT sub-class  constructors,destructor,operator
//    
ReactorDetector::PMT::PMT(){
  npmt=0;
  for (int i=0;i<3;i++)xyz[i]=0; 
  TimeGen=0;
  TimeSmr=0;
  PHgen=0;
  PHsmr=0;
  PathGd=0;
  PathSc=0;
  Sfactor=0;
  Atten=0;
  Npe=0;
  Xpe=0;
  Q=0.;
  Parent="U";

  SubHits=0;
  SubHitsPtr = new PMT*[0];
}
  
ReactorDetector::PMT::~PMT(){
  delete[] SubHitsPtr;
}

ReactorDetector::PMT::PMT(const ReactorDetector::PMT& p){
  
  npmt=p.npmt; 
  for (int i=0;i<3;i++)xyz[i]=p.xyz[i]; 
  TimeGen=p.TimeGen;
  TimeSmr=p.TimeSmr;
  PHgen=p.PHgen;
  PHsmr=p.PHsmr;
  PathGd=p.PathGd;
  PathSc=p.PathSc;
  Sfactor=p.Sfactor;
  Atten=p.Atten;
  Npe=p.Npe;
  Xpe=p.Xpe;
  Q=p.Q;
  Parent=p.Parent;
  //
  SubHits=p.SubHits;
  SubHitsPtr = new PMT*[SubHits];
  PMT** pold = p.SubHitsPtr+SubHits;
  PMT** pnew = SubHitsPtr+SubHits;
  while(pnew>SubHitsPtr)*--pnew=*--pold;
}
//
// PMT sub-class equal operator
//    
ReactorDetector::PMT& 
ReactorDetector::PMT::operator=(const ReactorDetector::PMT& rhs){

  if(this == &rhs)return *this;

  npmt=rhs.npmt;
  for (int i=0;i<3;i++)xyz[i]=rhs.xyz[i]; 
  TimeGen=rhs.TimeGen;
  TimeSmr=rhs.TimeSmr;
  PHgen=rhs.PHgen;
  PHsmr=rhs.PHsmr;
  PathGd=rhs.PathGd;
  PathSc=rhs.PathSc;
  Sfactor=rhs.Sfactor;
  Atten=rhs.Atten;
  Npe=rhs.Npe;
  Xpe=rhs.Xpe;
  Q=rhs.Q;
  Parent=rhs.Parent;
  //
  SubHits=rhs.SubHits;
  delete[] SubHitsPtr;
  SubHitsPtr = new PMT*[SubHits];
  PMT** pold = rhs.SubHitsPtr+SubHits;
  PMT** pnew = SubHitsPtr+SubHits;
  while(pnew>SubHitsPtr)*--pnew=*--pold;

  return *this;
}
ReactorDetector::PMT 
ReactorDetector::PMT::operator+(const ReactorDetector::PMT& rhs){

  PMT sum(*this);
  if(npmt!=rhs.npmt)return sum;
  sum.npmt = npmt;

  double w1=Xpe/(Xpe+rhs.Xpe);
  double w2=1-w1;

  for (int i=0;i<3;i++)sum.xyz[i]=w1*xyz[i]+w2*rhs.xyz[i]; 
  sum.TimeGen=w1*TimeGen+w2*rhs.TimeGen;
  sum.TimeSmr=w1*TimeSmr+w2*rhs.TimeSmr;
  sum.PHgen=w1*PHgen+w2*rhs.PHgen;
  sum.PHsmr=w1*PHsmr+w2*rhs.PHsmr;
  sum.PathGd=w1*PathGd+w2*rhs.PathGd;
  sum.PathSc=w1*PathSc+w2*rhs.PathSc;
  sum.Sfactor=w1*Sfactor+w1*rhs.Sfactor;
  sum.Atten=w1*Atten+w2*rhs.Atten;
  sum.Npe=Npe+rhs.Npe;
  sum.Xpe=Xpe+rhs.Xpe;
  if(Parent==rhs.Parent)sum.Parent=rhs.Parent;
  else sum.Parent="U";

  sum.SubHits = SubHits+rhs.SubHits;
  delete[] sum.SubHitsPtr;
  sum.SubHitsPtr = new PMT*[sum.SubHits];
  PMT** p = sum.SubHitsPtr+sum.SubHits;
  PMT** q = SubHitsPtr+SubHits;
  PMT** r = rhs.SubHitsPtr+rhs.SubHits;
  while(p>sum.SubHitsPtr+SubHits)*--p=*--r;
  while(p>sum.SubHitsPtr)*--p=*--q;

  return sum;
}
ReactorDetector::PMT& 
ReactorDetector::PMT::operator+=(const ReactorDetector::PMT& rhs){

  if(npmt!=rhs.npmt)return *this;

  double w1=Xpe/(Xpe+rhs.Xpe);
  double w2=1-w1;

  for (int i=0;i<3;i++)xyz[i]=w1*xyz[i]+w2*rhs.xyz[i]; 
  TimeGen=w1*TimeGen+w2*rhs.TimeGen;
  TimeSmr=w1*TimeSmr+w2*rhs.TimeSmr;
  PHgen=w1*PHgen+w2*rhs.PHgen;
  PHsmr=w1*PHsmr+w2*rhs.PHsmr;
  PathGd=w1*PathGd+w2*rhs.PathGd;
  PathSc=w1*PathSc+w2*rhs.PathSc;
  Sfactor=w1*Sfactor+w1*rhs.Sfactor;
  Atten=w1*Atten+w2*rhs.Atten;
  Npe+=rhs.Npe;
  Xpe+=rhs.Xpe;
  Q+=rhs.Q;
  if(Parent!=rhs.Parent)Parent="U";
  //
  PMT** SubHitsTmp = new PMT*[SubHits];
  PMT** p = SubHitsTmp+SubHits;
  PMT** q = SubHitsPtr+SubHits;
  while(p>SubHitsTmp)*--p=*--q;
  delete[] SubHitsPtr;
  SubHitsPtr = new PMT*[SubHits+rhs.SubHits];
  p = SubHitsPtr+SubHits+rhs.SubHits;
  q = SubHitsTmp+SubHits;
  PMT** r = rhs.SubHitsPtr+rhs.SubHits;
  while(p>SubHitsPtr+SubHits)*--p=*--r;
  while(p>SubHitsPtr)*--p=*--q;
  SubHits += rhs.SubHits;
  delete[] SubHitsTmp;
  //
  return *this;
}
void ReactorDetector::PMT::SetSubHitsPtr(int subhits){
  delete[] SubHitsPtr;
  SubHits = subhits;
  SubHitsPtr = new PMT*[subhits];
  return;
}


//
// Detector simulation function
//
void ReactorDetector::LightsOut(ReactorEvent& Event, int eventnum){

  PMTlen=0;
  delete[] PMTdata;
  PMTdata = new PMT[PMTsize];
  CleanPMTOutputArray();
  //  
  // Detector simulation routines.
  //
  GenerateSecondaries(Event);
  GenerateGammas(Event);
  GenerateResponse(Event);

  ConsolidatePMT();
  if(PMTDebugOption){
    if(eventnum == 0){
      ofstream file ( "testdump.txt");
      if(!file.is_open()){
        cout << "File failure, testdump.txt may include old data" << endl;
      }
      else{
        file << "Event \tPMTid \tTime \tEnergy" << endl;
        file.close();
      }
    }
    PMTOutputArray[10]->testdump(eventnum);
    PMTOutputArray[50]->testdump(eventnum);
    PMTOutputArray[100]->testdump(eventnum);
    }
  /* Reconstruction code.
     Position and energy reconstruction only done for positron
     and neutron.  Other particle types have ideal position
     information from GenerateSecondaries and a simple energy
     reconstruction using ideal position information and some
     effects such as PMT smearing and attenuation done in
     GenerateResponse.
  */
  CalculateQPosition("P");
  CalculateQPosition("N");

  ImproveQPosition("P");
  ImproveQPosition("N");

  CalculateEnergy("P");
  CalculateEnergy("N");

}
//
// Access to PMT data
//
void ReactorDetector::GetPMTdata(int npmt,double* XYZpmt,
                                 int& nele,double* PHele,double* Tele,
                                 int& npos,double* PHpos,double* Tpos,
                                 int& nneu,double* PHneu,double* Tneu,
                                 int& ntha,double* PHtha,double* Ttha,
                                 int& nbis,double* PHbis,double* Tbis,
                                 int& ncal,double* PHcal,double* Tcal,
                                 int& nmuo,double* PHmuo,double* Tmuo,
                                 int* npepos, int* npeneu, int* npetha,
                                 int* npebis, int* npecal, int* npemuo,
                                 int* npeele){
  
  *(XYZpmt+0) = *(Xpmt+npmt);
  *(XYZpmt+1) = *(Ypmt+npmt);
  *(XYZpmt+2) = *(Zpmt+npmt);

  nele=0;
  npos=0;
  nneu=0;
  ntha=0;
  nbis=0;
  ncal=0;
  nmuo=0;

  for(PMT* PMTptr=PMTdata;PMTptr<PMTdata+PMTlen;PMTptr++){
    if(npmt==(*PMTptr).npmt){
      if((*PMTptr).Parent=="E"){
        *(PHele+nele) = (*PMTptr).PHsmr;
        *(Tele+nele) = (*PMTptr).TimeSmr;
        *(npeele+nele) = (*PMTptr).Npe;
        nele++;
      }
      if((*PMTptr).Parent=="P"){
        *(PHpos+npos) = (*PMTptr).PHsmr;
        *(Tpos+npos) = (*PMTptr).TimeSmr;
        *(npepos+npos) = (*PMTptr).Npe;
        npos++;
      }
      if((*PMTptr).Parent=="N"){
        *(PHneu+nneu) = (*PMTptr).PHsmr;
        *(Tneu+nneu) = (*PMTptr).TimeSmr;
        *(npeneu+nneu) = (*PMTptr).Npe;
        nneu++;
      }
      if((*PMTptr).Parent=="Tl"){
        *(PHtha+ntha) = (*PMTptr).PHsmr;
        *(Ttha+ntha) = (*PMTptr).TimeSmr;
        *(npetha+ntha) = (*PMTptr).Npe;
        ntha++;
      }
      if((*PMTptr).Parent=="Bi"){
        *(PHbis+nbis) = (*PMTptr).PHsmr;
        *(Tbis+nbis) = (*PMTptr).TimeSmr;
        *(npebis+nbis) = (*PMTptr).Npe;
        nbis++;
      }
      if((*PMTptr).Parent=="Cf"){
        *(PHcal+ncal) = (*PMTptr).PHsmr;
        *(Tcal+ncal) = (*PMTptr).TimeSmr;
        *(npecal+ncal) = (*PMTptr).Npe;
        ncal++;
      }
      if((*PMTptr).Parent=="muon"){
        *(PHmuo+nmuo) = (*PMTptr).PHsmr;
        *(Tmuo+nmuo) = (*PMTptr).TimeSmr;
        *(npemuo+nmuo) = (*PMTptr).Npe;
        nmuo++;
      }
    } 
  }
  return;
}
// Return information about a PMT for a given secondary
void ReactorDetector::GetPMTdata(std::string parent,int pmtindex,
                                 double* XYZpmt, int* hits,
                                 double* PH, double* Q, double* Time,
                                 int* npe){

  *(XYZpmt+0) = *(Xpmt+pmtindex);
  *(XYZpmt+1) = *(Ypmt+pmtindex);
  *(XYZpmt+2) = *(Zpmt+pmtindex);


  for(PMT* PMTptr=PMTdata;PMTptr<PMTdata+PMTlen;PMTptr++){
    if(pmtindex==(*PMTptr).npmt){
      if((*PMTptr).Parent==parent){
        *PH += (*PMTptr).PHsmr;
        *Time += (*PMTptr).TimeSmr;
        *npe += (*PMTptr).Npe;
       *Q += (*PMTptr).Q;
        ++*hits;
      }
    }
  }
  return;
}

int ReactorDetector::GetHitPMTsPos(){
  return HitPmtsPos;
}
int ReactorDetector::GetHitPMTsNeu(){
  return HitPmtsNeu;
}
int ReactorDetector::GetHitPMTsTha(){
  return HitPmtsTha;
}
int ReactorDetector::GetHitPMTsBis(){
  return HitPmtsBis;
}
int ReactorDetector::GetHitPMTsCal(){
  return HitPmtsCal;
}
int ReactorDetector::GetHitPMTsMuo(){
  return HitPmtsMuo;
}
int ReactorDetector::GetHitPMTsEle(){
  return HitPmtsEle;
}
void ReactorDetector::GenerateSecondaries(ReactorEvent& Event){

  //cout << "GenerateSecondaries(Event)" << endl;
  //
  // Displace the positron vertex by its range along the positron direction.
  //
  int Npositron = Event.GetNumPositron();
  //cout << Npositron << " positron(s):" << endl;

  double* Rpos = new double[Event.Rdim*Npositron];

  // loop over the positrons
  for(int n=0;n<Npositron;n++){

    double kepos = Event.GetPositronKE(n);
    double tpos = 0.;
    double rangepos = 0.;
    PositronRange(kepos,rangepos,tpos);
    tpos+=Event.GetPositronTime(n);
    //
    double cospos = Event.GetPositronCosTheta(n);
    double phipos = Event.GetPositronPhi(n);

    double rint[3];
    for(int i=0;i<3;i++){
      rint[i] = *(Event.GetPositronVertexXYZ()+(i+n*Event.Rdim));
    }
    //
    double rpos[3];
    rpos[0]=rint[0]+rangepos*sqrt(1-cospos*cospos)*cos(phipos);
    rpos[1]=rint[1]+rangepos*sqrt(1-cospos*cospos)*sin(phipos);
    rpos[2]=rint[2]+rangepos*cospos;
    double rrpos = sqrt(rpos[0]*rpos[0]+rpos[1]*rpos[1]+rpos[2]*rpos[2]);
    //
    // set positron vertex in Event class
    //
    Rpos[0+n*Event.Rdim] = tpos;
    for(int i=1;i<4;i++)Rpos[i+n*Event.Rdim]=rpos[i-1];
    Rpos[4+n*Event.Rdim] = rrpos;
    Rpos[5+n*Event.Rdim] = rpos[2]/rrpos;
    Rpos[6+n*Event.Rdim] = atan2(rpos[1],rpos[0]);
    if(Rpos[6+n*Event.Rdim]<0)Rpos[6+n*Event.Rdim]+=2*PI;
    Event.SetPositronVertex(n,Rpos);
  }
  //  for(int n=0;n<Event.Rdim*Npositron;n++){
  //    cout << " Rpos[" << n << "] " << Rpos[n] << endl;
  //  }
  // done with positrons

  int Nneutron = Event.GetNumNeutron();
  //cout << Nneutron << " neutron(s):" << endl;

  delete[] Absorber;
  delete[] NeutronSteps;

  Absorber = new double[Nneutron];
  NeutronSteps = new double[Nneutron];

  double* Rneu = new double[Event.Rdim*Nneutron];

  // loop over the neutrons
  for(int n=0;n<Nneutron;n++){
    //
    double rneu[3];
    double tneu = 0.;
    if(FastNeutronOption){
      //
      // Throw the neutron vertex via a simple Gaussian
      //
      float rn[3];
      int len=3;
      rnormx_(rn,len,ranlux_);
      //
      // Random for throwing neutron time
      //
      len=1;
      float rv[1];
      ranlux_(rv,len);
      //
      //  Simple scheme that is not right at boundaries
      //  Neglects discontinuity in mean free path;
      //  Time will be taken as proportional to sqrt(path)
      //
      double rint[3];
      for(int i=0;i<3;i++){
        rint[i] = *(Event.GetNeutronVertexXYZ()+(i+n*Event.Rdim));
      }
      //
      double rrint = sqrt(rint[0]*rint[0]+rint[1]*rint[1]+rint[2]*rint[2]);
      double path = 0.;
      if(rrint<=R0){
        for (int i=0;i<3;i++)rneu[i]=rint[i]+mfpGd*rn[i]/sqrt(3.);
        path = mfpGd*sqrt(rn[0]*rn[0]+rn[1]*rn[1]+rn[2]*rn[2]);
        tneu = tGd*sqrt(path/mfpGd)*log(1/rv[0]);
      }
      else if(rrint<R2){
        for (int i=0;i<3;i++)rneu[i]=rint[i]+mfpSc*rn[i]/sqrt(3.);
        path = mfpSc*sqrt(rn[0]*rn[0]+rn[1]*rn[1]+rn[2]*rn[2]);
        tneu = tSc*sqrt(path/mfpSc)*log(1/rv[0]);
      }
      else{
        for (int i=0;i<3;i++)rneu[i]=999999;
        tneu = 999999.;
      }
      //
      // Shift z displacement by mean Chooz value
      //
      rneu[2]+=MeanNeuDispl;
    }
    else{
      double pneu[3];
      for(int i=0;i<3;i++){
        pneu[i]=*(Event.GetNeutronPxyz()+(i+n*Event.Pdim));
        //cout << "pneu[" << i << "] " << pneu[i] << endl;
      }
      for(int i=0;i<3;i++){
        rneu[i]=*(Event.GetNeutronVertexXYZ()+(i+n*Event.Rdim));
        //cout << "rneu[" << i << "] " << rneu[i] << endl;
      }
      double keneu = Event.GetNeutronKE(n);
      NeutronSteps[n]=0.;
      Absorber[n]=0.;
      NeutronPropagator(R0,R2,keneu,Absorber[n],NeutronSteps[n],
                        pneu,rneu,tneu,Temperature,a,z,nn);
      //cout << " Absorber[" << n << "] " << Absorber[n] << endl;
      //cout << " NeutronSteps[" << n << "] " << NeutronSteps[n] << endl;
      tneu+=Event.GetNeutronTime(n);
      //cout << " tneu " << tneu << endl;
    }
    //
    // set neutron vertex in Event class
    //
    Rneu[0+n*Event.Rdim] = tneu;
    for(int i=1;i<4;i++)Rneu[i+n*Event.Rdim]=rneu[i-1];
    double rrneu = sqrt(rneu[0]*rneu[0]+rneu[1]*rneu[1]+rneu[2]*rneu[2]);
    Rneu[4+n*Event.Rdim] = rrneu;
    Rneu[5+n*Event.Rdim] = rneu[2]/rrneu;
    Rneu[6+n*Event.Rdim] = atan2(rneu[1],rneu[0]);
    if(Rneu[6+n*Event.Rdim]<0)Rneu[6+n*Event.Rdim]+=2*PI;
    Event.SetNeutronVertex(n,Rneu);
  }
  //  for(int n=0;n<Event.Rdim*Nneutron;n++){
  //    cout << " Rneu[" << n << "] " << Rneu[n] << endl;
  //  }
  // done with neutrons
  delete[] Rpos;
  delete[] Rneu;
}

void ReactorDetector::GenerateResponse(ReactorEvent& Event){

  //cout << "GenerateResponse(Event)" << endl;
  //
  PHelectron = 0;
  PHpositron = 0;
  PHneutron = 0;
  PHthallium = 0;
  PHbismuth = 0;
  PHcalifornium = 0;
  PHmuon = 0;

  PHeleReco = 0;
  PHposReco = 0;
  PHneuReco = 0;
  PHthaReco = 0;
  PHbisReco = 0;
  PHcalReco = 0;
  PHmuoReco = 0;

  HitPmtsPos = 0;
  HitPmtsNeu = 0;
  HitPmtsTha = 0;
  HitPmtsBis = 0;
  HitPmtsCal = 0;
  HitPmtsMuo = 0;
  HitPmtsEle = 0;

  for(int i=0;i<7;i++){
    MeanSfactor[i] = 0;
    MeanAtten[i] = 0;
    MeanNpe[i] = 0;
    MeanQ[i] = 0;
  }
  //
  //
  //
  int pmtindex=0;
  double* xpmt=Xpmt;
  double* ypmt=Ypmt;
  double* zpmt=Zpmt;
  
  PMT* PMTptr = PMTdata;

  //cout << Ngamma << " gammas" << endl;
  for(int i=0;i<Ncosbins;i++){
    for(int j=0;j<Nphibins;j++){
      double rpmt[3];
      rpmt[0] = *xpmt++;
      rpmt[1] = *ypmt++;
      rpmt[2] = *zpmt++;
      //for (int l=0;l<3;l++) cout << "  rpmt[" << l << "] " << rpmt[l] << endl;
      double r[3];
      double dr[3];
      double tr[3];
      //      
      double sumele[7]={0,0,0,0,0,0,0};
      double sumpos[7]={0,0,0,0,0,0,0};
      double sumneu[7]={0,0,0,0,0,0,0};
      double sumtha[7]={0,0,0,0,0,0,0};
      double sumbis[7]={0,0,0,0,0,0,0};
      double sumcal[7]={0,0,0,0,0,0,0};
      double summuo[7]={0,0,0,0,0,0,0};
      //
      double* rgptr=Rgamma;
      double* egptr=Egamma;
      double* tgptr=Tgamma;
      std::string* ogptr=Ogamma;
      //
      int nelegt0=0;
      int nposgt0=0;
      int nneugt0=0;
      int nthagt0=0;
      int nbisgt0=0;
      int ncalgt0=0;
      int nmuogt0=0;
      //
      for(int k=0;k<Ngamma;k++){
        //
        for (int l=0;l<3;l++)r[l]=*rgptr++;
        double rdotr = r[0]*r[0]+r[1]*r[1]+r[2]*r[2];
        //cout << i << " " << j << " " << k << "  r " << sqrt(rdotr) << endl;
        //
        // nothing to do if r>R1: cycle through useless info
        //
        if(sqrt(rdotr)>R1){
          double dummy = *egptr++;
          dummy = *tgptr++;
          std::string sdummy = *ogptr++;
          continue;
        }
        //
        for (int l=0;l<3;l++)dr[l]=rpmt[l]-r[l];
        double ddr = sqrt(dr[0]*dr[0]+dr[1]*dr[1]+dr[2]*dr[2]);
        //cout << "  ddr " << ddr;
        for (int l=0;l<3;l++)tr[l]=dr[l]/ddr;
        double tdotr = r[0]*tr[0]+r[1]*tr[1]+r[2]*tr[2];
        //cout << "  tdotr " << tdotr;
        //
        // solve for intersection with inner radius
        //
        double sGd;
        double sSc;
        //
        // check for no intersections
        //
        double test = R0*R0+tdotr*tdotr-rdotr;
        bool inter = (test>=0);
        //
        // A straight line from the interaction vertex to the pmt
        // goes through the inner radius at least once.  In this case,
        // the light will see Gd-scint. and unloaded scint.
        //
        //cout << "  " << inter << endl;
        if(inter){
          double sint1 = -tdotr+sqrt(test);
          double sint2 = -tdotr-sqrt(test);
          if(sint1>0&&sint2<0){     // 1 intersection at soln 1
            sGd = sint1;
          }
          else if(sint2>0&&sint1<0){     // 1 intersection at soln 2
            sGd = sint2;
          }
          else if(sint2>0&&sint1>0){     // 2 intersections 
            sGd = sint1-sint2;
            if(sGd<0)sGd*=-1;
          }
          else{                          // no intersections towards PMT
            sGd = 0;
          }
          sSc = ddr-sGd;
        }
        //
        //  otherwise the light only goes through unloaded scintillator
        //
        else{
          sGd = 0;
          sSc = ddr;
        }
        //cout << "       sGd " << sGd << " sSc " << sSc << endl;
        //
        //  increment PH-- make atten. relative to center
        //
        double dsGd = sGd-R0;
        double dsSc = sSc-R2+R0;
        double atten0 = exp(-sGd/attenlGd-sSc/attenlSc);     
        double atten = exp(-dsGd/attenlGd-dsSc/attenlSc);     
        //
        // solid angle factor
        //
        double sfactor=0;
        for (int l=0;l<3;l++){sfactor+=tr[l]*rpmt[l]/R2;}
        sfactor *= R2*R2/ddr/ddr;
        //
        // photostatistics
        //
        double phgen = *egptr++;
        //cout << "phgen " << phgen << endl;
        //
        //
        // Now throw number of photons as gaussian
        // around mean of phgen*PhotonsPerMeV
        //
        int len = 1;
        float photons[1];
        rnormx_(photons,len,ranlux_);
        photons[0]*=sqrt(phgen*PhotonsPerMeV);
        float xpe = (phgen*PhotonsPerMeV) + (double) photons[0];
        xpe *= (atten0*sfactor);
        xpe *= (PMTcoverage/Npmt*PMTqe);
        //
        int npe;
        int error;
        rnpssn_(xpe,npe,error);
        //cout << "npe " << npe << endl;
        //
        float Q = 0.;
        Q = GenerateQ(npe);
        double phsmr = Q/PMTqe/PMTcoverage/PhotonsPerMeV;   
        //cout << "phsmr " << phsmr << endl;
        //        
        double tgen = *tgptr++;
        //cout << "tgen " << tgen << endl;
        double tsmr = refracGd*sGd/c+refracSc*sSc/c + tgen; 
        //cout << "tsmr " << tsmr << endl;
        //
        std::string type = *ogptr++;
        //cout << "type " << type << endl;
        if(type == "E"){
          nelegt0++;
          sumele[0]+=phsmr;
          sumele[1]+=phgen;
          sumele[2]+=phgen*atten0*sfactor;
          sumele[3]+=npe;
          sumele[4]+=sfactor;
          sumele[5]+=atten;
          sumele[6]+=Q;
          //
          PHelectron+=phsmr;
        }
        else if(type == "P"){
          nposgt0++;
          sumpos[0]+=phsmr;
          sumpos[1]+=phgen;
          sumpos[2]+=phgen*atten0*sfactor;
          sumpos[3]+=npe;
          sumpos[4]+=sfactor;
          sumpos[5]+=atten;
          sumpos[6]+=Q;
          //
          PHpositron+=phsmr;
        }
        else if(type == "N"){
          nneugt0++;
          sumneu[0]+=phsmr;
          sumneu[1]+=phgen;
          sumneu[2]+=phgen*atten0*sfactor;
          sumneu[3]+=npe;
          sumneu[4]+=sfactor;
          sumneu[5]+=atten;
          sumneu[6]+=Q;
          //      
          PHneutron+=phsmr;
        }
        else if(type == "Tl"){
          nthagt0++;
          sumtha[0]+=phsmr;
          sumtha[1]+=phgen;
          sumtha[2]+=phgen*atten0*sfactor;
          sumtha[3]+=npe;
          sumtha[4]+=sfactor;
          sumtha[5]+=atten;
          sumtha[6]+=Q;
          //      
          PHthallium+=phsmr;
        }
        else if(type == "Bi"){
          nbisgt0++;
          sumbis[0]+=phsmr;
          sumbis[1]+=phgen;
          sumbis[2]+=phgen*atten0*sfactor;
          sumbis[3]+=npe;
          sumbis[4]+=sfactor;
          sumbis[5]+=atten;
          sumbis[6]+=Q;
          //      
          PHbismuth+=phsmr;
        }
        else if(type == "Cf"){
          ncalgt0++;
          sumcal[0]+=phsmr;
          sumcal[1]+=phgen;
          sumcal[2]+=phgen*atten0*sfactor;
          sumcal[3]+=npe;
          sumcal[4]+=sfactor;
          sumcal[5]+=atten;
          sumcal[6]+=Q;
          //      
          PHcalifornium+=phsmr;
        }
        else if(type == "muon"){
          nmuogt0++;
          summuo[0]+=phsmr;
          summuo[1]+=phgen;
          summuo[2]+=phgen*atten0*sfactor;
          summuo[3]+=npe;
          summuo[4]+=sfactor;
          summuo[5]+=atten;
          summuo[6]+=Q;
          //      
          PHmuon+=phsmr;
        }
        else{
          cout << "  ERROR: GenerateResponse has unrecognized type " 
               << type << endl;
        }
        //        
        PMT PMTtmp;
        PMTtmp.npmt = pmtindex;
        for(int l=0;l<3;l++)PMTtmp.xyz[l] = rpmt[l];
        PMTtmp.PHgen = phgen;
        PMTtmp.PHsmr = phsmr;
        PMTtmp.PathGd = sGd;
        PMTtmp.PathSc = sSc;
        PMTtmp.Atten = atten;
        PMTtmp.Sfactor = sfactor;
        PMTtmp.TimeGen = tgen;
        PMTtmp.TimeSmr = tsmr;
        PMTtmp.Xpe = xpe;
        PMTtmp.Npe = npe;
        PMTtmp.Q = Q;
        PMTtmp.Parent = type;
        
        if(PMTptr<PMTdata+PMTsize){
          *PMTptr++=PMTtmp;
          PMTlen++;
        }
        else{
          //
          // expand the data array first
          //
          PMTptr = ResizePMT();
          *PMTptr++=PMTtmp;
          PMTlen++;
        }
      }
      //cout << "PHpositron " << PHpositron << endl;
      //cout << "PHneutron  " << PHneutron << endl;
      //
      //  Crude estimate of reconstructed PH
      //  Includes poisson npe smearing and fluctuation in atten length
      //
      /*  PHposReco, PHneuReco, etc., are recalculated in CalculateEnergy 
          in order to use reconstructed position for energy 
          reconstruction.  These calculcations are done with ideal
          knowledge of position.
      */
      if(sumpos[2]>0){
        PHposReco+=sumpos[0]*sumpos[1]/sumpos[2];
        MeanNpe[0]+=sumpos[3]/Npmt;
        MeanQ[0]+=sumpos[6]/Npmt;
        MeanSfactor[0]+=sumpos[4]/Npmt/nposgt0;
        MeanAtten[0]+=sumpos[5]/Npmt/nposgt0;
      }
      if(sumneu[2]>0){
        PHneuReco+=sumneu[0]*sumneu[1]/sumneu[2];
        MeanNpe[1]+=sumneu[3]/Npmt;
        MeanQ[1]+=sumneu[6]/Npmt;
        MeanSfactor[1]+=sumneu[4]/Npmt/nneugt0;
        MeanAtten[1]+=sumneu[5]/Npmt/nneugt0;
      }
      if(sumtha[2]>0){
        PHthaReco+=sumtha[0]*sumtha[1]/sumtha[2];
        MeanNpe[2]+=sumtha[3]/Npmt;
        MeanQ[2]+=sumtha[6]/Npmt;
        MeanSfactor[2]+=sumtha[4]/Npmt/nthagt0;
        MeanAtten[2]+=sumtha[5]/Npmt/nthagt0;
      }
      if(sumbis[2]>0){
        PHbisReco+=sumbis[0]*sumbis[1]/sumbis[2];
        MeanNpe[3]+=sumbis[3]/Npmt;
        MeanQ[3]+=sumbis[6]/Npmt;
        MeanSfactor[3]+=sumbis[4]/Npmt/nbisgt0;
        MeanAtten[3]+=sumbis[5]/Npmt/nbisgt0;
      }
      if(sumcal[2]>0){
        PHcalReco+=sumcal[0]*sumcal[1]/sumcal[2];
        MeanNpe[4]+=sumcal[3]/Npmt;
        MeanQ[4]+=sumcal[6]/Npmt;
        MeanSfactor[4]+=sumcal[4]/Npmt/ncalgt0;
        MeanAtten[4]+=sumcal[5]/Npmt/ncalgt0;
      }
      if(summuo[2]>0){
        PHmuoReco+=summuo[0]*summuo[1]/summuo[2];
        MeanNpe[5]+=summuo[3]/Npmt;
        MeanQ[5]+=summuo[6]/Npmt;
        MeanSfactor[5]+=summuo[4]/Npmt/nmuogt0;
        MeanAtten[5]+=summuo[5]/Npmt/nmuogt0;
      }
      if(sumele[2]>0){
        PHeleReco+=sumele[0]*sumele[1]/sumele[2];
        MeanNpe[6]+=sumele[3]/Npmt;
        MeanQ[6]+=sumele[6]/Npmt;
        MeanSfactor[6]+=sumele[4]/Npmt/nelegt0;
        MeanAtten[6]+=sumele[5]/Npmt/nelegt0;
      }
      if(sumpos[6]>0){
        HitPmtsPos++;
      }
      if(sumneu[6]>0){
        HitPmtsNeu++;
      }
      if(sumtha[6]>0){
        HitPmtsTha++;
      }
      if(sumbis[6]>0){
        HitPmtsBis++;
      }
      if(sumcal[6]>0){
        HitPmtsCal++;
      }
      if(summuo[6]>0){
        HitPmtsMuo++;
      }
      if(sumele[6]>0){
        HitPmtsEle++;
      }
      //
      // increment PMT index
      //
      pmtindex++;
    }
  }
}

void ReactorDetector::GenerateGammas(ReactorEvent& Event){

  //cout << "GenerateGammas(Event)" << endl;
  //
  // first check for any gammas produced in the event itself
  int ngamma = Event.GetNumGamma();
  //cout << " " << ngamma << " gammas from the Event" << endl;
  //
  int maxgamma = 100+ngamma;
  double* egamma = new double[maxgamma];
  double* tgamma = new double[maxgamma];
  double* rgamma = new double[3*maxgamma];
  std::string* ogamma = new std::string[maxgamma];
  //
  double* egptr=egamma;
  double* rgptr=rgamma;
  double* tgptr=tgamma;
  std::string* ogptr=ogamma;
  //
  // event gammas
  //
  for(int n=0;n<ngamma;n++){

    *egptr++ = Event.GetGammaKE(n);
    //
    for(int i=0;i<3;i++) 
      *rgptr++ = *(Event.GetGammaVertexXYZ()+(i+n*Event.Rdim));
    //
    *tgptr++ = Event.GetGammaTime(n);
    //
    if(Event.GetGammaParentProcess(n) == 1){
      cout << "ERROR: gammas are not produced by inverse-beta decay" << endl;
    }
    else if(Event.GetGammaParentProcess(n) == 2){
      *ogptr++ = "Cf";
    }
    else if(Event.GetGammaParentProcess(n) == 3){
      *ogptr++ = "muon";
    }
    else if(Event.GetGammaParentProcess(n) == 4){
      *ogptr++ = "muon";
    }
    else{
      cout << "Process Id " << Event.GetGammaParentProcess(n) << " is unknown" 
           << endl;
    }
  }
  //
  // radioactive source gammas
  //
  if(Event.GetPmtRad() == "on"){

    // pick a PMT location for the decay
    const int len = 2;
    float r[len];
    ranlux_(r,len);
    int pmtId = int(r[0]*Npmt);

    // pick decay material and isotope 
    std::string Stuff;
    int Isotope;

    // this assumes even fractions of decays from all isotopes
    //
    if(r[1] < 0.25){
      Stuff = "thallium"; Isotope = 208; // thallium 208
    }
    else if(0.25 <= r[1] && r[1] < 0.5){
      Stuff = "thallium"; Isotope = 210; // thallium 210
    }
    else if(0.5 <= r[1] && r[1] < 0.75){
      Stuff = "bismuth"; Isotope = 212; // bismuth 212
    }
    else{
      Stuff = "bismuth"; Isotope = 214; // bismuth 214
    }
    //cout << Stuff << "(" << Isotope << ")" << endl;
    //
    // Thallium
    //
    if(Stuff == "thallium"){
      MyTlSource Thallium(Isotope);

      //cout << " " << Thallium.GetNumTlGammas() << " gammas" << endl;

      // loop over the decay gammas
      for(int n=0;n<Thallium.GetNumTlGammas();n++){

        // pick a direction for each gamma
        const int len=2;
        float rv[len];
        ranlux_(rv,len);
        double cosg = -1+2*rv[0];
        double phig = 2*PI*rv[1];
        double t[3];
        t[0] = cos(phig)*sqrt(1-cosg*cosg);
        t[1] = sin(phig)*sqrt(1-cosg*cosg);
        t[2] = cosg;
        //for(int i=0;i<3;i++) cout << "t["<<i<<"] " << t[i] << " ";
        //cout << endl;

        // get the energy, time, r and p for each Tl gamma
        double eg = Thallium.GetTlGammaEnergy(n); 
        double tg = 0.;
        //cout << " energy " << eg << " time " << tg << endl;
        //
        double rg[3];
        double* rgp = rg;
        rg[0] = Xpmt[pmtId];
        rg[1] = Ypmt[pmtId];
        rg[2] = Zpmt[pmtId];
        //for(int i=0;i<3;i++) cout << " rg["<<i<<"] " << rg[i] << " ";
        //cout << endl;
        //
        // move the "PMT" in 30 cm (for R5912 8" PMTs) from the outer vessel
        //
        rgp = TranslateRadialDistance(Xpmt[pmtId],Ypmt[pmtId],
                                      Zpmt[pmtId],-30.);
        for(int i=0;i<3;i++) rg[i] = *rgp++;
        //for(int i=0;i<3;i++) cout << " rg["<<i<<"] " << rg[i] << " ";
        //cout << endl;
        //
        double pg[3];
        for(int i=0;i<3;i++) pg[i] = eg*t[i];
        //for(int i=0;i<3;i++) cout << " pg["<<i<<"] " << pg[i] << " ";
        //cout << endl;
        //
        // compton scatter the gammas through the oil
        //
        ReactorScint Scint(eg,tg,rg,pg,R0,R1,R2);
        //
        int scatters = Scint.GetPoints();
        for(int s=0;s<scatters;s++){
          *egptr++=Scint.GetNextEnergy();
          *tgptr++=Scint.GetNextTime();
          for(int j=0;j<3;j++) *rgptr++=*(Scint.GetNextXYZ()+s);
          *ogptr++ = "Tl";
          ngamma++;
        }
      }
      bool inscint = false;
      double rdotr = 0.;
      for(int n=0;n<ngamma;n++){
        rdotr = rgamma[3*n]*rgamma[3*n] +
          rgamma[3*n+1]*rgamma[3*n+1] + 
          rgamma[3*n+2]*rgamma[3*n+2];
        if(sqrt(rdotr)<R1) inscint = true;
      }
      if(inscint){
        pmtRadCount++;
        cout << "PMTrad Tl " << pmtRadCount << " radius " << sqrt(rdotr) 
             << endl;
      }
    }
    //
    // Bismuth
    //
    else if(Stuff == "bismuth"){
      MyBiSource Bismuth(Isotope);

      //cout << " " << Bismuth.GetNumBiGammas() << " gammas" << endl;

      // loop over the decay gammas
      for(int n=0;n<Bismuth.GetNumBiGammas();n++){

        // pick a direction for each gamma
        const int len=2;
        float rv[len];
        ranlux_(rv,len);
        double cosg = -1+2*rv[0];
        double phig = 2*PI*rv[1];
        double t[3];
        t[0] = cos(phig)*sqrt(1-cosg*cosg);
        t[1] = sin(phig)*sqrt(1-cosg*cosg);
        t[2] = cosg;
        //for(int i=0;i<3;i++) cout << "t["<<i<<"] " << t[i] << " ";
        //cout << endl;

        // get the energy, time, r and p for each Bi gamma
        double eg = Bismuth.GetBiGammaEnergy(n); 
        double tg = 0.;
        //cout << " energy " << eg << " time " << tg << endl;
        //
        double rg[3];
        double* rgp = rg;
        rg[0] = Xpmt[pmtId];
        rg[1] = Ypmt[pmtId];
        rg[2] = Zpmt[pmtId];
        //for(int i=0;i<3;i++) cout << " rg["<<i<<"] " << rg[i] << " ";
        //cout << endl;
        //
        // move the "PMT" in 30 cm (for R5912 8" PMTs) from the outer vessel
        //
        rgp = TranslateRadialDistance(Xpmt[pmtId],Ypmt[pmtId],
                                     Zpmt[pmtId],-30.);
        for(int i=0;i<3;i++) rg[i] = *rgp++;
        //for(int i=0;i<3;i++) cout << " rg["<<i<<"] " << rg[i] << " ";
        //cout << endl;
        //
        double pg[3];
        for(int i=0;i<3;i++) pg[i] = eg*t[i];
        //for(int i=0;i<3;i++) cout << " pg["<<i<<"] " << pg[i] << " ";
        //cout << endl;
        //
        // compton scatter the gammas through the oil
        //
        ReactorScint Scint(eg,tg,rg,pg,R0,R1,R2);
        //
        int scatters = Scint.GetPoints();
        for(int s=0;s<scatters;s++){
          *egptr++=Scint.GetNextEnergy();
          *tgptr++=Scint.GetNextTime();
          for(int j=0;j<3;j++) *rgptr++=*(Scint.GetNextXYZ()+s);
          *ogptr++ = "Bi";
          ngamma++;
        }
      }
      bool inscint = false;
      double rdotr = 0.;
      for(int n=0;n<ngamma;n++){
        rdotr = rgamma[3*n]*rgamma[3*n] + 
          rgamma[3*n+1]*rgamma[3*n+1] + 
          rgamma[3*n+2]*rgamma[3*n+2];
        if(sqrt(rdotr)<R1) inscint = true;
      }
      if(inscint){
        pmtRadCount++;
        cout << "PMTrad Bi " << pmtRadCount << " radius " << sqrt(rdotr) 
             << endl;
      }
    } 
  }
  //
  // electron gammas, needs improvement
  //
  int Nelectron = Event.GetNumElectron();
  //cout << Nelectron << " electron(s):" << endl;

  // loop over the electrons
  for(int n=0;n<Nelectron;n++){

    double rele[3];
    for(int i=0;i<3;i++){
      rele[i] = *(Event.GetElectronVertexXYZ()+(i+n*Event.Rdim));
      //cout << " rele[" << i << "] " << rele[i] << endl;
    }
    double tele = Event.GetElectronTime(n);
    //cout << " tele " << tele << endl;
    double keele = Event.GetElectronKE(n);
    //cout << " keele " << keele << endl;
    //
    // generate a "fake" gamma with E=electron KE generated at vertex.
    //
    for(int i=0;i<3;i++)*rgptr++=rele[i];
    *tgptr++ = tele;
    *egptr++ = keele;
    *ogptr++ = "E";
    ngamma++;
  } // done with electrons
  //cout << "  " << ngamma << " gammas, so far" << endl;
  //
  // positron gammas
  //
  int Npositron = Event.GetNumPositron();
  //cout << Npositron << " positron(s):" << endl;

  // loop over the positrons
  for(int n=0;n<Npositron;n++){

    double rpos[3];
    for(int i=0;i<3;i++){
      rpos[i] = *(Event.GetPositronVertexXYZ()+(i+n*Event.Rdim));
      //cout << " rpos[" << i << "] " << rpos[i] << endl;
    }
    double ppos[3];
    for(int i=0;i<3;i++){
      ppos[i] = *(Event.GetPositronPxyz()+(i+n*Event.Pdim));
      //cout << " ppos[" << i << "] " << ppos[i] << endl;
    }
    double tpos = Event.GetPositronTime(n);
    //cout << " tpos " << tpos << endl;
    double kepos = Event.GetPositronKE(n);
    //cout << " kepos " << kepos << endl;
    //
    // the first is a "fake" gamma with E=positron KE generated at positron
    // vertex.
    //
    for(int i=0;i<3;i++)*rgptr++=rpos[i];
    *tgptr++ = tpos;
    *egptr++ = kepos;
    *ogptr++ = "P";
    ngamma++;
    //
    // Now the two annihilation gammas
    //
    int len=4;
    float rv[4];
    ranlux_(rv,len);
    double cosg = -1+2*rv[0];
    double phig = 2*PI*rv[1];
    double t[3];
    t[0] = cos(phig)*sqrt(1-cosg*cosg);
    t[1] = sin(phig)*sqrt(1-cosg*cosg);
    t[2] = cosg;
    for (int i=0;i<2;i++){
      //
      // handle multiple compton scatters
      //
      ReactorScint Scint(MELECTRON,tpos,rpos,ppos,R0,R1,R2);
      //
      int scatters = Scint.GetPoints();
      for(int s=0;s<scatters;s++){
        *egptr++=Scint.GetNextEnergy();
        *tgptr++=Scint.GetNextTime();
        for(int j=0;j<3;j++) *rgptr++=*(Scint.GetNextXYZ()+s);
        *ogptr++ = "P";
        ngamma++;
      }
    }
  } // done with positrons
  //cout << "  " << ngamma << " gammas, so far" << endl;
  //
  // Generate neutron gammas
  //
  Nneutron = Event.GetNumNeutron();
  //cout << Nneutron << " neutron(s):" << endl;

  // loop over the neutrons
  for(int n=0;n<Nneutron;n++){

    double rneu[3];
    for(int i=0;i<3;i++){
      rneu[i] = *(Event.GetNeutronVertexXYZ()+(i+n*Event.Rdim));
      //cout << " rneu[" << i << "] " << rneu[i] << endl;
    }
    double tneu = Event.GetNeutronTime(n);
    //cout << " tneu " << tneu << endl;
    //
    // pick H or Gd, then which Gd peak
    //
    double emax=Hpeak;
    if(FastNeutronOption){
      //cout << "in FastNeutronOption" << endl;
      Absorber[n]=1;
      double rrneu = sqrt(rneu[0]*rneu[0]+rneu[1]*rneu[1]+rneu[2]*rneu[2]);
      if(rrneu<R0){//in Gd region
        int len=2;
        float rv[2];
        ranlux_(rv,len);
        if(rv[0]<=GdCaptureFraction){
          //
          // model Gd spectrum by Gd155 + Gd157
          //
          if(rv[1]<=Gd155frac){
            emax = Gd155peak;
            Absorber[n]=155;
          }
          else{
            emax = Gd157peak;
            Absorber[n]=157;
          }
        }
      }
    }
    else{
      //cout << "Absorber[" << n << "] " << Absorber[n] << endl;
      if(Absorber[n]==1)emax=Hpeak;
      if(Absorber[n]==12)emax=Cpeak;
      if(Absorber[n]==155)emax=Gd155peak;
      if(Absorber[n]==157)emax=Gd157peak;
    }
    //
    // One photon from an H or C capture
    //
    if(emax==Hpeak || emax==Cpeak){
      //cout << " H or C gammas" << endl;
      int len=3;
      float rv[3];
      ranlux_(rv,len);
      std::string material = "scintillator";
      double range = GammaComptonRange(material,emax);
      range*=log(1/rv[0]);
      double cosg = -1+2*rv[1];
      double phig = 2*PI*rv[2];
      double t[3];
      t[0] = cos(phig)*sqrt(1-cosg*cosg);
      t[1] = sin(phig)*sqrt(1-cosg*cosg);
      t[2] = cosg;
      for(int j=0;j<3;j++)*rgptr++ = rneu[j]+range*t[j];
      *egptr++ = emax;
      *tgptr++ = tneu+range/c*refracSc;
      *ogptr++ = "N";
      ngamma++;
      //cout << "  " << ngamma << " gammas" << endl;
    }
    //
    // otherwise model Gd photons
    //
    else{
      //cout << " Gd gammas" << endl;
      int ngd=0;
      double* pgd = new double[3*maxgamma];
      MyGdDecayModel(emax,ngd,pgd);
      float* rv2 = new float[ngd];
      ranlux_(rv2,ngd);
      double* qgd=pgd;
      double check[4]={0,0,0,0};
      for(int i=0;i<ngd;i++){
        double p[3];
        for(int j=0;j<3;j++)p[j]=*qgd++;
        double e = sqrt(p[0]*p[0]+p[1]*p[1]+p[2]*p[2]);
        std::string material = "scintillator";
        double range = GammaComptonRange(material,e);
        range*=log(1/rv2[i]);
        for(int j=0;j<3;j++)*rgptr++ = rneu[j]+range*p[j]/e;
        //
        for(int j=0;j<3;j++)check[j]+=p[j];
        check[3]+=e;
        //
        *egptr++ = e;
        *tgptr++ = tneu+range/c*refracGd;
        *ogptr++ = "N";
        ngamma++;
        //cout << "  " << ngamma << " gammas" << endl;
      }
        delete[] pgd;
        delete[] rv2;
    }
  } // done with neutrons
  //cout << "  " << ngamma << " gammas, total" << endl;
  //
  // Transfer temp data to storage
  //
  delete[] Rgamma;
  delete[] Egamma;
  delete[] Tgamma;
  delete[] Ogamma;
  
  Ngamma = ngamma;
  Rgamma = new double[3*ngamma];
  Egamma = new double[ngamma];
  Tgamma = new double[ngamma];
  Ogamma = new std::string[ngamma];

  double* ptr;

  ptr = Rgamma+3*ngamma;
  while(ptr>Rgamma)*--ptr=*--rgptr;

  ptr = Egamma+ngamma;
  while(ptr>Egamma)*--ptr=*--egptr;

  ptr = Tgamma+ngamma;
  while(ptr>Tgamma)*--ptr=*--tgptr;

  std::string* qtr = Ogamma+ngamma;
  while(qtr>Ogamma)*--qtr=*--ogptr;

  /*
  cout << "  " << Ngamma << " gammas" << endl;
  for(int n=0;n<Ngamma;n++){
    for(int i=0;i<3;i++) cout << "  Rgamma[" << 3*n+i << "] " 
                              << Rgamma[3*n+i];
    cout << endl;
    cout << "  Egamma[" << n << "] " << Egamma[n] 
         << "  Tgamma[" << n << "] " << Tgamma[n]
         << "  Ogamma[" << n << "] " << Ogamma[n] << endl;
  }
  */

  // clean up
  delete[] rgamma;
  delete[] egamma;
  delete[] tgamma;
  delete[] ogamma;    
}

float ReactorDetector::QSpectrum(float const& Q){
  float m = 8.1497;
  float ng1 = 0.2735E-01;
  float ng2 = 0.7944E-03;
  float nexp = 0.81228E-01;
  float G2 = 4.5; //Relative gain for 2nd Polya for R1408 spectrum
  float Q2 = Q/G2;
  float Q0 = 0.61;
  float gmratio = m/exp(gamma(m));


  float Qpol1 = gmratio*pow((m*Q),m-1)*exp(-m*Q);
  float Qpol2 = gmratio*pow((m*Q2),m-1)*exp(-m*Q2);
  return  (ng1*Qpol1 + ng2*Qpol2 + nexp*exp(-Q/Q0));
}

float ReactorDetector::GenerateQ(int npe){

    float pedwidth = 0.1;
    float qtot = 0.;

    if (npe>0) {
     float* qran = new float[npe];
     float* qsmear= new float[npe];
     rnormx_(qsmear,npe,ranlux_);
     funlux_(Qspace,qran[0],npe);
      for (int ipe=0; ipe<npe; ipe++){
            qtot+=(qran[ipe]+pedwidth*qsmear[ipe]);
      }
        delete[] qran;
        delete[] qsmear;
    }
    else {
      float qsmear[1];
      int ipe = 1;
      rnormx_(qsmear,ipe,ranlux_);
      qtot+=pedwidth*qsmear[0];
    }
    return qtot;
 }



ReactorDetector::PMT* ReactorDetector::ResizePMT(){

  int oldsize = PMTsize;
  int newsize = 2*oldsize;
  PMT* PMThold = new PMT[newsize];
  PMT* PMTold = PMTdata+oldsize;
  PMT* PMTnew = PMThold+oldsize;
  while(PMTnew>PMThold)*--PMTnew=*--PMTold;
  delete[] PMTdata;
  PMTdata = new PMT[newsize];
  PMTold = PMThold+newsize;
  PMTnew = PMTdata+newsize;
  while(PMTnew>PMTdata)*--PMTnew=*--PMTold;
  delete[] PMThold;
  PMTsize = newsize;
  return PMTdata+oldsize;
}
//
// Fetch number of gammas from positron
//
int ReactorDetector::GetNgamma(std::string parent){
  int gamma=0;
  for(std::string* optr=Ogamma;optr<Ogamma+Ngamma;optr++){
    if (*optr==parent)gamma++;
  }
  return gamma;
}
//
// Fetch array of positron gammas
//
void ReactorDetector::GetGamma(std::string parent,double* xyz){

  double* Rptr=Rgamma;
  double* rptr=xyz;
  //
  for(std::string* optr=Ogamma;optr<Ogamma+Ngamma;optr++){
    if (*optr==parent){
      for(int i=0;i<3;i++)*rptr++ = *Rptr++;
    }
  }
}  
void ReactorDetector::GetGamma(std::string parent,double* e,
                               double* t,double* r,
                               double* c,double* f){

  //cout << "GetGamma(" << parent << ")" << endl;
  double* Eptr=Egamma;
  double* Rptr=Rgamma;
  double* Tptr=Tgamma;
  //double* eptr=e;
  //double* rptr=r;
  //double* tptr=t;
  //double* cptr=c;
  //double* fptr=f;
  //
  for(std::string* optr=Ogamma;optr<Ogamma+Ngamma;optr++){
    if (*optr==parent){
      *e++=*Eptr;
      *t++=*Tptr;
      double x=*(Rptr+0);
      double y=*(Rptr+1);
      double z=*(Rptr+2);
      *r++=sqrt(x*x+y*y+z*z);
      *c++=z/sqrt(x*x+y*y+z*z);
      *f++=atan2(y,x);
      if((*f)<0)*f+=2*PI;
    }
    Eptr++;
    Tptr++;
    Rptr+=3;
  }
}
void ReactorDetector::SetNominalParameters(){
  //
  // Set nominal detector parameters from ReactorConstants
  //
  R0 = RD0;
  R1 = RD1;
  R2 = RD2;
  //
  GdConcentration=GDCONCENTRATION;
  //
  refracGd = REFRACGD;
  refracSc = REFRACSC;
  //
  mfpGd = MFPGD;
  mfpSc = MFPSC;
  //
  MeanNeuDispl = MEANNEUDISPL;
  //
  FastNeutronOption = FASTNEUTRONOPTION;
  Temperature = TEMPERATURE;
  //
  tGd = TGD;
  tSc = TSC;
  //
  GdCaptureFraction = GDCAPTUREFRACTION;
  //
  GammasPerGd = GAMMASPERGD; 
  //
  attenlGd = ATTENLGD;
  attenlSc = ATTENLSC;
  //
  PhotonsPerMeV = PHOTONSPERMEV;
  //
  ScintDecayTime = SCINTDECAYTIME;
  //
  PMTcoverage = PMTCOVERAGE;
  PMTdiameter = PMTDIAMETER;
  //
  PMTqe = PMTQE;
  EScale = ESCALE;
}
void ReactorDetector::SetPMT(){
  //
  // determine the number of PMT
  //
  float num_pmt = 16*R2*R2*PMTcoverage/PMTdiameter/PMTdiameter;
  Ncosbins = int(sqrt(num_pmt/PI));
  Nphibins = int(sqrt(num_pmt*PI));
  Npmt = Ncosbins*Nphibins;
  //cout << "  Set Npmt " << Npmt << endl;

  delete[] Xpmt;
  delete[] Ypmt;
  delete[] Zpmt;
  delete[] PMTOutputArray;

  Xpmt = new double[Npmt];
  Ypmt = new double[Npmt];
  Zpmt = new double[Npmt];
  PMTOutputArray = new PMToutput*[Npmt];
  for(int i=0;i<Npmt;i++){
    PMTOutputArray[i]=new PMToutput (i);
    }

  //
  // Make a guess at PMT size to avoid too much re-sizing
  //
  delete[] PMTdata;
  PMTlen = 0;
  PMTsize = 10*Npmt;
  PMTdata = new PMT[PMTsize];
  //
  // loop over cotheta, then phi
  //
  double* xpmt=Xpmt;
  double* ypmt=Ypmt;
  double* zpmt=Zpmt;
  
  double dphi = 2*PI/Nphibins;
  double dz = 2.0/Ncosbins;
  
  for(int i=0;i<Ncosbins;i++){
    double z = -1+i*dz+dz/2;
    for(int j=0;j<Nphibins;j++){
      double phi = j*dphi+dphi/2;
      *xpmt++ = R2*sqrt(1-z*z)*cos(phi);
      *ypmt++ = R2*sqrt(1-z*z)*sin(phi);
      *zpmt++ = R2*z;
      //      cout << "z,phi  " << z << " " << phi << endl;
    }
  }
}
void ReactorDetector::SetParam_GdConcentration(double x){
  GdConcentration =x;
  double y =(GdConcentration/GdConcentrationRef);
  double z = GdCaptureFraction/(1-GdCaptureFraction);
  //
  GdCaptureFraction = y*z/(1+y*z);
  //
  mfpGd*=(1+z)/(1+y*z);
  tGd*=(1+z)/(1+y*z);
  SetNeutronPropStuff();
}
void ReactorDetector::SetNeutronPropStuff(){
  //
  a[0] = A0;
  a[1] = A1;
  a[2] = A2;
  a[3] = A3;
  //
  z[0] = Z0;
  z[1] = Z1;
  z[2] = Z2;
  z[3] = Z3;
  //
  nn[0]=NAVOGADRO*f0*density/A0;
  nn[1]=NAVOGADRO*f1*density/A1;
  nn[2]=NAVOGADRO*GdConcentration/100*f2*density/A2;
  nn[3]=NAVOGADRO*GdConcentration/100*f3*density/A3;
  //
}
double ReactorDetector::GetHitFrac(std::string parent){
  bool* hit = new bool[Npmt];
  for(int i=0;i<Npmt;i++)hit[i]=0;
  for(PMT* pPMT=PMTdata;pPMT<PMTdata+PMTlen;pPMT++){
    if(pPMT->Parent==parent&&pPMT->Npe>0)hit[pPMT->npmt]=1;
  }
  int nhit=0;
  for(int i=0;i<Npmt;i++)nhit+=hit[i];
  delete[] hit;
  return 1.0*nhit/Npmt;
}

void ReactorDetector::CalculateEnergy(std::string parent){

  // so far this only works for positron and neutron
  //
  //double rpmt[3];
  double revent[3];
  if(parent=="P")
    for(int i=0;i<3;i++)revent[i]=DipolePositron[i];
  else if(parent=="N")
    for(int i=0;i<3;i++)revent[i]=DipoleNeutron[i];
  else
    cout << "ERROR: CalculateEnergy does not work for parent type: "
         << parent << endl;

  double rdotr = revent[0]*revent[0]+revent[1]*revent[1]+revent[2]*revent[2];
  double* xpmt=Xpmt;
  double* ypmt=Ypmt;
  double* zpmt=Zpmt;
  double dr[3];
  double tr[3];
  //
  //
  // Begin by calculating the probability of photon detection
  // integrated over the entire PMT sphere.  Event position is
  // reconstructed position.  Ultimately, we'd like to include the
  // wavelength and angular PMT response here, rather than the flat
  // PMTqe.  Most of this was pasted from GenerateResponse.
  //
  //
  double detprob = 0.;
  double sGd;
  double sSc;
  for(int i=0;i<Ncosbins;i++){
    for(int j=0;j<Nphibins;j++){
      double rpmt[3];
      rpmt[0] = *xpmt++;
      rpmt[1] = *ypmt++;
      rpmt[2] = *zpmt++;
      for (int l=0;l<3;l++)dr[l]=rpmt[l]-revent[l];
      double ddr = sqrt(dr[0]*dr[0]+dr[1]*dr[1]+dr[2]*dr[2]);
      for (int l=0;l<3;l++)tr[l]=dr[l]/ddr;
      double tdotr = revent[0]*tr[0]+revent[1]*tr[1]+revent[2]*tr[2];
      //
      // solve for intersection with inner radius
      //
      //
      // check for no intersections
      //
      double test = R0*R0+tdotr*tdotr-rdotr;
      bool inter = (test>=0);
      //
      // A straight line from the interaction vertex to the pmt
      // goes through the inner radius at least once.  In this case,
      // the light will see Gd-scint. and unloaded scint.
      //
      if(inter){
        double sint1 = -tdotr+sqrt(test);
        double sint2 = -tdotr-sqrt(test);
        if(sint1>0&&sint2<0){     // 1 intersection at soln 1
          sGd = sint1;
        }
        else if(sint2>0&&sint1<0){     // 1 intersection at soln 2
          sGd = sint2;
        }
        else if(sint2>0&&sint1>0){     // 2 intersections
          sGd = sint1-sint2;
          if(sGd<0)sGd*=-1;
        }
        else{                          // no intersections towards PMT
          sGd = 0;
        }
        sSc = ddr-sGd;
      }
      //
      //  otherwise the light only goes through unloaded scintillator
      //
      else{
        sGd = 0;
        sSc = ddr;
      }
      // Now we increment detection probability, including
      // solid angle factor (sfactor).
      double atten = exp(-sGd/attenlGd-sSc/attenlSc);
      double sfactor=0;
      for (int l=0;l<3;l++){sfactor+=tr[l]*rpmt[l]/R2;}
      sfactor *= R2*R2/ddr/ddr;
      detprob+=sfactor*atten*PMTqe*(PMTcoverage/Npmt);
    }
  }
  // Now we find out how many photons we actually detected.
  double q = 0.;
  for(PMT* pPMT=PMTdata;pPMT<PMTdata+PMTlen;pPMT++){
//    if(pPMT->Parent==parent&&pPMT->Q>0){
    if(pPMT->Parent==parent){
      q+=pPMT->Q;
    }
  }

  // Now we can calculate most probable energy, including
  // division by energy scale.
  double energy = 0.;
  energy = q/(detprob*PhotonsPerMeV*EScale);
  //cout << " Escale " << EScale << endl;

  if(parent=="E") PHeleReco=energy;
  if(parent=="P") PHposReco=energy;
  if(parent=="N") PHneuReco=energy;
  if(parent=="Tl") PHthaReco=energy;
  if(parent=="Bi") PHbisReco=energy;
  if(parent=="Cf") PHcalReco=energy;
  if(parent=="muon") PHmuoReco=energy;

}

void ReactorDetector::CalculateQPosition(std::string parent){

  double d[3] = {0,0,0};
  double q=0;
  for(PMT* pPMT=PMTdata;pPMT<PMTdata+PMTlen;pPMT++){
    if(pPMT->Parent==parent&&pPMT->Q>0){
      q+=pPMT->PHsmr;
      for(int i=0;i<3;i++)d[i]+=(pPMT->PHsmr)*(pPMT->xyz[i]);
    }
  }
  if(q>0)for(int i=0;i<3;i++)d[i]/=q;

  if(parent=="P"){
    for(int i=0;i<3;i++)DipolePositron[i] = d[i];
  }
  if(parent=="N"){
    for(int i=0;i<3;i++)DipoleNeutron[i] = d[i];
  }
}
void ReactorDetector::ImproveQPosition(std::string parent){

  double d[3];
  double k = 0.;
  PMT* qPMT;
  if(parent=="P"){
    for(int i=0;i<3;i++)d[i]=DipolePositron[i];
    k = PHpositron;
    qPMT=PMTpositron;
  }
  if(parent=="N"){
    for(int i=0;i<3;i++)d[i]=DipoleNeutron[i];
    k = PHneutron;
    qPMT=PMTneutron;
  }
  //
  double C= PMTqe*PMTdiameter*PMTdiameter/16*PhotonsPerMeV;
  //
  double sumlast = 999999;
  double test=999999;
  double tol=0.01;
  int sign=1;
  bool first=1;
  double dev=0.1;
  while(test>tol){
  //
    double dlast[3];
    for(int i=0;i<3;i++)dlast[i]=d[i];
    double klast=k;
    double sum[3]={0,0,0};
    for(PMT* pPMT=qPMT;pPMT<qPMT+Npmt;pPMT++){
      if(pPMT->Parent!=parent)continue;
      double r[3];
      double rn[3];
      double t[3];
      for(int i=0;i<3;i++)rn[i]=pPMT->xyz[i];
      for(int i=0;i<3;i++)r[i]=rn[i]-d[i];
      double rdotr = r[0]*r[0]+r[1]*r[1]+r[2]*r[2];
      double rdotrn = r[0]*rn[0]+r[1]*rn[1]+r[2]*rn[2];
      for(int i=0;i<3;i++)t[i]=r[i]/sqrt(rdotr);
      //
      double tdotd=d[0]*t[0]+d[1]*t[1]+d[2]*t[2];
      double ddotd=d[0]*d[0]+d[1]*d[1]+d[2]*d[2];
      double test2=tdotd*tdotd-ddotd+R0*R0;
      double sSc;
      double sGd;
      //
      if(test2<0){//no intersections with inner shell
        sSc=sqrt(rdotr);
        sGd=0;
      }
      else{
        double s1=-tdotd+sqrt(test2);
        double s2=-tdotd-sqrt(test2);
        if(s1>0&&s2>0){//2 interesections
          sSc=sqrt(rdotr)-s1+s2;
          sGd=s1-s2;
        }
        else if(s1>0&&s2<0){//1 interestion
          sSc=sqrt(rdotr)-s1;
          sGd=s1;
        }
        else {//no interesctions
          sSc=sqrt(rdotr);
          sGd=0;
        }
      }
      //
      double mn=pPMT->Q;
      double w0=C*rdotrn/R2/sqrt(rdotr)/rdotr*
        exp(-sGd/attenlGd-sSc/attenlSc);
      sum[0]+=mn;
      sum[1]+=w0;
      sum[2]+=w0*klast-mn*log(w0*klast);
    }
    if(first){
      k = sum[0]/sum[1];
      for(int i=0;i<3;i++)d[i]*=(1+dev);
      first=0;
    }
    else{
      k = sum[0]/sum[1];
      if(sum[2]<sumlast){
        for(int i=0;i<3;i++)d[i]*=(1+sign*dev);
      }
      else{
        sign*=-1;
        dev/=2;
        for(int i=0;i<3;i++)d[i]*=(1+sign*dev);
      }
    }
    test=1-sum[2]/sumlast;
    if(test<0)test*=-1;
    sumlast=sum[2];
  }
  if(parent=="P")for(int i=0;i<3;i++)DipolePositron[i]=d[i];
  if(parent=="N")for(int i=0;i<3;i++)DipoleNeutron[i]=d[i];
}  
//
//
//
void ReactorDetector::ConsolidatePMT(){
  //
  // first sum the total xpe
  //
  double *xpeele = new double[Npmt];
  double *Qele = new double[Npmt];
  double *xpepos = new double[Npmt];
  double *Qpos = new double[Npmt];
  double *xpeneu =  new double[Npmt];
  double *Qneu = new double[Npmt];
  double *xpetha = new double[Npmt];
  double *Qtha = new double[Npmt];
  double *xpebis = new double[Npmt];
  double *Qbis = new double[Npmt];
  double *xpecal = new double[Npmt];
  double *Qcal = new double[Npmt];
  double *xpemuo = new double[Npmt];
  double *Qmuo = new double[Npmt];
  int* subhitsele = new int[Npmt];
  int* subhitspos = new int[Npmt];
  int* subhitsneu = new int[Npmt];
  int* subhitstha = new int[Npmt];
  int* subhitsbis = new int[Npmt];
  int* subhitscal = new int[Npmt];
  int* subhitsmuo = new int[Npmt];
  //
  for(int i=0;i<Npmt;i++){
    xpeele[i]=0;
    xpepos[i]=0;
    xpeneu[i]=0;
    xpetha[i]=0;
    xpebis[i]=0;
    xpecal[i]=0;
    xpemuo[i]=0;
    Qele[i]=0;
    Qpos[i]=0;
    Qneu[i]=0;
    Qtha[i]=0;
    Qbis[i]=0;
    Qcal[i]=0;
    Qmuo[i]=0;
    subhitsele[i]=0;
    subhitspos[i]=0;
    subhitsneu[i]=0;
    subhitstha[i]=0;
    subhitsbis[i]=0;
    subhitscal[i]=0;
    subhitsmuo[i]=0;
  }
  //
  for(PMT* pPMT=PMTdata;pPMT<PMTdata+PMTlen;pPMT++){
    int n=pPMT->npmt;
    PMTOutputArray[n]->incout(pPMT, MergeTime);
    if(pPMT->Parent=="E"){
      xpeele[n]+=pPMT->Npe;
      Qele[n]+=pPMT->Q;
      subhitsele[n]++;
    }
    if(pPMT->Parent=="P"){
      xpepos[n]+=pPMT->Npe;
      Qpos[n]+=pPMT->Q;
      subhitspos[n]++;
    }
    if(pPMT->Parent=="N"){
      xpeneu[n]+=pPMT->Npe;
      Qneu[n]+=pPMT->Q;
      subhitsneu[n]++;
    }
    if(pPMT->Parent=="Tl"){
      xpetha[n]+=pPMT->Npe;
      Qtha[n]+=pPMT->Q;
      subhitstha[n]++;
    }
    if(pPMT->Parent=="Bi"){
      xpebis[n]+=pPMT->Npe;
      Qbis[n]+=pPMT->Q;
      subhitsbis[n]++;
    }
    if(pPMT->Parent=="Cf"){
      xpecal[n]+=pPMT->Npe;
      Qcal[n]+=pPMT->Q;
      subhitscal[n]++;
    }
    if(pPMT->Parent=="muon"){
      xpemuo[n]+=pPMT->Npe;
      Qmuo[n]+=pPMT->Q;
      subhitsmuo[n]++;
    }
  }
  //   
  delete[] PMTelectron;
  PMTelectron = new PMT[Npmt];
  delete[] PMTpositron;
  PMTpositron = new PMT[Npmt];
  delete[] PMTneutron;
  PMTneutron = new PMT[Npmt];
  delete[] PMTthallium;
  PMTthallium = new PMT[Npmt];
  delete[] PMTbismuth;
  PMTbismuth = new PMT[Npmt];
  delete[] PMTcalifornium;
  PMTcalifornium = new PMT[Npmt];
  delete[] PMTmuon;
  PMTmuon = new PMT[Npmt];
  //
  for(int i=0;i<Npmt;i++){
    (*(PMTelectron+i)).npmt=i;
    (*(PMTelectron+i)).Parent="E";
    (PMTelectron+i)->SetSubHitsPtr(subhitsele[i]);
    //
    (*(PMTpositron+i)).npmt=i;
    (*(PMTpositron+i)).Parent="P";
    (PMTpositron+i)->SetSubHitsPtr(subhitspos[i]);
    //
    (*(PMTneutron+i)).npmt=i;
    (*(PMTneutron+i)).Parent="N";
    (PMTneutron+i)->SetSubHitsPtr(subhitsneu[i]);
    //
    (*(PMTthallium+i)).npmt=i;
    (*(PMTthallium+i)).Parent="Tl";
    (PMTthallium+i)->SetSubHitsPtr(subhitstha[i]);
    //
    (*(PMTbismuth+i)).npmt=i;
    (*(PMTbismuth+i)).Parent="Bi";
    (PMTbismuth+i)->SetSubHitsPtr(subhitsbis[i]);
    //
    (*(PMTcalifornium+i)).npmt=i;
    (*(PMTcalifornium+i)).Parent="Cf";
    (PMTcalifornium+i)->SetSubHitsPtr(subhitscal[i]);
    //
    (*(PMTmuon+i)).npmt=i;
    (*(PMTmuon+i)).Parent="muon";
    (PMTmuon+i)->SetSubHitsPtr(subhitsmuo[i]);
  }
  //
  for(PMT* pPMT=PMTdata;pPMT<PMTdata+PMTlen;pPMT++){
    int n=pPMT->npmt;
    PMT* qPMT;
    if(pPMT->Parent=="E"){
      qPMT = PMTelectron+n;
      *qPMT+=*pPMT;
    }
    if(pPMT->Parent=="P"){
      qPMT = PMTpositron+n;
      *qPMT+=*pPMT;
    }
    if(pPMT->Parent=="N"){
      qPMT = PMTneutron+n;
      *qPMT+=*pPMT;
    }
    if(pPMT->Parent=="Tl"){
      qPMT = PMTthallium+n;
      *qPMT+=*pPMT;
    }
    if(pPMT->Parent=="Bi"){
      qPMT = PMTbismuth+n;
      *qPMT+=*pPMT;
    }
    if(pPMT->Parent=="Cf"){
      qPMT = PMTcalifornium+n;
      *qPMT+=*pPMT;
    }
    if(pPMT->Parent=="muon"){
      qPMT = PMTmuon+n;
      *qPMT+=*pPMT;
    }
  }
  delete[] xpepos;
  delete[] Qpos;
  delete[] xpeneu;
  delete[] Qneu;
  delete[] xpeele;
  delete[] Qele;
  delete[] xpetha;
  delete[] Qtha;
  delete[] xpebis;
  delete[] Qbis;
  delete[] Qcal;
  delete[] xpecal;
  delete[] Qmuo;
  delete[] xpemuo;
}    

double* ReactorDetector::TranslateRadialDistance(double x,double y,
                                                 double z,double d){

  // translate a point along the radial axis
  // x,y,z cartesian coordinates of point to translate
  // d distance to translate along the radial axis (negative -> move inward)

  double p[3];
  double* ptr = p;
  double r, costheta, phi;

  // convert to spherical coordinates
  //
  r = sqrt(x*x + y*y + z*z);
  if(r != 0.){
    costheta = z/r;
  }
  else{
    costheta = 0.;
    cout << " ERROR: TranslateRadialDistance initial r = 0!" << endl;
  }
  phi = atan2(y,x);
  if(phi < 0) phi += 2*PI;

  //cout << " " << r << "," << costheta << "," << phi << endl;

  // move a distance d along the radial axis
  //
  r+=d;

  // return to cartesian
  //
  p[0] = r*sqrt(1-costheta*costheta)*cos(phi);
  p[1] = r*sqrt(1-costheta*costheta)*sin(phi);
  p[2] = r*costheta;

  //for(int i=0;i<3;i++) cout << " p["<<i<<"] " << p[i] << " ";
  //cout << endl;

  // for some reason this empty cout statement is required to
  // make this funtion work and I don't like it AT ALL
  cout << "";

  return(ptr);
}

void ReactorDetector::CleanPMTOutputArray(){
  for(int j=0; j<Npmt; j++)
    PMTOutputArray[j]->cleanup();
  }

//PMToutput constructor, initializes empty vector and array
PMToutput::PMToutput(int ID){
  PMTid=ID;
  eventsin=0;
  eventsdetected=0;
}

//PMToutput destructor
PMToutput::~PMToutput(){
}
//PMToutput copy constructor
PMToutput::PMToutput(const PMToutput& PMTout){
  PMTid=PMTout.PMTid;
  eventsin=PMTout.eventsin;
  eventsdetected=PMTout.eventsdetected;
  temp=PMTout.temp;
  copy(PMTout.events.begin(),PMTout.events.end(),events.begin());
  copy(PMTout.output.begin(),PMTout.output.end(),output.begin());
  }

//PMToutput overloaded = operator
  PMToutput& PMToutput::operator=(const PMToutput& rhs){
  PMTid=rhs.PMTid;
  eventsin=rhs.eventsin;
  eventsdetected=rhs.eventsdetected;
  int i;
  for (i=0;i<eventsdetected;i++) output.push_back(rhs.output[i]);
  for (i=0;i<eventsin;i++) events.push_back(rhs.events[i]);
  return *this;
  }

//function incout - adds a PMT event into the string
void PMToutput::incout(ReactorDetector::PMT* input, double MergeTime){
  temp.energy=input->PHsmr;
  if(temp.energy==0)return;
  temp.time = input->TimeSmr;
  events.push_back(input);
  eventsin++;
  if(eventsdetected==0) {
    output.push_back(temp);
    eventsdetected++;
  }
  else{
    bool done=false;
    int x,y,z;
    x=0;
    z=output.size()-1;
    if(temp.time < output[0].time + MergeTime){
      if(abs(temp.time - output[0].time) < MergeTime) output[0]+=temp;
      else output.insert(output.begin(),temp);
      done=true;
      }
    else if(temp.time > output[z].time - MergeTime){
      if(abs(temp.time - output[z].time) < MergeTime) output[z]+=temp;
      else output.push_back(temp);
      done=true;
      }
    while(!done && z-x>1){
      y=(x+z)/2;
      if(temp.time > output[y].time) x=y;
      else z=y;
      }
    if(!done){
      if(abs(temp.time - output[x].time) < MergeTime){
        output[x]+=temp;
        done=true;
        }
      else if(abs(temp.time-output[z].time) < MergeTime){
        output[z]+=temp;
        done=true;
        }
      }
    if(!done){
      std::vector<PMTinfo>::iterator it1;
      it1=output.begin();
      it1+=z;
      output.insert(it1,temp);
      eventsdetected++;
      }
/*  <Algorithm> implementation
    std::vector<PMTinfo>::iterator it1;
    it2= lower_bound(output.begin(), output.end(), temp, SortByTime);
    if ( it1 != output.begin() )
      it1--;
    if ( temp.time - it1->time < MergeTime ) {
      (*it1)+=temp;
    }
    else if ( it2 != output.end() && it2->time - temp.time < MergeTime ) {
      (*it2)+=temp;
    }
    else {
      output.insert(it2, temp);
      eventsdetected++;
    }
*/}
}

void PMToutput::testdump(int event){
  ofstream file ( "testdump.txt", ios::app );
  if(!file.is_open()){
    cout << "File failure" << endl;
    return;
    }
  else{
    std::vector<PMTinfo>::iterator it1;
    for (it1 = output.begin(); it1 != output.end(); it1++)
      file << event << "\t" << PMTid << "\t" << it1->time << "\t" << it1->energy << endl;
    }
}


void PMToutput::cleanup(){
  output.clear();
  events.clear();
  eventsin=0;
  eventsdetected=0;
  }

PMTinfo&
PMTinfo::operator+=(const PMTinfo& rhs){
  energy+=rhs.energy;
  if(time>rhs.time) time=rhs.time;
  return *this;
}

---