sdecay-sys 0.2.0+cd75314

/* SandiaDecay: a library that provides nuclear decay info and calculations.
 
 Copyright 2018 National Technology & Engineering Solutions of Sandia, LLC
 (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the U.S.
 Government retains certain rights in this software.
 For questions contact William Johnson via email at wcjohns@sandia.gov, or
 alternative email of interspec@sandia.gov.
 
 This library is free software; you can redistribute it and/or
 modify it under the terms of the GNU Lesser General Public
 License as published by the Free Software Foundation; either
 version 2.1 of the License, or (at your option) any later version.
 
 This library is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 Lesser General Public License for more details.
 
 You should have received a copy of the GNU Lesser General Public
 License along with this library; if not, write to the Free Software
 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 */

#include <map>
#include <cmath>
#include <cerrno>
#include <math.h>
#include <vector>
#include <string>
#include <locale>
#include <limits>
#include <cstring>
#include <sstream>
#include <fstream>
#include <ctype.h>
#include <float.h>
#include <iostream>
#include <assert.h>
#include <stdexcept>
#include <algorithm>

// If you run with CalcFloatType==__float128 on GNU, you'll need this next
//  include for `qexp(...)`, and you'll need to link against libquadmath
// #include <quadmath.h>

#include "rapidxml/rapidxml.hpp"

#include "SandiaDecay.h"


/* The sandia.decay.xml file normally has elements like <nuclide/>, <element/>
    etc., but if ENABLE_SHORT_NAME is enabled, then either these element names
    can be used, or much shorter ones like <n/>, <el/>, etc.  Similar story for
    attributes.
  As of 20180106 there is no notable difference in parsing times of the original
  sandia.decay.xml file if this is enabled or disabled, and the results look
  identical - but leaving this compile switch in (and associated code) until
  next release incase any problems arise it will help deal with.
 */
#define ENABLE_SHORT_NAME 1

/* Previous to 20201118 nuclides with no <transition /> elements in sandia.decay.xml would get left
 out of the Bateman coefficients when making a SandiaDecay::NuclideMixture, so those nuclides
 activities wouldn't be present in decay results.  This wasn't a big deal as you wouldn't observe
 those nuclides in data anyway, and only a few (around 18) nuclides has this issue, and they are all
 extremely short half-lives that its questionable if they should even be in sandia.decay.xml (they
 probably don't have transitions because the nuclides haven't been characterized well), but
 none-the-less, its fixed up now.
 
 I tested that all nuclides in DB decayed to 3.5 lives yields the exact same gammas with and without
 this fix, and that all activities of nuclides, and their children are the same, except for the ~18
 affected nuclides.

 However, leaving in this fixed compile-time switch until the next release to make it easier to
 debug if any issues popup.
 */
#define DO_EMPTY_TRANSITION_FIX 1

// Ignore this warning. It shouldn't be important, and seems to be Windows-only.
// warning C4244: 'initializing' : conversion from 'std::streamoff' to 'size_t', possible loss of data
#pragma warning(disable:4244)

using namespace std;

// Workaround for Windows portability.
#if ( defined(WIN32) || defined(UNDER_CE) || defined(_WIN32) || defined(WIN64) )
#include <stdarg.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <float.h>
#define isnan(x) _isnan(x)
#define isinf(x) (!_finite(x))
#define fpu_error(x) (isinf(x) || isnan(x))
#endif

#if defined(_MSC_VER) && _MSC_VER < 1900
#define snprintf c99_snprintf
namespace
{
//from http://stackoverflow.com/questions/2915672/snprintf-and-visual-studio-2010
inline int c99_snprintf(char* str, size_t size, const char* format, ...)
{
  int count;
  va_list ap;
  va_start( ap, format );
  count = c99_vsnprintf( str, size, format, ap );
  va_end( ap );
  return count;
}
}//namespace
#endif

#if __cplusplus > 199711L
#define IsInf(x) std::isinf(x)
#define IsNan(x) std::isnan(x)
#else
#define IsInf(x) isinf(x)
#define IsNan(x) isnan(x)
#endif



namespace
{
  //Using sscanf costs 75ms over atof for opening sandia.decay.xml on late 2018
  //  mbp.  Using sscanf would be best for error checking (I think strtod
  //  returns a zero for non-numbers, and does not set errno, except out of
  //  range, and atof is UB if not a valid float).  I guess after checking the
  //  xml that all values properly parse, we'll go with the fastest one that
  //  doesnt cause UB.  Using stod is about the same speed as atof
  double parse_double( const char *str )
  {
    //return atof( str );
  
    errno = 0;
    const double answer = strtod(str,NULL);
    if( errno )
      throw runtime_error( "Could not convert '" + string(str) + "' to a double" );
    return answer;
    
    //double val;
    //const int nread = sscanf( str, "%lf", &val );
    //if( nread != 1 )
    //  throw runtime_error( "Could not convert '" + string(str) + "' to a double" );
    //return static_cast<float>(val);
  }
  
  float parse_float( const char *str )
  {
    // This function is the primary bottleneck of parsing; to initualize
    //  SandiaDecayDataBase with sandia.decay.min.xml (i.e., with coincidences, but minimzed tags),
    //  on an M1 macbook it takes:
    // - atof:   80ms
    // - strtof: 110ms
    // - sscanf: 150ms
    //
    // Even using atof, this function takes up almost 20% of the CPU time when constructing
    //  with sandia.decay.min.xml.
    //
    // Some notes about atof:
    //  - If input is not a valid float, will return 0.0; doesnt set `errno`.
    //  - If input is out of the range, its undefined behavior
    float answer = (float)atof( str );
    if( answer != 0.0 )
      return answer;
    
    // If we got zero from atof, it could actually be a zero value, or it could be an error,
    //  so we'll check this using strtof (we dont expect zero very often at all, and never expect
    //  an error, so this second check doesnt add any real time).
    errno = 0;
    answer = strtof(str,NULL);
    if( errno )
      throw runtime_error( "Could not convert '" + string(str) + "' to a float" );
    return answer;
    
    /*
    float val;
    const int nread = sscanf( str, "%f", &val );
    if( nread != 1 )
      throw runtime_error( "Could not convert '" + string(str) + "' to a float" );
    return val;
     */
  }
  
  short int parse_short_int( const char *str )
  {
    errno = 0;
    const long int answer = strtol( str, NULL, 10 );
    if( errno )
      throw runtime_error( "Could not convert '" + string(str) + "' to a short" );
    //ToDo: make sure answer is in short int range.
    return static_cast<short int>( answer );
    
    //return (short int)atoi( str );
  }
  
  int parse_int( const char *str )
  {
    errno = 0;
    const long int answer = strtol( str, NULL, 10 );
    if( errno )
      throw runtime_error( "Could not convert '" + string(str) + "' to a int" );
    //ToDo: make sure int is in range.
    return static_cast<int>( answer );
    
    //return atoi( str );
  }
  
//a struct so that we can sort an array using an extanal array of indexes,
//  with out modifying the data array.
template<class T> struct index_compare_assend
{
  index_compare_assend(const T arr) : arr(arr) {} //pass the actual values you want sorted into here
  bool operator()(const size_t a, const size_t b) const
  {
    return arr[a] < arr[b];
  }
  const T arr;
};//struct index_compare

  
bool convert( const std::string& arg, SandiaDecay::ProductType &s )
{
  if( arg == "beta" || arg == "b" )                 s = SandiaDecay::BetaParticle;
  else if( arg == "gamma" || arg == "g" )           s = SandiaDecay::GammaParticle;
  else if( arg == "alpha" || arg == "a" )           s = SandiaDecay::AlphaParticle;
  else if( arg == "positron" || arg == "p" )        s = SandiaDecay::PositronParticle;
  else if( arg == "electronCapture" || arg == "ec" ) s = SandiaDecay::CaptureElectronParticle;
  else if( arg == "xray" || arg == "x" )            s = SandiaDecay::XrayParticle;
  else return false;
  return true;
}//bool convert( const std::string& arg, ProductType &s )

  
SandiaDecay::DecayMode decaymode_fromstr( const std::string &decayMode )
{
  if( decayMode == "b-" )        return SandiaDecay::BetaDecay;
  else if( decayMode == "it" )   return SandiaDecay::IsometricTransitionDecay;
  else if( decayMode == "b-n" )  return SandiaDecay::BetaAndNeutronDecay;
  else if( decayMode == "b+" )   return SandiaDecay::BetaPlusDecay;
  else if( decayMode == "ec" )   return SandiaDecay::ElectronCaptureDecay;
  else if( decayMode == "b-a" )  return SandiaDecay::BetaAndAlphaDecay;
  else if( decayMode == "b-2n" ) return SandiaDecay::BetaAndTwoNeutronDecay;
  else if( decayMode == "ecp" )  return SandiaDecay::ElectronCaptureAndProtonDecay;
  else if( decayMode == "eca" )  return SandiaDecay::ElectronCaptureAndAlphaDecay;
  else if( decayMode == "b+p" )  return SandiaDecay::BetaPlusAndProtonDecay;
  else if( decayMode == "ec2p" ) return SandiaDecay::ElectronCaptureAndTwoProtonDecay;
  else if( decayMode == "b+2p" ) return SandiaDecay::BetaPlusAndTwoProtonDecay;
  else if( decayMode == "b+3p" ) return SandiaDecay::BetaPlusAndThreeProtonDecay;
  else if( decayMode == "b+a" )  return SandiaDecay::BetaPlusAndAlphaDecay;
  else if( decayMode == "2b-" )  return SandiaDecay::DoubleBetaDecay;
  else if( decayMode == "2ec" )  return SandiaDecay::DoubleElectronCaptureDecay;
  else if( decayMode == "a" )    return SandiaDecay::AlphaDecay;
  else if( decayMode == "p" )    return SandiaDecay::ProtonDecay;
  else if( decayMode == "14c" )  return SandiaDecay::Carbon14Decay;
  else if( decayMode == "sf" )   return SandiaDecay::SpontaneousFissionDecay;
  else if( decayMode == "2p" )   return SandiaDecay::DoubleProton;
  else if( decayMode == "Undefined" ) return SandiaDecay::UndefinedDecay;
  return SandiaDecay::UndefinedDecay;
}//DecayMode decaymode_fromstr( const char *str )
  
  
SandiaDecay::ForbiddennessType forbiddenness_fromstr( const char *str )
{
  const size_t len = strlen(str);
  if( len == 1 )
  {
    if( str[0]=='1' )
      return SandiaDecay::FirstForbidden;
    if( str[0]=='2' )
      return SandiaDecay::SecondForbidden;
    if( str[0]=='3' )
      return SandiaDecay::ThirdForbidden;
    if( str[0]=='4' )
      return SandiaDecay::FourthForbidden;
  }else if( len==2 && str[1]=='u' )
  {
    if( str[0]=='1' )
      return SandiaDecay::FirstUniqueForbidden;
    if( str[0]=='2' )
      return SandiaDecay::SecondUniqueForbidden;
    if( str[0]=='3' )
      return SandiaDecay::ThirdUniqueForbidden;
  }
  
  return SandiaDecay::NoForbiddenness;
}//ForbiddennessType forbiddenness_fromstr( const char *str )
  
  
/** Revision status in the source XML data for this particle.
*/
enum RevisionType
{
  NoRevision,
  EditedRevision,
  InsertedRevision,
  DeletedRevision
};//enum RevisionType
  
  
RevisionType revision_fromstr( const char *str )
{
  const size_t len = strlen(str);
  if( !len )
    return NoRevision;
  if( !strcmp(str,"edited") )
    return EditedRevision;
  if( !strcmp(str,"inserted") )
    return InsertedRevision;
  if( !strcmp(str,"deleted") )
    return DeletedRevision;
  return NoRevision;
}//RevisionType revision_fromstr( const char *str )

  
bool lessThanBySymbol( const SandiaDecay::Nuclide *lhs, const std::string &rhs )
{
  if( !lhs )
    return false;
  return (lhs->symbol < rhs);
}//bool lessThanBySymbol( const Nuclide *lhs, const std::string &rhs )

  
bool pointerLessThanBySymbol( const SandiaDecay::Nuclide *lhs, const SandiaDecay::Nuclide *rhs )
{
  if( !lhs )
    return false;
  if( !rhs )
    return true;
  return (lhs->symbol < rhs->symbol);
}//bool pointerLessThanBySymbol( const Nuclide *lhs, const Nuclide *lhs )
  
  
vector<const SandiaDecay::Nuclide *>::const_iterator find(
                            const vector<const SandiaDecay::Nuclide *> &data,
                            const std::string &symbol )
{
  vector<const SandiaDecay::Nuclide *>::const_iterator pos
          = lower_bound( data.begin(), data.end(), symbol, &lessThanBySymbol );
    
  if( (pos == data.end()) || ((*pos)->symbol != symbol) )
    return data.end();
    
  return pos;
}//find(...)

  
struct BatemanWorkingSpace
{
  std::vector< std::vector<const SandiaDecay::Nuclide *> > nuclide_path;
  std::vector< std::vector< std::vector<SandiaDecay::CalcFloatType> > > decay_coeffs;
};//struct BatemanWorkingSpace
  
//The following nuclides are known to give nan or inf coeficients in
//  BatemanWorkingSpace::decay_coeffs :  Sm136, Pt183, Ir172, Hg179, Eu136
//  (this issue was found 20121011, but not investigated further - I think
//  its been fixed (20180402), but I didnt check that)
void calc_bateman_coef( std::vector< vector<SandiaDecay::CalcFloatType> > &coefs,
                        std::vector<const SandiaDecay::Transition *> decay_path,
                        BatemanWorkingSpace &ws )
{
  assert( decay_path.size() );
  const SandiaDecay::Transition * const trans = decay_path.back();
  assert( trans );
  
  const SandiaDecay::Nuclide * const child = trans->child;
#if( !DO_EMPTY_TRANSITION_FIX )
  assert( child );
#endif
  
  const size_t row = coefs.size();
  coefs.push_back( vector<SandiaDecay::CalcFloatType>(row+1, 0.0) );  //13.5% of time
  
  for( size_t col = 0; col < row; ++col )
  {
#if( !DO_EMPTY_TRANSITION_FIX )
    assert( decay_path[row-1]->child );
#endif
    assert( decay_path[row-1]->parent );
    
    const SandiaDecay::CalcFloatType lambda_iminus1 = decay_path[row-1]->parent->decayConstant();
#if( DO_EMPTY_TRANSITION_FIX )
    const SandiaDecay::CalcFloatType lambda_i = (decay_path[row-1]->child ? decay_path[row-1]->child->decayConstant() : 0.0);
#else
    const SandiaDecay::CalcFloatType lambda_i = decay_path[row-1]->child->decayConstant();
#endif
    const SandiaDecay::CalcFloatType lambda_j = decay_path[col]->parent->decayConstant();
    const SandiaDecay::CalcFloatType br = decay_path[row-1]->branchRatio;
    
    coefs[row][col] = br * (lambda_iminus1/(lambda_i - lambda_j)) * coefs[row-1][col];
    coefs[row][row] -= coefs[row][col];
  }//for( loop over 'col' of matrix A )
  
  
  //We have to get rid of any transition without a child for efficiency sake
  vector<const SandiaDecay::Transition *> decays;
#if( DO_EMPTY_TRANSITION_FIX )
  if( child )
#endif
  {
    decays.reserve( child->decaysToChildren.size() );
  
    for( size_t t = 0; t < child->decaysToChildren.size(); ++t )
    {
#if( !DO_EMPTY_TRANSITION_FIX )
      if( child->decaysToChildren[t]->child )
#endif
        decays.push_back( child->decaysToChildren[t] );
    }//for( loop over children )
  }//if( child )
  
  if( decays.empty() )
  {
    const size_t ndecaypath = decay_path.size();
    ws.nuclide_path.push_back( vector<const SandiaDecay::Nuclide *>() );
    vector<const SandiaDecay::Nuclide *> &decay_nuclides = ws.nuclide_path.back();
    decay_nuclides.resize( ndecaypath + 1 );
    for( size_t i = 0; i < ndecaypath; ++i )
      decay_nuclides[i] = decay_path[i]->parent;
    
    decay_nuclides[ndecaypath] = child;
    ws.decay_coeffs.push_back( coefs );  //17.2% of time
    
    coefs.resize( row );
    
    return;
  }//if( decays.empty() )
  
  const size_t ndecays = decays.size();
  for( size_t t = 0; t < ndecays; ++t )
  {
    const size_t ndecaypath = decay_path.size();
    vector<const SandiaDecay::Transition *> new_path( ndecaypath + 1 );
    for( size_t i = 0; i < ndecaypath; ++i )
      new_path[i] = decay_path[i];
    new_path[ndecaypath] = decays[t];
    
    calc_bateman_coef( coefs, new_path, ws );
  }//for( loop over decaysToChildren )
  
  coefs.resize( row );
}//void calc_bateman_coef(...)
}//namespace


namespace SandiaDecay
{

const char *to_str( SandiaDecay::ProductType s )
{
  switch( s )
  {
    case SandiaDecay::BetaParticle:
      return "beta";
    case SandiaDecay::GammaParticle:
      return "gamma";
    case SandiaDecay::AlphaParticle:
      return "alpha";
    case SandiaDecay::PositronParticle:
      return "positron";
    case SandiaDecay::CaptureElectronParticle:
      return "electronCapture";
    case SandiaDecay::XrayParticle:
      return "xray";
  }//switch( s )

  return "InvalidProductType";
}//const char *to_str( ProductType s )

const char *to_str( const DecayMode &s )
{
  switch( s )
  {
    case AlphaDecay:
      return "Alpha";
    case BetaDecay:
      return "Beta";
    case BetaPlusDecay:
      return "Beta+";
    case ProtonDecay:
      return "Proton";
    case IsometricTransitionDecay:
      return "Isometric";
    case BetaAndNeutronDecay:
      return "Beta and Neutron";
    case BetaAndTwoNeutronDecay:
      return "Beta and 2 Neutron";
    case ElectronCaptureDecay:
      return "Electron Capture";
    case ElectronCaptureAndProtonDecay:
      return "Electron Capture and Proton";
    case ElectronCaptureAndAlphaDecay:
      return "Electron Capture and Alpha";
    case ElectronCaptureAndTwoProtonDecay:
      return "Electron Capture and 2 Proton";
    case BetaAndAlphaDecay:
      return "Beta and Alpha";
    case BetaPlusAndProtonDecay:
      return "Beta Plus and Proton";
    case BetaPlusAndTwoProtonDecay:
      return "Beta Plus and 2 Proton";
    case BetaPlusAndThreeProtonDecay:
      return "Beta Plus and 3 Proton";
    case BetaPlusAndAlphaDecay:
      return "Beta Plus and Alpha";
    case DoubleBetaDecay:
      return "2 Beta+";
    case DoubleElectronCaptureDecay:
      return "2 Electron Capture";
    case Carbon14Decay: //Carbon-14 ?
      return "Carbon-14";
    case SpontaneousFissionDecay:   //I think this is spontaneous fission
      return "Spontaneous Fission";
    case ClusterDecay:
      return "Cluster Emission";
    case DoubleProton:
      return "Double Proton";
    case UndefinedDecay:
      return "Undefined";
    break;
  };//

  return "";
}//const char *to_str( DecayMode s )
  
std::istream& operator>>( std::istream& input, ProductType &s )
{
  std::string arg;
  input >> arg;

  if( !convert( arg, s ) )
    input.setstate( ios::failbit );

  return input;
}//istream & operator>>( istream &, ProductType & )


std::string human_str_summary( const Nuclide &obj )
{
  stringstream ostr;
    
  ostr << obj.symbol << " Atomic Number " << obj.atomicNumber <<", Atomic Mass "
    << obj.massNumber << ", Isomer Number " << obj.isomerNumber << " "
    << obj.atomicMass << " AMU, HalfLife=" << obj.halfLife << " seconds";
  const size_t nParents = obj.decaysFromParents.size();
  if( nParents )
    ostr << "\n  Parent";
  if( nParents > 1 )
    ostr << "s";
  if( nParents )
    ostr << ": ";
    
  for( size_t i = 0; i < nParents; ++i )
  {
    if( i )
      ostr << ", ";
    if( obj.decaysFromParents[i] && obj.decaysFromParents[i]->parent )
      ostr << obj.decaysFromParents[i]->parent->symbol;
  }//for( loop over parents )
    
  const size_t nChilds = obj.decaysToChildren.size();
    
  for( size_t i = 0; i < nChilds; ++i )
    ostr << "\n    " << human_str_summary(*obj.decaysToChildren[i]);
    
  return ostr.str();
}//std::ostream& operator<<( std::ostream& ostr, const Nuclide &obj )


std::string human_str_summary( const Transition &obj )
{
  stringstream ostr;
    
  ostr << "Transition ";
  if( obj.parent )
    ostr << obj.parent->symbol;
  ostr << "&rarr;";
  if( obj.child )
    ostr << obj.child->symbol;
  else
    ostr << "various";
  
  ostr << ": mode=" << obj.mode << " branchRatio=" << obj.branchRatio;
  if( obj.products.size() )
    ostr << "; Products:";
  for( size_t i = 0; i < obj.products.size(); ++i )
    ostr << "\n    " << SandiaDecay::human_str_summary( obj.products[i] );
    
  return ostr.str();
}//ostream& operator<<( ostream& ostr, const Transition &obj )

  
std::string human_str_summary( const RadParticle &obj )
{
  stringstream ostr;
  
  switch( obj.type )
  {
    case BetaParticle:   ostr << "beta:"; break;
    case GammaParticle:  ostr << "gamma:"; break;
    case AlphaParticle:           ostr << "alpha:"; break;
    case PositronParticle:        ostr << "positron:"; break;
    case CaptureElectronParticle: ostr << "electronCapture:"; break;
    case XrayParticle:           ostr << "xray:"; break;
  };//switch( obj.type )
    
  ostr << " energy=" << obj.energy << "keV intensity=" << obj.intensity;
  switch( obj.type )
  {
    case GammaParticle:
      break;
      
    case AlphaParticle:
      ostr << " hinderence=" << obj.hindrance;
      break;
      
    case BetaParticle: case PositronParticle: case CaptureElectronParticle:
      ostr << " forbiddenness=" << obj.forbiddenness << " logFT=" << obj.logFT;
      break;

    case XrayParticle:
      break;
  };//switch( obj.type )
    
  return ostr.str();
}//std::string human_str_summary( const RadParticle &obj )

  
  


RadParticle::RadParticle( const ::rapidxml::xml_node<char> *node )
{
  set( node );
}

RadParticle::RadParticle(ProductType p_type, float p_energy, float p_intensity)
  : type( p_type ),
    energy( p_energy ),
    intensity( p_intensity ),
    hindrance( 0.0f ),
    logFT( 0.0f ),
    forbiddenness( NoForbiddenness )
    //, revision( RadParticle::NoRevision )
{
}


void RadParticle::set( const ::rapidxml::xml_node<char> *node )
{
  //Note: assumes rapidxml::parse_no_string_terminators has NOT been used
  using ::rapidxml::internal::compare;
  typedef ::rapidxml::xml_attribute<char> Attribute;

  const std::string name( node->name(), node->name()+node->name_size() );
  if( !convert( name, type ) )
  {
    const string msg = "Failed converting '" + name + "' to ProductType";
    throw runtime_error( msg );
  }//if( !convert( name, type ) )

#if( ENABLE_SHORT_NAME )
  const bool shortname = (name.size() <= 2);
  
  const Attribute *energy_att        = shortname ? node->first_attribute("e",1) : node->first_attribute( "energy", 6 );
  const Attribute *intensity_att     = shortname ? node->first_attribute("i",1) : node->first_attribute( "intensity", 9 );
  const Attribute *hindrance_att     = shortname ? node->first_attribute("h",1) : node->first_attribute( "hindrance", 9 );
  const Attribute *forbiddenness_att = shortname ? node->first_attribute("f",1) : node->first_attribute( "forbiddenness", 13 );
  const Attribute *logFT_att         = shortname ? node->first_attribute( "lft", 3 ) : node->first_attribute( "logFT", 5 );
  //const Attribute *revision_att      = node->first_attribute( "revision", 8 );
#else
  const Attribute *energy_att        = node->first_attribute( "energy", 6 );
  const Attribute *intensity_att     = node->first_attribute( "intensity", 9 );
  const Attribute *hindrance_att     = node->first_attribute( "hindrance", 9 );
  const Attribute *forbiddenness_att = node->first_attribute( "forbiddenness", 13 );
  const Attribute *logFT_att         = node->first_attribute( "logFT", 5 );
  //const Attribute *revision_att      = node->first_attribute( "revision", 8 );
#endif

  if( energy_att ) energy = parse_float( energy_att->value() );
  else             energy = 0.0f;

  if( intensity_att ) intensity = parse_float( intensity_att->value() );
  else                intensity = 0.0f;

  if( hindrance_att ) hindrance = parse_float( hindrance_att->value() );
  else                hindrance = 0.0f;

  if( forbiddenness_att )
    forbiddenness = forbiddenness_fromstr( forbiddenness_att->value() );
  else forbiddenness = NoForbiddenness;

  if( logFT_att ) logFT = parse_float( logFT_att->value() );
  else logFT = 0.0f;

  //if( revision_att )
  //  revision = revision_fromstr( revision_att->value() );
  //else revision = RadParticle::NoRevision;
}//void set( ::rapidxml::xml_node<char> *node )



//Transition::Transition()
//{
//  parent = child = NULL;
//  mode = UndefinedDecay;
//  branchRatio = 0.0;
//}//default Transition constructor


Transition::Transition( const ::rapidxml::xml_node<char> *node,
                        const vector<const Nuclide *> &nuclides )
{
  set( node, nuclides );
}

  

void Transition::set( const ::rapidxml::xml_node<char> *node,
                      const vector<const Nuclide *> &nuclides )
{
  products.clear();

  //Note: assumes ::rapidxml::parse_no_string_terminators has NOT been used
  using ::rapidxml::internal::compare;
  typedef ::rapidxml::xml_attribute<char> Attribute;

  assert( compare( node->name(), node->name_size(), "transition", 10, true )
         || compare( node->name(), node->name_size(), "t", 1, true ) );

#if( ENABLE_SHORT_NAME )
  const bool shortnames = (node->name_size()==1);
  
  const Attribute *parent_att      = shortnames ? node->first_attribute("p",1) : node->first_attribute( "parent", 6 );
  const Attribute *child_att       = shortnames ? node->first_attribute("c",1) : node->first_attribute( "child", 5 );
  const Attribute *mode_att        = shortnames ? node->first_attribute("m",1) : node->first_attribute( "mode", 4 );
  const Attribute *branchRatio_att = shortnames ? node->first_attribute("br",2) : node->first_attribute( "branchRatio", 11 );
#else
  const Attribute *parent_att      = node->first_attribute( "parent", 6 );
  const Attribute *child_att       = node->first_attribute( "child", 5 );
  const Attribute *mode_att        = node->first_attribute( "mode", 4 );
  const Attribute *branchRatio_att = node->first_attribute( "branchRatio", 11 );
#endif
  
  if( parent_att )
  {
    const std::string parentstr = parent_att->value();
    vector<const Nuclide *>::const_iterator iter = find( nuclides, parentstr );
    if( (parentstr != "") && (iter != nuclides.end()) )
      parent = (*iter);
    else parent = NULL;
  }else parent = NULL;

  if( child_att )
  {
    const std::string childstr = child_att->value();
    vector<const Nuclide *>::const_iterator iter = find( nuclides, childstr );
    if( (childstr != "") && (iter != nuclides.end()) )
      child = (*iter);
    else child = NULL;
  }else child = NULL;


  if( mode_att )
    mode = decaymode_fromstr( mode_att->value() );
  else mode = UndefinedDecay;


  if( branchRatio_att ) branchRatio = parse_float( branchRatio_att->value() );
  else                  branchRatio = 0.0f;

  //In order to link coincidences correctly, we will need to loop over decay
  //  products twice since we're using a index based mecahnism.
  std::vector<RadParticle> new_particles;
  std::vector< std::pair<const char *,size_t> > new_particle_ids;
  std::vector<const ::rapidxml::xml_node<char> *> new_particle_nodes;
  
  for( const ::rapidxml::xml_node<char> *particle = node->first_node();
      particle;
      particle = particle->next_sibling() )
  {
    if( compare( particle->name(), particle->name_size(), "edit", 4, true )
        || compare( particle->name(), particle->name_size(), "insertion", 9, true ) )
      continue;

    try
    {
      const Attribute *revision_att = particle->first_attribute( "revision", 8 );
      if( revision_att
          && (revision_fromstr(revision_att->value())==DeletedRevision) )
          continue;
     
      new_particles.push_back( RadParticle( particle ) );
      
      const rapidxml::xml_attribute<char> *idattrib = particle->first_attribute("id");
      if( idattrib && idattrib->value_size() )
        new_particle_ids.push_back( std::make_pair( (const char *)idattrib->value(), idattrib->value_size()) );
      else
        new_particle_ids.push_back( std::make_pair( (const char *)0, size_t(0)) );
    
      new_particle_nodes.push_back( particle );
    }catch( std::exception &e )
    {
      cerr << "Caught: " << e.what()
//           << " on transition from "
//           << (parent ? parent->symbol : string("null"))
//           << " to "
//           << (child ? child->symbol : string("null"))
           << endl;
    }
  }//for( loop over decaysToChildren )

  assert( new_particles.size() == new_particle_ids.size() );
  assert( new_particles.size() == new_particle_nodes.size() );
  
  
  for( size_t i = 0; i < new_particle_nodes.size(); ++i )
  {
    RadParticle &particle = new_particles[i];
    
    const ::rapidxml::xml_node<char> *gamma_node = new_particle_nodes[i];
    
#if( ENABLE_SHORT_NAME )
    const ::rapidxml::xml_node<char> *coinc = shortnames ? gamma_node->first_node( "c", 1 ) : gamma_node->first_node( "coincidentGamma", 15 );
#else
    const ::rapidxml::xml_node<char> *coinc = gamma_node->first_node( "coincidentGamma", 15 );
#endif
    
    for( ; coinc; coinc = coinc->next_sibling( coinc->name(), coinc->name_size() ) )
    {
      const ::rapidxml::xml_attribute<char> *idattr = coinc->first_attribute("id",2);
      const char * const id_val = idattr ? idattr->value() : NULL;
      const size_t id_len = idattr ? idattr->value_size() : std::size_t(0);
      
#if( ENABLE_SHORT_NAME )
      const ::rapidxml::xml_attribute<char> *intensityattr = shortnames ? coinc->first_attribute("i",1)
      : coinc->first_attribute("intensity",9);
#else
      const ::rapidxml::xml_attribute<char> *intensityattr = coinc->first_attribute("intensity",9);
#endif
      const char * const intensity_val = intensityattr ? intensityattr->value() : NULL;
      const size_t intensity_len = intensityattr ? intensityattr->value_size() : std::size_t(0);
      
      if( !id_len || !intensity_len )
        continue;
      
      bool found_partner = false;
      const float intensity = parse_float( intensity_val );

#if( ENABLE_SHORT_NAME )
      // Here we will optimistically assume the "id" value is a string representing an integer
      //  that gives the index of the matching particle - this assumes the input XML file was
      //  made for this - which `minimize_xml_file` will do with the '--shrink-coinc' option.
      //  If this assumption doesnt pan-out, we will instead do the full search, so not that
      //  much will be lost.
      //
      //  Including the check for `shortnames`, either runtime or compiletime isnt really necassary,
      //    just currently not 
      if( shortnames && (id_len <= 3) )
      {
        unsigned short int trial_index = (id_val[id_len - 1] - '0');
        if( id_len >= 2 )
          trial_index += 10*(id_val[id_len - 2] - '0');
        if( id_len >= 3 )
          trial_index += 100*(id_val[id_len - 3] - '0');
        
        if( trial_index < new_particle_ids.size() )
        {
          const char * const trial_val = new_particle_ids[trial_index].first;
          const size_t trial_len = new_particle_ids[trial_index].second;
          
          if( rapidxml::internal::compare( id_val, id_len, trial_val, trial_len, true) )
          {
            particle.coincidences.push_back( std::make_pair(trial_index,intensity) );
            found_partner = true;
          }
        }//if( trial_index < new_particle_ids.size() )
      }//if( shortnames && (id_len <= 3) )
#endif //#if( ENABLE_SHORT_NAME )
      
      if( !found_partner )
      {
        for( unsigned short int j = 0; j < new_particle_ids.size(); ++j )
        {
          const char * const trial_val = new_particle_ids[j].first;
          const size_t trial_len = new_particle_ids[j].second;
          
          if( rapidxml::internal::compare( id_val, id_len, trial_val, trial_len, true) )
          {
            particle.coincidences.push_back( std::make_pair(j,intensity) );
            found_partner = true;
            break;
          }
        }
      }//if( !found_partner )
      
      if( !found_partner )
      {
      // As of 20221027, there are about 250 missed matches... we'll not print out for the moment.
      //  const char * const parent = (parent_att ? parent_att->value() : "null");
      //  const rapidxml::xml_attribute<char> *energy_attrib = gamma_node ? gamma_node->first_attribute("energy") : nullptr;
      //  const char * const energy = ((energy_attrib && energy_attrib->value()) ? energy_attrib->value() : "null");
      //  cerr << "SandiaDecay: Failed to find coincident gamma for " << parent
      //       << " with id=\"" << uuid << "\"" << " for gamma energy " << energy << " keV" << endl;
      }//if( !found_partner )
    }//for( loop over <coincidentGamma> )
  }//for( size_t i = 0; i < new_particle_nodes.size(); ++i )
  
  products.swap( new_particles );
}//void set( ::rapidxml::xml_node<char> *node )


bool Nuclide::lessThanForOrdering( const Nuclide *lhs, const Nuclide *rhs )
{
  if( !lhs || !rhs )
    return lhs < rhs;
  
  if( (lhs->massNumber == rhs->massNumber)
     && (lhs->atomicNumber == rhs->atomicNumber)
     && (lhs->isomerNumber == rhs->isomerNumber) )
  {
    return false;
  }

  if( lhs->massNumber != rhs->massNumber )
    return (lhs->massNumber < rhs->massNumber);
  
  if( lhs->atomicNumber == rhs->atomicNumber )
    return (lhs->isomerNumber < rhs->isomerNumber);

  return lhs->atomicNumber < rhs->atomicNumber;
}


bool Nuclide::greaterThanForOrdering( const Nuclide *lhs, const Nuclide *rhs )
{
  return lessThanForOrdering( rhs, lhs );
}


bool Nuclide::lessThanByDecay( const Nuclide *lhs, const Nuclide *rhs )
{
  if( !lhs || !rhs )
    return lhs < rhs;
  
  if( (lhs->massNumber == rhs->massNumber)
     && (lhs->atomicNumber == rhs->atomicNumber)
     && (lhs->isomerNumber == rhs->isomerNumber) )
  {
    return false;
  }
    
  //is 'this' a child of 'rhs' ? If not, is 'this' lighter than 'rhs
  if( lhs->massNumber != rhs->massNumber )
    return (lhs->massNumber < rhs->massNumber);
  
  if( lhs->atomicNumber == rhs->atomicNumber )
    return (lhs->isomerNumber < rhs->isomerNumber);

  // If the atomic numbers differ more than 7, then we know which way the decay goes (I tested
  //  commenting this particular test out will give identical results, just take more cpu).
  const int an_diff = ((lhs->atomicNumber > rhs->atomicNumber)
                        ? (lhs->atomicNumber - rhs->atomicNumber) : (rhs->atomicNumber - lhs->atomicNumber));
  if( an_diff > 7 )
    return (lhs->atomicNumber < rhs->atomicNumber);
  
  // This next test was verified to give identical results with or without it, but saves CPU with
  const float am_diff = fabs(lhs->atomicMass - rhs->atomicMass);
  if( (am_diff > 1.0f) && (an_diff > 4) )
    return lhs->atomicNumber < rhs->atomicNumber;
  
  // \TODO: We could do a few more tests to avoid calling into Nuclide::branchRatioToDecendant,
  //    but this is decent for now
  assert( lhs->massNumber == rhs->massNumber );
  assert( (an_diff > 0) && (an_diff < 8) );
  assert( (am_diff <= 1.0f) || (an_diff <= 4) );
  
  const float lhsToRhsBr = lhs->branchRatioToDecendant( rhs );
  const float rhsToLhsBr = rhs->branchRatioToDecendant( lhs );

  if( lhsToRhsBr == rhsToLhsBr ) //These nuclides dont decay into each other.
    return (lhs->atomicNumber < rhs->atomicNumber);
  
  return (lhsToRhsBr < rhsToLhsBr);
}//bool lessThanByDecay( const Nuclide *lhs, const Nuclide *rhs )


bool Nuclide::greaterThanByDecay( const Nuclide *lhs, const Nuclide *rhs )
{
  return lessThanByDecay( rhs, lhs );
}

bool  Nuclide::operator==( const Nuclide &rhs ) const
{
  return ((atomicNumber==rhs.atomicNumber) && (massNumber==rhs.massNumber) && (isomerNumber==rhs.isomerNumber));
}

bool  Nuclide::operator!=( const Nuclide &rhs ) const
{
  return ((atomicNumber!=rhs.atomicNumber) || (massNumber!=rhs.massNumber) || (isomerNumber!=rhs.isomerNumber));
}

template <typename T>
size_t nelements( const T &container )
{
  return container.size();
  //return container.capacity();
}
  
size_t Nuclide::memsize() const
{
  size_t size = sizeof(Nuclide);
  size += nelements(symbol)*sizeof(symbol[0]);
  size += nelements(decaysToChildren)*sizeof(decaysToChildren[0]);
  size += nelements(decaysFromParents)*sizeof(decaysFromParents[0]);

  return size;
}//size_t memsize() const


size_t RadParticle::memsize() const
{
  return sizeof(RadParticle) + nelements(coincidences)*sizeof(std::pair<unsigned short int,float>);
}//size_t memsize() const
  
  
size_t Transition::memsize() const
{
  size_t size = sizeof(Transition) + nelements(products)*sizeof(RadParticle);
  
  for( size_t i = 0; i < products.size(); ++i )
    size += (products[i].memsize()-sizeof(products[i]));
  
  return size;
}
  
size_t Element::memsize() const
{
  size_t size = sizeof(Element);
  size += nelements(symbol)*sizeof(symbol[0]);
  size += nelements(name)*sizeof(name[0]);
  size += nelements(isotopes)*sizeof(isotopes[0]);
  size += nelements(xrays)*sizeof(xrays[0]);
  
  return size;
}

size_t SandiaDecayDataBase::memsize() const
{
  size_t size = sizeof(SandiaDecayDataBase);
  
  cout << "m_nuclides.size()=" << m_nuclides.size() << endl;
  cout << "m_elements.size()=" << m_elements.size() << endl;
  cout << "m_transitionStore.size()=" << m_transitionStore.size() << endl;
  
  size_t pre = size;
  size += nelements(m_nuclides)*sizeof(m_nuclides[0]);
  for( size_t i = 0; i < m_nuclideStore.size(); ++i )
    size += (m_nuclideStore[i].memsize()-sizeof(m_nuclideStore[i]));
  size += nelements(m_nuclideStore)*sizeof(m_nuclideStore[0]);
  size_t post = size;
  
  cout << "Nuclides contrib " << post-pre << endl;
  pre = size;
  size += nelements(m_elements)*sizeof(m_elements[0]);
  for( size_t i = 0; i < m_elements.size(); ++i )
    size += (m_elements[i]->memsize()-sizeof(m_elements[i]));
  size += nelements(m_elementStore)*sizeof(m_elementStore[0]);
  post = size;
  
  cout << "Elements contrib " << post-pre << endl;
  pre = size;
  for( size_t i = 0; i < m_transitionStore.size(); ++i )
    size += (m_transitionStore[i].memsize()-sizeof(m_transitionStore[i]));
  size += nelements(m_transitionStore)*sizeof(m_transitionStore[0]);
  post = size;
  
  cout << "Trans contrib " << post-pre << endl;
  
  return size;
}//size_t memsize() const
  
  
size_t Nuclide::numDecays() const
{
  return decaysToChildren.size();
}

bool Nuclide::isStable() const
{
  return IsInf(halfLife);
}
  
double Nuclide::decayConstant() const
{
  //0.5 = exp( -decay_const*halfLife )
  //IsInf() dosnt seem to be available in Microsoft VC++
  if( !(halfLife <= DBL_MAX && halfLife >= -DBL_MAX) || (halfLife<=0.0) ) //is this check really neaded?
    return 0.0;

  return 0.693147180559945286 / halfLife;
}//double decayConstant()

double Nuclide::partialDecayConstant( const size_t transition_num ) const
{
  //0.5 = exp( -(decay_const_1 + decay_const_2 + ...) * halfLife )
  const double total_decay_constant = decayConstant();
  return total_decay_constant * decaysToChildren.at(transition_num)->branchRatio;
}//double partialDecayConstant( const size_t transition_num )

float Nuclide::branchingRatio( const size_t transition_num ) const
{
  return decaysToChildren.at( transition_num )->branchRatio;
}//double branchingRatio( const size_t transition_num ) const


const Nuclide *Nuclide::child( const size_t transition_num ) const
{
  return decaysToChildren.at( transition_num )->child;
}



CalcFloatType Nuclide::numAtomsToActivity( const CalcFloatType num_atoms ) const
{
  return num_atoms * decayConstant();
}//double numAtomsToActivity( const double num_atoms ) const

CalcFloatType Nuclide::activityToNumAtoms( const CalcFloatType activity ) const
{
  return activity / decayConstant();
}//CalcFloatType activityToNumAtoms( const CalcFloatType activity ) const


// XXX - Barely tested
// XXX - If there is a cycle: Nuclide_1 --> Nuclide_2 --> Nuclide_1, then
//       this will cause an infinite recurtion
float Nuclide::branchRatioToDecendant( const Nuclide *descendant ) const
{
  if( this == descendant )
    return 1.0f;

  if( massNumber < descendant->massNumber )
    return 0.0f;

  float br_sum = 0.0;
  for( size_t i = 0; i < decaysToChildren.size(); ++i )
  {
    const Nuclide *child = decaysToChildren[i]->child;
    if( child )
    {
      const float br = decaysToChildren[i]->branchRatio;
      br_sum += br * child->branchRatioToDecendant( descendant );
    }//if( child )
  }//for( loop over decay paths )

  return br_sum;
}//CalcFloatType branchRatioToDecendant( const Nuclide *descendant ) const


// XXX - barels tested
// XXX - If there is a cylcle: Nuclide_1 --> Nuclide_2 --> Nuclide_1, then
//       this will cause an infinite recurtion
float Nuclide::branchRatioFromForebear( const Nuclide *ancestor ) const
{
  //I think the below would work, but
  // return ancestor->branchRatioToDecendant( this );

  if( this == ancestor )
    return 1.0f;

  if( massNumber > ancestor->massNumber )
    return 0.0f;

  float br_sum = 0.0;
  for( size_t i = 0; i < decaysFromParents.size(); ++i )
  {
    const Nuclide *parent = decaysFromParents[i]->parent;
    const float br = decaysFromParents[i]->branchRatio;
    br_sum += br * parent->branchRatioFromForebear( ancestor );
  }//for( loop over decay paths )

  return br_sum;
}//CalcFloatType branchRatioFromForebear( const Nuclide *ancestor ) const



vector<const Nuclide *> Nuclide::descendants() const
{
  vector<const Nuclide *> children( 1, this );

  for( size_t decN = 0; decN < decaysToChildren.size(); ++decN )
  {
    const Transition * const transition = decaysToChildren[decN];
    const Nuclide * const child = transition->child;

    if( !child )
      continue;

    const vector<const Nuclide *> results = child->descendants();

    for( size_t resN = 0; resN < results.size(); ++resN )
    {
      const Nuclide * const result = results[resN];
      const vector<const Nuclide *>::iterator begin = children.begin();
      const vector<const Nuclide *>::iterator end = children.end();
      vector<const Nuclide *>::iterator pos;
      pos = lower_bound( begin, end, result, &Nuclide::greaterThanForOrdering );

      if( (pos==end) || ((*pos)!=result) )
        children.insert( pos, result );
    }//for( size_t resN = 0; resN < results.size(); ++resN )
  }//for( size_t decN = 0; decN < decaysToChildren.size(); ++decN )


  return children;
}//std::vector<const Nuclide *> descendants() const


std::vector<const Nuclide *> Nuclide::forebearers() const
{
  std::vector<const Nuclide *> parents( 1, this );

  //
  for( size_t decN = 0; decN < decaysFromParents.size(); ++decN )
  {
    const Transition * const transition = decaysFromParents[decN];
    const Nuclide * const parent = transition->parent;
    const vector<const Nuclide *> results = parent->forebearers();

    for( size_t resN = 0; resN < results.size(); ++resN )
    {
      const Nuclide * const result = results[resN];
      const vector<const Nuclide *>::iterator begin = parents.begin();
      const vector<const Nuclide *>::iterator end = parents.end();

      vector<const Nuclide *>::iterator pos;
      pos = lower_bound( begin, end, result, &Nuclide::greaterThanForOrdering );

      if( (pos==end) || ((*pos)!=result) )
        parents.insert( pos, result );
    }//for( size_t resN = 0; resN < results.size(); ++resN )
  }//for( size_t decN = 0; decN < decaysToChildren.size(); ++decN )

  return parents;
}//std::vector<const Nuclide *> forebearers() const



double Nuclide::secularEquilibriumHalfLife() const
{
  //20111012 Verified gives correct correct for U235, U238, Pu240, Pu242, Th232
  if( IsInf(halfLife) )
    return numeric_limits<double>::infinity();

  double secHalflife = 0.0;
  for( size_t i = 0; i < decaysToChildren.size(); ++i )
  {
    const Nuclide *child = decaysToChildren[i]->child;
    if( child && (child != this) )
    {
      if( !IsInf(child->halfLife) )
        secHalflife = max( secHalflife,
                         max( child->halfLife,
                              child->secularEquilibriumHalfLife() ) );
    }
  }//for( size_t i = 0; i < decaysToChildren.size(); ++i )

  return secHalflife;
}//double Nuclide::secularEquilibriumHalfLife() const


bool Nuclide::canObtainSecularEquilibrium() const
{
  return (secularEquilibriumHalfLife() < halfLife);
}//bool canObtainSecularEquilibrium() const


double Nuclide::promptEquilibriumHalfLife() const
{
  //20111012 Verified gives correct correct for U235, U238, Pu240, Pu242, Th232

  //XXX
  //  shouldnt this function just return the max 1/2 life of the child elements?
  //  Right now I'll leave below implementation, since this implinetation roughly
  //  follows some notes I found from by a fellow sandian, but I dont necassarily
  //  trust.
  if( IsInf(halfLife) )
    return 0.0;

  double promtHalflife = 0.0;

  for( size_t i = 0; i < decaysToChildren.size(); ++i )
  {
    const Nuclide *child = decaysToChildren[i]->child;
    if( child && (child != this) )
    {
      if( !IsInf(child->halfLife)
          && child->halfLife < this->halfLife )
        promtHalflife = max( promtHalflife,
                         max( child->halfLife,
                              child->promptEquilibriumHalfLife() ) );
    }
  }//for( size_t i = 0; i < decaysToChildren.size(); ++i )

  return promtHalflife;
}//double Nuclide::promptEquilibriumHalfLife() const


bool Nuclide::canObtainPromptEquilibrium() const
{
  return (promptEquilibriumHalfLife() > DBL_MIN);
}//bool Nuclide::canObtainPromptEquilibrium() const


double Nuclide::atomsPerGram() const
{
  //1 mole of C12 weighs 12 grams
  const double mole = 6.02214179E+23;
  return mole/atomicMass;
}//double Nuclide::atomsPerGram() const


double Nuclide::activityPerGram() const
{
  const double num_atoms_in_gram = atomsPerGram();
  return numAtomsToActivity( num_atoms_in_gram );
}//double Nuclide::activityPerGram() const


bool Nuclide::decaysToStableChildren() const
{
  for( size_t i = 0; i < decaysToChildren.size(); ++i )
  {
    const Transition *trans = decaysToChildren[i];
    if( trans->child && !IsInf(trans->child->halfLife) )
      return false;
  }//for( size_t i = 0; i < decaysToChildren.size(); ++i )

  return true;
}//bool decaysToStableChildren() const


Nuclide::Nuclide( const ::rapidxml::xml_node<char> *node )
{
  set( node );
}

//Nuclide::Nuclide()
//{
//};

Nuclide::~Nuclide()
{
}//~Nuclide()



void Nuclide::set( const ::rapidxml::xml_node<char> *node )
{
  //Note: assumes ::rapidxml::parse_no_string_terminators has NOT been used
  using ::rapidxml::internal::compare;
  typedef ::rapidxml::xml_attribute<char> Attribute;

  assert( compare( node->name(), node->name_size(), "nuclide", 7, true )
         || compare( node->name(), node->name_size(), "n", 1, true ) );

  decaysToChildren.clear();

  const Attribute *symbol_att, *atomicNumber_att, *massNumber_att;
  const Attribute *isomerNumber_att, *atomicMass_att, *halfLife_att;

#if( ENABLE_SHORT_NAME )
  const bool shortnames = (node->name_size() == 1);
  
  symbol_att       = shortnames ? node->first_attribute( "s", 1 ) : node->first_attribute( "symbol", 6 );
  atomicNumber_att = shortnames ? node->first_attribute( "an", 2 ) : node->first_attribute( "atomicNumber", 12 );
  massNumber_att   = shortnames ? node->first_attribute( "mn", 2 ) : node->first_attribute( "massNumber", 10 );
  isomerNumber_att = shortnames ? node->first_attribute( "iso", 3 ) : node->first_attribute( "isomerNumber", 12 );
  atomicMass_att   = shortnames ? node->first_attribute( "am", 2 ) : node->first_attribute( "atomicMass", 10 );
  halfLife_att     = shortnames ? node->first_attribute( "hl", 2 ) : node->first_attribute( "halfLife", 8 );
#else
  symbol_att       = node->first_attribute( "symbol", 6 );
  atomicNumber_att = node->first_attribute( "atomicNumber", 12 );
  massNumber_att   = node->first_attribute( "massNumber", 10 );
  isomerNumber_att = node->first_attribute( "isomerNumber", 12 );
  atomicMass_att   = node->first_attribute( "atomicMass", 10 );
  halfLife_att     = node->first_attribute( "halfLife", 8 );
#endif
  
  if( symbol_att ) symbol = symbol_att->value();
  else             symbol = "";

  if( atomicNumber_att ) atomicNumber = parse_short_int( atomicNumber_att->value() );
  else                   atomicNumber = 0;

  if( massNumber_att )   massNumber = parse_short_int( massNumber_att->value() );
  else                   massNumber = 0;

  if( isomerNumber_att ) isomerNumber = parse_short_int( isomerNumber_att->value() );
  else                   isomerNumber = 0;

  if( atomicMass_att ) atomicMass = parse_float( atomicMass_att->value() );
  else                 atomicMass = 0.0f;

  
  if( halfLife_att )
  {
    if( sscanf( halfLife_att->value(), "%lf", &halfLife ) != 1 )
    {
      if( !compare( halfLife_att->value(), halfLife_att->value_size(), "INF", 3, true )  )
        cerr << "Non-INF, non-numeric halfLife: " << halfLife_att->value() << endl;
      halfLife = numeric_limits<double>::infinity();
    }//if( ss.fail() )
  }else
  {
    halfLife = numeric_limits<double>::infinity();
  }
}//void set( ::rapidxml::xml_node<char> *node )




Element::Element( ::rapidxml::xml_node<char> *node,
                  const vector<const Nuclide *> &nuclides )
{
  set( node, nuclides );
}


void Element::set( ::rapidxml::xml_node<char> *node,
                   const vector<const Nuclide *> &nuclides )
{
  //Note: assumes ::rapidxml::parse_no_string_terminators has NOT been used
  using ::rapidxml::internal::compare;
  typedef ::rapidxml::xml_attribute<char> Attribute;

  assert( compare( node->name(), node->name_size(), "element", 7, true )
         || compare( node->name(), node->name_size(), "el", 2, true ) );

  isotopes.clear();

#if( ENABLE_SHORT_NAME )
  const bool shortname = (node->name_size()==2);
  Attribute *symbol_att       = shortname ? node->first_attribute("s",1) : node->first_attribute("symbol",6);
  Attribute *name_att         = shortname ? node->first_attribute("n",1) : node->first_attribute("name",4);
  Attribute *atomicNumber_att = shortname ? node->first_attribute("an",2) : node->first_attribute("atomicNumber",12);
#else
  Attribute *symbol_att       = node->first_attribute("symbol",6);
  Attribute *name_att         = node->first_attribute("name",4);
  Attribute *atomicNumber_att = node->first_attribute("atomicNumber",12);
#endif

  if( symbol_att ) symbol = symbol_att->value();
  else             symbol = "";

  if( name_att ) name = name_att->value();
  else           name = "";

  if( atomicNumber_att ) atomicNumber = parse_short_int( atomicNumber_att->value() );
  else                   atomicNumber = 0;

#if( ENABLE_SHORT_NAME )
  for( ::rapidxml::xml_node<char> *isotope = node->first_node( (shortname ? "iso" : "isotope") );
      isotope;
      isotope = isotope->next_sibling( isotope->name(), isotope->name_size() ) )
#else
    for( ::rapidxml::xml_node<char> *isotope = node->first_node("isotope",7);
        isotope;
        isotope = isotope->next_sibling("isotope",7) )
#endif
  {
#if( ENABLE_SHORT_NAME )
    Attribute *symbol_att = shortname ? isotope->first_attribute("s",1) : isotope->first_attribute( "symbol", 6 );
    Attribute *abundance_att = shortname ? isotope->first_attribute("a", 1 ) : isotope->first_attribute( "abundance", 9 );
#else
    Attribute *symbol_att = isotope->first_attribute( "symbol", 6 );
    Attribute *abundance_att = isotope->first_attribute( "abundance", 9 );
#endif

    if( !symbol_att || !abundance_att )
      throw runtime_error( "<element>\n        <isotope> node ill formed" );
    
    NuclideAbundancePair iso;
    const string sym = symbol_att->value();
    vector<const Nuclide *>::const_iterator pos = find( nuclides, sym );
    if( pos == nuclides.end() )
    {
      const string msg = "Could not find the symbol '"
                          + sym + "' in <element>-><isotope> node";
      throw runtime_error( msg );
    }//if( pos == nuclides.end() )

    iso.nuclide = (*pos);
    iso.abundance = parse_double( abundance_att->value() );

    isotopes.push_back( iso );
  }//for( loop over isotopes )

#if( ENABLE_SHORT_NAME )
  for( ::rapidxml::xml_node<char> *xray = node->first_node( (shortname ? "x" : "xray") );
       xray;
       xray = xray->next_sibling( xray->name(), xray->name_size() ) )
#else
    for( ::rapidxml::xml_node<char> *xray = node->first_node("xray",4);
        xray;
        xray = xray->next_sibling("xray",4) )
#endif
  {
#if( ENABLE_SHORT_NAME )
    Attribute *energy_att = shortname ? xray->first_attribute("e",1) : xray->first_attribute( "energy", 6 );
    Attribute *intensity_att = shortname ? xray->first_attribute("i",1) : xray->first_attribute( "relintensity", 12 );
#else
    Attribute *energy_att = xray->first_attribute( "energy", 6 );
    Attribute *intensity_att = xray->first_attribute( "relintensity", 12 );
#endif
    if( energy_att && intensity_att )
    {
      xrays.push_back( EnergyIntensityPair( parse_double(energy_att->value()), parse_double(intensity_att->value()) ) );
    }
  }
}//void Element::set(...)


double Element::atomicMass() const
{
  double atomicMass = 0.0;
  for( size_t i = 0; i < isotopes.size(); ++i )
  {
    const NuclideAbundancePair &p = isotopes[i];
    atomicMass += p.abundance * p.nuclide->atomicMass;
  }//for( loop over isotopes )


  //If the isotope is not natrally occuring, then atomicMass==0.0, so lets 
  //  supliment this.  Note that I got these atomic masses from CERNs ROOT
  //  using the code:
  // TGeoElementTable *t = new TGeoElementTable();
  // t->BuildDefaultElements()
  // for( int i = 1; i < 112; ++i){ cout << t->GetElement(i)->A() << ", ";}
  
  static const double atomic_masses[] = 
  { 
    0.0,  1.00794, 4.0026, 6.941, 9.01218, 10.811, 12.0107, 14.0067, 15.9994, 
    18.9984, 20.1797, 22.9898, 24.305, 26.9815, 28.0855, 30.9738, 32.066, 
    35.4527, 39.948, 39.0983, 40.078, 44.9559, 47.867, 50.9415, 51.9961, 54.938, 
    55.845, 58.9332, 58.6934, 63.546, 65.39, 69.723, 72.61, 74.9216, 78.96, 
    79.904, 83.8, 85.4678, 87.62, 88.9059, 91.224, 92.9064, 95.94, 98, 
    101.07, 102.906, 106.42, 107.868, 112.411, 114.818, 118.71, 121.76, 
    127.6, 126.904, 131.29, 132.905, 137.327, 138.905, 140.116, 140.908, 144.24, 
    145, 150.36, 151.964, 157.25, 158.925, 162.5, 164.93, 167.26, 168.934, 
    173.04, 174.967, 178.49, 180.948, 183.84, 186.207, 190.23, 192.217, 
    195.078, 196.967, 200.59, 204.383, 207.2, 208.98, 209, 210, 222, 223, 226, 
    227, 232.038, 231.036, 238.029, 237, 244, 243, 247, 247, 251, 252, 257, 
    258, 259, 262, 261, 262, 263, 262, 265, 266, 269, 272 
  };//static const float atomic_masses[] = {...}

  if( atomicMass<1.0 )
    atomicMass = static_cast<float>( atomic_masses[atomicNumber] );

/*
  if( atomicMass<1.0 )
  {
  //XXX - isotopes is actually empty
    double maxHalfLife = 0.0;
    for( size_t i = 0; i < isotopes.size(); ++i )
    {
      const NuclideAbundancePair &p = isotopes[i];
      if( p.nuclide->halfLife > maxHalfLife )
      {
        maxHalfLife = p.nuclide->halfLife;
        atomicMass = p.nuclide->atomicMass;
      }
    }//for( loop over isotopes )
  }//if( atomicMass<1.0 )
*/
  
  return atomicMass;
}//double atomicMass() const


bool Element::lessThan( const Element *lhs, const Element *rhs )
{
  if( !lhs || !rhs )
    return false;

  return (lhs->atomicNumber < rhs->atomicNumber);
}//bool lessThan( const Element *lhs, const Element *rhs )


bool Element::lessThanForAtomicNum( const Element *lhs, const int atomicNum )
{
  if( !lhs )
    return false;

  return (lhs->atomicNumber < atomicNum);
}//bool lessThanForAtomicNum( const Element *lhs, const int atomicNum )


NuclideMixture::NuclideMixture()
{
}

NuclideMixture::~NuclideMixture()
{
}


void NuclideMixture::clear()
{
  m_originalNuclides.clear();
  m_decayedToNuclides.clear();
}//void NuclideMixture::clear()

void NuclideMixture::addNuclideByAbundance( const Nuclide *nuclide, CalcFloatType num_initial_atom )
{
  addNuclide( NuclideNumAtomsPair( nuclide, num_initial_atom )  );
}


void NuclideMixture::addNuclideByActivity( const Nuclide *nuclide, CalcFloatType activity )
{
  const CalcFloatType num_initial_atom = nuclide->activityToNumAtoms( activity );
  addNuclide( NuclideNumAtomsPair( nuclide, num_initial_atom ) );
}


void NuclideMixture::addAgedNuclideByActivity( const Nuclide *nuclide,
                                              CalcFloatType activity, double age )
{
  NuclideMixture ager;
  ager.addNuclideByActivity( nuclide, activity );
  const std::vector<NuclideActivityPair> aged_activities = ager.activity( age );

  CalcFloatType age_sf = 1.0;
  for( size_t i = 0; i < aged_activities.size(); ++i )
  {
    const NuclideActivityPair &red = aged_activities[i];
    if( red.nuclide == nuclide )
    {
      age_sf = activity / red.activity;
      i = aged_activities.size();
    }
  }//for( size_t i = 0; i < aged_activities.size(); ++i )

  for( size_t i = 0; i < aged_activities.size(); ++i )
  {
    const NuclideActivityPair &red = aged_activities[i];
    addNuclideByActivity( red.nuclide, age_sf * red.activity );
  }
}//void addAgedNuclideByActivity(...)

  
void NuclideMixture::addAgedNuclideByNumAtoms( const Nuclide *nuclide,
                                              CalcFloatType number_atoms,
                                              double age_in_seconds )
{
  if( nuclide->isStable() )
  {
    addNuclideByAbundance( nuclide, number_atoms );
    return;
  }
  
  NuclideMixture ager;
  // We will use 1 initial atom, so we arent sensitive so much to value of `number_atoms`
  ager.addNuclideByAbundance( nuclide, 1.0 );
  const std::vector<NuclideNumAtomsPair> aged_atoms = ager.numAtoms( age_in_seconds );
  
  CalcFloatType age_sf = 1.0;
  for( size_t i = 0; i < aged_atoms.size(); ++i )
  {
    const NuclideNumAtomsPair &red = aged_atoms[i];
    if( red.nuclide == nuclide )
    {
      //Lets check for at least some numerical accuracy:
      //  epsilon: the difference between 1.0 and the next representable value of the given floating-point type
      //  min: returns the smallest finite, normalized, value of the given type
      // 100: arbitrary
      // This test seems to trigger for age at around 47 half-lives of  parent nuclide
      if( (red.numAtoms < 100.0*numeric_limits<CalcFloatType>::epsilon())
         || (red.numAtoms < 100.0*numeric_limits<CalcFloatType>::min()) )
      {
        stringstream msg;
        msg << "Call to NuclideMixture::addAgedNuclideByNumAtoms(" << nuclide->symbol
        << ", " << number_atoms << ", " << age_in_seconds << ")"
        << " results in too large of numerical imprecision.";
        
        throw runtime_error( msg.str() );
      }
      
      age_sf = number_atoms / red.numAtoms;
      i = aged_atoms.size(); //stop this loop
    }
  }//for( size_t i = 0; i < aged_activities.size(); ++i )


  for( size_t i = 0; i < aged_atoms.size(); ++i )
  {
    const NuclideNumAtomsPair &red = aged_atoms[i];
    addNuclideByAbundance( red.nuclide, age_sf * red.numAtoms );
  }
}//void addAgedNuclideByNumAtoms(...)
  

void NuclideMixture::addNuclide( const NuclideNumAtomsPair &nuclide )
{
  m_decayedToNuclides.clear();
  m_originalNuclides.push_back( nuclide );
}


void NuclideMixture::addNuclide( const NuclideActivityPair &nucidePair )
{
  const Nuclide *nuclide = nucidePair.nuclide;
  const CalcFloatType num_atoms = nuclide->activityToNumAtoms( nucidePair.activity );
  addNuclide( NuclideNumAtomsPair( nuclide, num_atoms ) );
}



bool NuclideMixture::addNuclideInSecularEquilibrium( const Nuclide *parent,
                                                    CalcFloatType parent_activity )
{
  const double secEqHL = parent->secularEquilibriumHalfLife();
  if( (secEqHL >= parent->halfLife) || (secEqHL<=0.0)  )
  {
    cerr << "NuclideMixture::addNuclideInSecularEquilibrium( " << parent->symbol
         << ", " << static_cast<double>(parent_activity/becquerel) << "bq ): Nuclide "
         << parent->symbol << " can not reach secular equilibrium! I am "
         << "cowardly refusing to add it to the NuclideMixture." << endl;
    return false;
  }//if( (secEqHL >= parent->halfLife) || (secEqHL<=0.0)  )

#ifdef ALLOW_TRANSITION_MODIFICATION
  const vector<Transition *> &transitions = parent->decaysToChildren;
#else
  const vector<const Transition *> &transitions = parent->decaysToChildren;
#endif
  
  addNuclideByActivity( parent, parent_activity );

  for( size_t trans = 0; trans < transitions.size(); ++trans )
  {
    const Nuclide *child = transitions[trans]->child;
    const float branchRatio = transitions[trans]->branchRatio;

    if( child && (child!=parent) && !IsInf(child->halfLife))
      addNuclideInSecularEquilibrium( child, branchRatio*parent_activity );
  }//for( size_t trans = 0; trans < transitions.size(); ++trans )
  
  return true;
}//void NuclideMixture::addNuclideInSecularEquilibrium(...)


void NuclideMixture::addNuclideInPromptEquilibrium( const Nuclide *parent,
                                                   CalcFloatType activity )
{
  if( IsInf(parent->halfLife) )
    return;

  addNuclideByActivity( parent, activity );

  for( size_t i = 0; i < parent->decaysToChildren.size(); ++i )
  {
    const Transition *trans = parent->decaysToChildren[i];
    const Nuclide *child = trans->child;
    if( child && (child->halfLife < parent->halfLife) )
      addNuclideInPromptEquilibrium( child, trans->branchRatio*activity );
  }//for( size_t i = 0; i < decaysToChildren.size(); ++i )
}//void addNuclideInPromptEquilibrium(...)


int NuclideMixture::numSolutionNuclides() const
{
  if( m_decayedToNuclides.empty() )
    performTimeEvolution();
  return static_cast<int>( m_decayedToNuclides.size() );
}


CalcFloatType NuclideMixture::activity( double time_in_seconds, const Nuclide *nuclide )    const
{
  return activity( time_in_seconds, internalIndexNumber( nuclide ) );
}

CalcFloatType NuclideMixture::activity( double time_in_seconds, const std::string &symbol ) const
{
  return activity( time_in_seconds, internalIndexNumber( symbol ) );
}

CalcFloatType NuclideMixture::activity( double time_in_seconds, int z, int atomic_mass, int iso )    const
{
  return activity( time_in_seconds, internalIndexNumber( z, atomic_mass, iso ) );
}

CalcFloatType NuclideMixture::activity( double time_in_seconds, int index ) const
{
  if( m_decayedToNuclides.empty() )
    performTimeEvolution();

  const int n_nuclides = static_cast<int>( m_decayedToNuclides.size() );
  if( (index < 0) || (index >= n_nuclides) )
    throw std::runtime_error( "NuclideMixture::activity(...): hecka ish" );

  return m_decayedToNuclides[index].activity( time_in_seconds );
}//CalcFloatType activity( double time_in_seconds, int internal_index_number ) const


CalcFloatType NuclideMixture::totalActivity( double time ) const
{
  if( m_decayedToNuclides.empty() )
    performTimeEvolution();

  SandiaDecay::CalcFloatType activity = 0.0;
  for( size_t i = 0; i < m_decayedToNuclides.size(); ++i )
    activity += m_decayedToNuclides[i].activity( time );

  return static_cast<CalcFloatType>(activity);
}//CalcFloatType NuclideMixture::totalActivity( double time ) const


CalcFloatType NuclideMixture::totalMassInGrams( double time ) const
{
  if( m_decayedToNuclides.empty() )
    performTimeEvolution();

  SandiaDecay::CalcFloatType mass_amu = 0.0;
  for( size_t i = 0; i < m_decayedToNuclides.size(); ++i )
  {
    const NuclideTimeEvolution &evo = m_decayedToNuclides[i];
    const Nuclide *nuc = evo.nuclide;
    mass_amu += evo.numAtoms( time ) * nuc->atomicMass;
  }//for( loop over m_decayedToNuclides )

  const SandiaDecay::CalcFloatType mole = 6.02214179E+23;  //AMU/gram
  return static_cast<CalcFloatType>( mass_amu / mole );
}//CalcFloatType totalMassInGrams( double time )


CalcFloatType NuclideMixture::numAtoms( double time_in_seconds, const Nuclide *nuclide )    const
{
  return numAtoms( time_in_seconds, internalIndexNumber( nuclide ) );
}


CalcFloatType NuclideMixture::numAtoms( double time_in_seconds, const std::string &symbol ) const
{
  return numAtoms( time_in_seconds, internalIndexNumber( symbol ) );
}


CalcFloatType NuclideMixture::numAtoms( double time_in_seconds, int z, int atomic_mass, int iso )    const
{
  return numAtoms( time_in_seconds, internalIndexNumber( z, atomic_mass, iso ) );
}//double numAtoms( double time_in_seconds, int z, int atomic_mass )  const;


CalcFloatType NuclideMixture::numAtoms( double time_in_seconds, int index ) const
{
  if( m_decayedToNuclides.empty() )
    performTimeEvolution();

  const int n_nuclides = static_cast<int>( m_decayedToNuclides.size() );
  if( (index < 0) || (index >= n_nuclides) )
    throw std::runtime_error( "NuclideMixture::numAtoms(...): Invalid Index" );

  return m_decayedToNuclides[index].numAtoms( time_in_seconds );
}//double numAtoms( double time_in_seconds, int internal_index_number ) const;


vector<NuclideActivityPair> NuclideMixture::activity( double time_in_seconds )  const
{
  vector<NuclideActivityPair> answer;

  if( m_decayedToNuclides.empty() )
    performTimeEvolution();

  for( size_t i = 0; i < m_decayedToNuclides.size(); ++i )
  {
    const Nuclide *nuclide = m_decayedToNuclides[i].nuclide;
    
    CalcFloatType activity = m_decayedToNuclides[i].activity( time_in_seconds );
    
    /*
     //At time=0, we would expect only the original nuclides would have non-zero
     //  activity; however, because of numerical rounding in the bateman
     //  equations, we may get small amounts (like 1E-22) of child products.
     //  If this bothers you, you can un-comment out the next few lines of code
    if( time_in_seconds <= 0.0 && activity > 0.0 )
    {
      bool isorig = false;
      for( size_t i = 0; activity > 0.0 && i < m_originalNuclides.size(); ++i )
        isorig = (m_originalNuclides[i].nuclide == nuclide);
      if( !isorig )
        activity = 0.0;
    }//if( time_in_seconds <= 0.0 && activity > 0.0 )
     */
    
    answer.push_back( NuclideActivityPair( nuclide, static_cast<double>(activity) )  );
  }//for( loop over atoms decayed too, i )

  return answer;
}//vector<NuclideActivityPair> activity( double time_in_seconds )  const


vector<NuclideNumAtomsPair> NuclideMixture::numAtoms( double time_in_seconds )  const
{
  vector<NuclideNumAtomsPair> answer;
  if( m_decayedToNuclides.empty() )
    performTimeEvolution();

  for( size_t i = 0; i < m_decayedToNuclides.size(); ++i )
  {
    const Nuclide *nuclide = m_decayedToNuclides[i].nuclide;
    const CalcFloatType numAtoms = m_decayedToNuclides[i].numAtoms( time_in_seconds );
    answer.push_back( NuclideNumAtomsPair( nuclide, numAtoms )  );
  }//for( loop over atoms decayed too, i )

  return answer;
}//vector<NuclideNumAtomsPair> numAtoms( double time_in_seconds )  const

/*
bool includesNuclide( const std::vector<NuclideNumAtomsPair> &lhs, const Nuclide *nuc )
{
  for( size_t i = 0; i < lhs.size(); ++i )
  {
    if( lhs[i].nuclide == nuc )
      return true;
  }
  return false;
}
*/

vector<EnergyRatePair> NuclideMixture::decayParticle( double time,
                                                           ProductType type,
                                                           HowToOrder sortType ) const
{
  //Should make a vector of energies first, sort them, then a second vector
  //  of abundances made to correspond to the vector of energies

  //Pre 20121010 I had thought the call to activity was harmless (1.8% of time),
  //  but using "Instruments" in OSX, instead of "Activity Monitor" profiling
  //  shows it taking up close to 100% of the time of this function, at least
  //  for the case fitting shielding and source activities in the spectrum
  //  viewer - the inefficient function looks to be SandiaDecayDataBase::getTimeEvolution(...)
  const vector<NuclideActivityPair> activities = activity( time ); //takes up 1.8% of the time for this function call

  vector<double> energies, branchratios;
//  energies.reserve( 2048 );
//  branchratios.reserve( 2048 );

  for( size_t nucIndex = 0; nucIndex < activities.size(); ++nucIndex )
  {
    const Nuclide *nuclide = activities[nucIndex].nuclide;
    const double activity = activities[nucIndex].activity;
    
    //if( activity <= 0.0 )
    //  continue;

    const size_t n_decaysToChildren = nuclide->decaysToChildren.size();

    for( size_t decayIndex = 0; decayIndex < n_decaysToChildren; ++decayIndex )
    {
      const Transition *transition = nuclide->decaysToChildren[decayIndex];
      const size_t n_products = transition->products.size();

      for( size_t productNum = 0; productNum < n_products; ++productNum )
      {
        const RadParticle &particle = transition->products[productNum];
        if( particle.type == type )
        {
  //Comment from Greg T. in his code to read tori.db3:
  // The ToRI x-ray database will return x-rays for GS->isomeric state transitions,
  // even if the x-rays originate from the isomeric de-excitation
  // so, we don't want to repeat different isomeric states of the same child
  //
  //wcjohns: and example is Br83, which decays to Kr83 and Kr83m, which the
  //         database has the same xrays (energies and intensities) listed
  //         for both
          if( type == XrayParticle )
          {
            bool duplicate = false;
            
            for( size_t prevDecay = 0; prevDecay < decayIndex; ++prevDecay )
            {
              //I'm not totally happy with this next test - it seems like results
              //  could depend on the order of transistions in the vector...
              const Transition *prevTrans = nuclide->decaysToChildren[prevDecay];
              if( transition->parent && prevTrans->parent
                  && transition->child && prevTrans->child
                 && transition->parent->atomicNumber == prevTrans->parent->atomicNumber
                 && transition->parent->massNumber == prevTrans->parent->massNumber
                 && transition->parent->isomerNumber == prevTrans->parent->isomerNumber
                 && transition->child->atomicNumber == prevTrans->child->atomicNumber
                 )
              {
                duplicate = true;
                break;
              }
            }
            
            if( duplicate )
              continue;
            
            /*
             //20181220: below is how wcjohnson had been detecting duplicates,
             //          but on further review (and greater understanding of
             //          the issue), it probably isnt correct, so for the
             //          current time, will use the above solution reproducing
             //          Greg solution
            //XXX: Note below neglects situations where you add a nuclide to
            //  the NuclideMixture that is a iso>0 state, and its a decendant of
            //  another nuclide that you added
            if( transition->parent->isomerNumber
//               && !transition->child->isomerNumber
               && transition->parent && transition->child
               && transition->parent->atomicNumber == transition->child->atomicNumber
               && transition->parent->massNumber == transition->child->massNumber
               && !includesNuclide( m_originalNuclides, transition->parent )
               )
            {
              continue;
            }
             */
          }//if( type == XrayParticle )
          
          energies.push_back( particle.energy );
          branchratios.push_back( activity * particle.intensity * transition->branchRatio );
        }//if( particle.type == type )
      }//for( size_t productNum = 0; productNum < n_products; ++productNum )
    }//for( size_t decayIndex = 0; decayIndex < n_decaysToChildren; ++decayIndex )
  }//for( size_t nucIndex = 0; nucIndex < activities.size(); ++nucIndex )

  const size_t nenergies = energies.size();
  vector<size_t> sort_indices( nenergies );
  for( size_t i = 0; i < nenergies; ++i )
    sort_indices[i] = i;

  std::sort( sort_indices.begin(), sort_indices.end(),
             index_compare_assend<vector<double>&>(energies) );

  double current_energy = -1.0;
  vector<EnergyRatePair> answer;
  answer.reserve( energies.size() );

  for( size_t i = 0; i < nenergies; ++i )
  {
    const double energy = energies[sort_indices[i]];
    const double branchratio = branchratios[sort_indices[i]];

    if( energy != current_energy )
    {
      current_energy = energy;
      answer.push_back( EnergyRatePair(branchratio,energy) );
    }else
    {
      answer.back().numPerSecond += branchratio;
    }
  }//for( size_t i = 0; i < energies.size(); ++i )

  switch( sortType )
  {
    case OrderByAbundance:
      sort( answer.begin(), answer.end(),
           &EnergyRatePair::moreThanByNumPerSecond );
      break;

    case OrderByEnergy:
      //already sorted by energy
      break;
  }//switch( sortType )

  return answer;
}//vector<AbundanceEnergyPair> decayParticle( double time_in_seconds, ProductType type, SortType sortType = kByAbundance ) const



vector<EnergyRatePair> NuclideMixture::gammas( const double time_in_seconds,
                                                    const NuclideMixture::HowToOrder sortType,
                                                    const bool includeAnnihilation ) const
{
  if( !includeAnnihilation )
    return decayParticle( time_in_seconds, GammaParticle, sortType );

  vector<EnergyRatePair> gams = decayParticle( time_in_seconds, GammaParticle, sortType );
  const vector<EnergyRatePair> poss = decayParticle( time_in_seconds, PositronParticle, OrderByEnergy );

  EnergyRatePair possbr( 0.0, 510.998910 );
  
  for( size_t i = 0; i < poss.size(); ++i )
    possbr.numPerSecond += 2.0*poss[i].numPerSecond; //an annihilation event creates two photons
  
  vector<EnergyRatePair>::iterator pos;
  switch( sortType )
  {
    case OrderByAbundance:
      pos = lower_bound( gams.begin(), gams.end(), possbr, &EnergyRatePair::moreThanByNumPerSecond );
    break;
        
    case OrderByEnergy:
      pos = lower_bound( gams.begin(), gams.end(), possbr, &EnergyRatePair::lessThanByEnergy );
    break;
  }//switch( sortType )
    
  gams.insert( pos, possbr );
  
  return gams;
}//vector<AbundanceEnergyPair> gammas( double time_in_seconds, SortType sortType ) const


std::vector<EnergyRatePair> NuclideMixture::alphas( double time_in_seconds, NuclideMixture::HowToOrder sortType ) const
{
  return decayParticle( time_in_seconds, AlphaParticle, sortType );
}//vector<AbundanceEnergyPair> gammas( double time_in_seconds, SortType sortType ) const


std::vector<EnergyRatePair> NuclideMixture::betas( double time_in_seconds,  NuclideMixture::HowToOrder sortType ) const
{
  return decayParticle( time_in_seconds, BetaParticle, sortType );
}


std::vector<EnergyRatePair> NuclideMixture::betaPlusses( double time_in_seconds, NuclideMixture::HowToOrder sortType ) const
{
  return decayParticle( time_in_seconds, PositronParticle, sortType );
}


std::vector<EnergyRatePair> NuclideMixture::xrays( double time_in_seconds, NuclideMixture::HowToOrder sortType ) const
{
  return decayParticle( time_in_seconds, XrayParticle, sortType );
}

std::vector<EnergyRatePair> NuclideMixture::photons( const double time_in_seconds, const NuclideMixture::HowToOrder sortType ) const
{
  vector<EnergyRatePair> gam = gammas( time_in_seconds, sortType, true );
  const vector<EnergyRatePair> x = xrays( time_in_seconds, sortType );
  
  gam.insert( gam.begin(), x.begin(), x.end() );
  
  switch( sortType )
  {
    case OrderByAbundance:
      sort( gam.begin(), gam.end(), &EnergyRatePair::moreThanByNumPerSecond );
      break;
      
    case OrderByEnergy:
      sort( gam.begin(), gam.end(), &EnergyRatePair::lessThanByEnergy );
      break;
  }//switch( sortType )
  
  return gam;
}

  
std::vector<SandiaDecay::EnergyCountPair>
NuclideMixture::decayParticlesInInterval( const double initial_age,
                            const double interval_duration,
                            const ProductType type,
                            const HowToOrder sort_type,
                            const size_t characteristic_time_slices ) const
{
  // This function is rather niave, it just performs a very simple-minded integration
  //  at a fixed number of time-steps.
  //
  // TODO: figure out how many time slices are needed for reasonable accuracy, and use a more intelligent integration algorithm
  //       A first quick go at this, for In110 (hl=4.9h), over a 2.8 hour measurement,
  //       gave corrections of
  //            For 250: 0.826922  (which matches analytical answer of 0.826922)
  //            For 50:  0.82692
  //            For 25:  0.826913
  //            For 10:  0.826869
  //
  //  A spot check using Mn56 (hl=9283.8s), and a meas duration of 86423.86s, with 50 timeslices
  //    gives a correction factor of 0.15473519892011101, vs analytical answer of 0.1547364350135815
  
  const int num_source_nuclides = numInitialNuclides();
  if( num_source_nuclides < 1 )
    throw runtime_error( "decayParticlesInInterval:"
                        " passed in mixture must have at least one parent nuclide" );
  
  double minHalflife = std::numeric_limits<double>::max();
  for( int nuc_num = 0; nuc_num < num_source_nuclides; ++nuc_num )
  {
    const SandiaDecay::Nuclide *nuclide = initialNuclide(nuc_num);
    assert( nuclide );
    if( !nuclide )
      throw std::logic_error( "decayParticlesInInterval: nullptr nuc" );
  
    // TODO: the parent half-life may not be the relevant one; should check down the chain
    minHalflife = std::min(nuclide->halfLife, minHalflife);
  }
      
  const double characteristicTime = std::min( interval_duration, minHalflife );
  const double dt = characteristicTime / characteristic_time_slices;
  
  const int max_num_slices = 2000;
  const int min_num_slices = 50;
  const int niave_num_slices = static_cast<int>( std::ceil( interval_duration / dt ) );
      
  const int num_time_slices = std::min( max_num_slices, std::max( min_num_slices, niave_num_slices ) );
  
  const vector<SandiaDecay::EnergyRatePair> initial_particles
                  = decayParticle( initial_age, type, SandiaDecay::NuclideMixture::OrderByEnergy );
  
  const size_t num_energies = initial_particles.size();
  
  // Create the vector of particle {energy,counts} we will use to accumulate
  vector<EnergyCountPair> energy_count_pairs( num_energies, EnergyCountPair(0.0,0.0) );
  for( size_t i = 0; i < num_energies; ++i )
  {
    energy_count_pairs[i].energy = initial_particles[i].energy;
    energy_count_pairs[i].count = 0.0;
  }
        
  // Do a very niave integration, using the mid-point of the time interval for the average value,
  // and multiply by the duration of the interval, to get the total - this could be so much better
  for( int timeslice = 0; timeslice < num_time_slices; timeslice += 1 )
  {
    const double this_age = initial_age + interval_duration*(2.0*timeslice + 1.0)/(2.0*num_time_slices);
    const vector<SandiaDecay::EnergyRatePair> these_gammas
                        = decayParticle( this_age, type, SandiaDecay::NuclideMixture::OrderByEnergy );
    
    assert( these_gammas.size() == energy_count_pairs.size() );
    if( these_gammas.size() != num_energies )
      throw std::logic_error( "gamma result size doesn't match expected." );
      
    for( size_t i = 0; i < num_energies; ++i )
      energy_count_pairs[i].count += these_gammas[i].numPerSecond;
  }//for( loop over timeslices )
  
  const double time_delta = interval_duration / num_time_slices;
  for( size_t i = 0; i < num_energies; ++i )
    energy_count_pairs[i].count *= time_delta;
  
  switch( sort_type )
  {
    case OrderByAbundance:
      sort( energy_count_pairs.begin(), energy_count_pairs.end(),
           &EnergyCountPair::moreThanByCount );
      break;

    case OrderByEnergy:
      //already sorted by energy
      break;
  }//switch( sortType )
  
#ifndef NDEBUG
  // For debug builds we'll do a sanity check if we can easily compare to analytical answer
  // when input has a single nuclide, and it decays to stable children
  if( (num_source_nuclides == 1) && initialNuclide(0)->decaysToStableChildren() )
  {
    const SandiaDecay::Nuclide *nuclide = initialNuclide(0);
    
    bool found_issue = false;
    const double lambda = nuclide->decayConstant();
    const double corr_factor = (1.0 - exp(-1.0*lambda*interval_duration)) / (lambda * interval_duration);
    
    assert( initial_particles.size() == energy_count_pairs.size() );
    for( size_t i = 0; i < energy_count_pairs.size(); ++i )
    {
      assert( energy_count_pairs[i].energy == initial_particles[i].energy );
      
      const double numerical_answer = energy_count_pairs[i].count / interval_duration;
      const double uncorrected_answer = initial_particles[i].numPerSecond;
      if( (uncorrected_answer > DBL_EPSILON) || (uncorrected_answer > DBL_EPSILON) )
      {
        const double numerical_corr_factor = numerical_answer / uncorrected_answer;
        const double diff = fabs(numerical_corr_factor - corr_factor);
        if( (diff > 0.0001) || (0.0001*diff > std::max(numerical_corr_factor, corr_factor)) )
        {
          found_issue = true;
          cerr << "Found decay correction value of "
          << numerical_corr_factor << ", when a true value of "
          << corr_factor << " was expected for " << nuclide->symbol
          << " with half life " << nuclide->halfLife/SandiaDecay::hour
          << " hours and a measurement time "
          << interval_duration/SandiaDecay::hour
          << " hours (at energy " << energy_count_pairs[i].energy << " keV)"
          << endl;
        }//if( error is larger than expected )
      }//if( not a zero BR gamma )
    }//if( we can use standard formula to correct )
    
    assert( !found_issue );
  }//if( one input nuclide that decays to stable children )
#endif //NDEBUG
  
  return energy_count_pairs;
}//decayParticlesInInterval(...)
  
  
std::vector<SandiaDecay::EnergyCountPair>
NuclideMixture::decayGammasInInterval( const double initial_age,
                        const double interval_duration,
                        const bool includeAnnihilation,
                        const HowToOrder sort_type,
                        const size_t characteristic_time_slices ) const
{
  vector<EnergyCountPair> gams = decayParticlesInInterval( initial_age, interval_duration,
                                            GammaParticle, sort_type, characteristic_time_slices );
  
  if( !includeAnnihilation )
    return gams;

  const vector<EnergyCountPair> poss = decayParticlesInInterval( initial_age, interval_duration,
                                      PositronParticle, OrderByEnergy, characteristic_time_slices );

  EnergyCountPair possbr( 510.998910, 0.0 );
  
  for( size_t i = 0; i < poss.size(); ++i )
    possbr.count += 2.0*poss[i].count; //an annihilation event creates two photons
  
  vector<EnergyCountPair>::iterator pos;
  switch( sort_type )
  {
    case OrderByAbundance:
      pos = lower_bound( gams.begin(), gams.end(), possbr, &EnergyCountPair::moreThanByCount );
    break;
        
    case OrderByEnergy:
      pos = lower_bound( gams.begin(), gams.end(), possbr, &EnergyCountPair::lessThanByEnergy );
    break;
  }//switch( sortType )
    
  gams.insert( pos, possbr );
  
  return gams;
}//NuclideMixture::decayGammasInInterval(...)
  
  
std::vector<SandiaDecay::EnergyCountPair>
  NuclideMixture::decayPhotonsInInterval( const double initial_age,
                            const double interval_duration,
                            HowToOrder sort_type,
                            const size_t characteristic_time_slices ) const
{
  vector<EnergyCountPair> gam = decayGammasInInterval( initial_age, interval_duration, true, 
                                                          sort_type, characteristic_time_slices );
  const vector<EnergyCountPair> x = decayParticlesInInterval( initial_age, interval_duration, 
                                ProductType::XrayParticle, sort_type, characteristic_time_slices );
    
  gam.insert( gam.begin(), x.begin(), x.end() );
    
  switch( sort_type )
  {
    case OrderByAbundance:
      sort( gam.begin(), gam.end(), &EnergyCountPair::moreThanByCount );
      break;
        
    case OrderByEnergy:
      sort( gam.begin(), gam.end(), &EnergyCountPair::lessThanByEnergy );
      break;
  }//switch( sortType )
    
  return gam;
}//NuclideMixture::decayPhotonsInInterval(...)
  

//internal_index_number runs from 0 to numSolutionNuclides()
int NuclideMixture::internalIndexNumber( const Nuclide *nuclide ) const
{
  if( m_decayedToNuclides.empty() )
    performTimeEvolution();

  for( size_t i = 0; i < m_decayedToNuclides.size(); ++i )
    if( m_decayedToNuclides[i].nuclide->symbol == nuclide->symbol ) //we could just compare pointer values...
      return static_cast<int>( i );

  throw std::runtime_error( nuclide->symbol + " is not in this NuclideMixture" );
  return -1;
}//int internalIndexNumber( const Nuclide *nuclide )


int NuclideMixture::internalIndexNumber( const std::string &symbol ) const
{
  if( m_decayedToNuclides.empty() )
    performTimeEvolution();

  for( size_t i = 0; i < m_decayedToNuclides.size(); ++i )
    if( m_decayedToNuclides[i].nuclide->symbol == symbol )
      return static_cast<int>( i );

  const string msg = symbol + " is not in this NuclideMixture.  Did you perhaps"
                              " not put symbol into its normailzed form (ex. "
                              "Co60, U238m, etc)?";
  throw std::runtime_error( msg );
  return -1;
}//int internalIndexNumber( const std::string &symbol ) const


int NuclideMixture::internalIndexNumber(int z, int mass_number, int iso ) const
{
  if( m_decayedToNuclides.empty() )
    performTimeEvolution();

  for( size_t i = 0; i < m_decayedToNuclides.size(); ++i )
  {
    const Nuclide *nuclide = m_decayedToNuclides[i].nuclide;
    if( nuclide->massNumber == mass_number
        && nuclide->atomicNumber == z
        && nuclide->isomerNumber == iso )
      return static_cast<int>( i );
  }

  char buffer[256];
  snprintf( buffer, sizeof(buffer),
            "Z=%i MN=%i, ISO=%i is not in this NuclideMixture.",
            z, mass_number, iso );
  throw std::runtime_error( buffer );
  return -1;
}//int internalIndexNumber(int z, int atomic_mass ) const


int NuclideMixture::numInitialNuclides() const
{
  return static_cast<int>( m_originalNuclides.size() );
}//int NuclideMixture::numInitialNuclides() const

const Nuclide *NuclideMixture::initialNuclide( int index ) const
{
  return m_originalNuclides.at( index ).nuclide;
}//const Nuclide *initialNuclide( int index ) const

double NuclideMixture::numInitialAtoms( int index ) const
{
  return m_originalNuclides.at(index).numAtoms;
}//double NuclideMixture::numInitialAtoms( int index ) const
  
double NuclideMixture::initialActivity( int index ) const
{
  const Nuclide *nuclide = m_originalNuclides.at(index).nuclide;
  const double numAtoms = m_originalNuclides.at(index).numAtoms;
  return nuclide->numAtomsToActivity( numAtoms );
}

const Nuclide *NuclideMixture::solutionNuclide( int internal_index_number ) const
{
  if( m_decayedToNuclides.empty() )
    performTimeEvolution();

  return m_decayedToNuclides.at( internal_index_number ).nuclide;
}//const Nuclide *solutionNuclide( int internal_index_number ) const



std::string NuclideMixture::info( const double time ) const
{
  if( m_originalNuclides.empty() )
    return "";

  const vector<NuclideActivityPair> activities = activity( time );
  const vector<EnergyRatePair> gammasAbundances = gammas( time, NuclideMixture::OrderByAbundance, true );
  const vector<EnergyRatePair> alphasAbundances = alphas( time );
  const vector<EnergyRatePair> betasAbundances = betas( time );
  const vector<EnergyRatePair> betaPlussesAbundances = betaPlusses( time );

  stringstream infostrm;

  infostrm << "Starting from:";

  {//begin codeblock to put starting nuclides information into the stream
    stringstream tempstrm;
    tempstrm << "\n    ";

    for( size_t i = 0; i < m_originalNuclides.size(); ++i )
    {
      const NuclideNumAtomsPair &pair = m_originalNuclides[i];
      if( i ) tempstrm << ",";
      if( tempstrm.str().length() > 78 )
      {
        infostrm << tempstrm.str();
        tempstrm.clear();
        tempstrm << "\n    ";
      }//if( we've reached our length limit )

      tempstrm << static_cast<double>(pair.nuclide->numAtomsToActivity( pair.numAtoms ) / becquerel)
               << " Bq " << pair.nuclide->symbol;
    }//for( loop over orignal nuclides )

    infostrm << tempstrm.str();
  }//end codeblock to put starting nuclides information into the stream


  infostrm << "\nThe following nuclides are present at " << time/second
           << " seconds:";


  {//begin codeblock to put decayed to nuclides information into the stream
    stringstream tempstrm;
    tempstrm << "\n    ";

    for( size_t i = 0; i < activities.size(); ++i )
    {
      const NuclideActivityPair &pair = activities[i];
      if( i ) tempstrm << ",";
      if( tempstrm.str().length() > 78 )
      {
        infostrm << tempstrm.str();
        tempstrm.clear();
        tempstrm << "\n    ";
      }//if( we've reached our length limit )

      tempstrm << " " << static_cast<double>(pair.activity / becquerel) << " Bq " << pair.nuclide->symbol;
    }//for( loop over activities )

    infostrm << tempstrm.str();
  }//end codeblock to put decayed to nuclides information into the stream

  if( gammasAbundances.size() )
  {
    infostrm << "\nGammas Present:";
    for( size_t i = 0; i < gammasAbundances.size(); ++i )
      infostrm << "\n    " << gammasAbundances[i].energy/keV << " keV\t-\t"
               << gammasAbundances[i].numPerSecond << " per second";
  }//if( gammasAbundances.size() )

  if( alphasAbundances.size() )
  {
    infostrm << "\nAlphas Present:";
    for( size_t i = 0; i < alphasAbundances.size(); ++i )
      infostrm << "\n    " << alphasAbundances[i].energy/keV << " keV\t-\t"
              << alphasAbundances[i].numPerSecond << " per second";
  }//if( alphasAbundances.size() )

  if( betasAbundances.size() )
  {
    infostrm << "\nBetas Present:";
    for( size_t i = 0; i < betasAbundances.size(); ++i )
      infostrm << "\n    " << betasAbundances[i].energy/keV << " keV\t-\t"
               << betasAbundances[i].numPerSecond << " per second";
  }//if( alphasAbundances.size() )


  if( betaPlussesAbundances.size() )
  {
    infostrm << "\nBeta+'s Present:";
    for( size_t i = 0; i < betaPlussesAbundances.size(); ++i )
      infostrm << "\n    " << betaPlussesAbundances[i].energy/keV << " keV\t-\t"
               << betaPlussesAbundances[i].numPerSecond << " per second";
  }//if( betaPlussesAbundances.size() )


  return infostrm.str();
}//string info() const

const std::vector<NuclideTimeEvolution> &NuclideMixture::decayedToNuclidesEvolutions() const
{
  if( m_decayedToNuclides.empty() )
    performTimeEvolution();

  return m_decayedToNuclides;
}//const std::vector<NuclideTimeEvolution> &NuclideMixture::decayedToNuclidesEvolutions() const



void NuclideMixture::performTimeEvolution() const
{
  m_decayedToNuclides = SandiaDecayDataBase::getTimeEvolution( m_originalNuclides );
}//void performTimeEvolution()

void SandiaDecayDataBase::read_file_contents( const std::string &filename, std::vector<char> &data )
{
  std::ifstream stream( filename.c_str(), ios::binary );
  if (!stream)
    throw runtime_error(string("Cannot open file ") + filename);
  
  stream.unsetf(ios::skipws);
  
  // Determine stream size
  stream.seekg(0, ios::end);
  size_t size = stream.tellg();
  stream.seekg(0);
  
  // Load data and add terminating 0
  data.resize( size + 1 );
  stream.read(&data.front(), static_cast<streamsize>(size));
  data[size] = 0;
}//void SandiaDecayDataBase::read_file_contents( std::string filename, std::vector<char> &data )


SandiaDecayDataBase::SandiaDecayDataBase( const std::string &filename )
  : m_xmlFileContainedDecayXrays( false ),
    m_xmlFileContainedElementalXrays( false )
{
  std::vector<char> data;
  read_file_contents( filename, data );
  
  parseSandiaDecayXml( data, m_nuclides, m_nuclideStore,
                        m_elements, m_elementStore, m_transitionStore );
  
  checkIfContainedXrays();
}

  
SandiaDecayDataBase::SandiaDecayDataBase()
  : m_xmlFileContainedDecayXrays( false ),
    m_xmlFileContainedElementalXrays( false )
{
}

  
void SandiaDecayDataBase::checkIfContainedXrays()
{
  m_xmlFileContainedDecayXrays = false;
  for( size_t i = 0; !m_xmlFileContainedDecayXrays && (i < m_transitionStore.size()); ++i )
    for( size_t j = 0; !m_xmlFileContainedDecayXrays && (j < m_transitionStore[i].products.size()); ++j )
      m_xmlFileContainedDecayXrays = (m_transitionStore[i].products[j].type == XrayParticle);
  
  m_xmlFileContainedElementalXrays = ((m_elements.size()>=93) && !(m_elements[92]->xrays.empty()));
}//void checkIfContainedXrays()
  
  
bool SandiaDecayDataBase::initialized() const
{
  return !m_nuclides.empty();
}//bool initialized() const


void SandiaDecayDataBase::initialize( const std::string &filename )
{
  std::vector<char> data;
  read_file_contents( filename, data );
  initialize( data );
}//void initialize( const std::string &filename )


void SandiaDecayDataBase::initialize( std::vector<char> &data )
{
  if( !m_nuclides.empty() )
    throw std::runtime_error( "SandiaDecayDataBase::initialize(...): Database "
                             "already initialized form XML file" );
  
  parseSandiaDecayXml( data, m_nuclides, m_nuclideStore,
                      m_elements, m_elementStore, m_transitionStore );
  
  checkIfContainedXrays();
}//void initialize( std::vector<char> &data );
  

void SandiaDecayDataBase::reset()
{
  m_nuclides.clear();
  m_nuclideStore.clear();
  
  m_elements.clear();
  m_elementStore.clear();

  m_transitionStore.clear();
  
  //Reclaim memory
  {
    vector<Element> tempElementStore;
    tempElementStore.swap( m_elementStore );
  }
  
  {
    vector<Nuclide> tempNuclideStore;
    tempNuclideStore.swap( m_nuclideStore );
  }
  
  {
    vector<Transition> tempTransitionStore;
    tempTransitionStore.swap( m_transitionStore );
  }
  
//#if __cplusplus <= 19971  1L
//#else
//  m_elementStore.shrink_to_fit();
//  m_nuclideStore.shrink_to_fit();
//  m_transitionStore.shrink_to_fit();
//#endif

  m_xmlFileContainedDecayXrays = false;
  m_xmlFileContainedElementalXrays = false;
}
  
  
SandiaDecayDataBase::~SandiaDecayDataBase()
{
  //unInitialize();
}//~SandiaDecayDataBase()



const vector<const Nuclide *> &SandiaDecayDataBase::nuclides() const
{
  return m_nuclides;
}

const std::vector<const Element *> &SandiaDecayDataBase::elements() const
{
  return m_elements;
}

const std::vector<Transition> &SandiaDecayDataBase::transitions() const
{
  return m_transitionStore;
}
  
const Element *SandiaDecayDataBase::element( const int atomicNumber ) const
{
  typedef vector<const Element *>::const_iterator ElementIter;

  const ElementIter begin = m_elements.begin();
  const ElementIter end = m_elements.end();

#ifdef _WIN32
  ElementIter pos = begin;
  while( pos != end && Element::lessThanForAtomicNum( *pos, atomicNumber ) )
    ++pos;
#else
  const ElementIter pos = lower_bound( begin, end, atomicNumber,
                                       &Element::lessThanForAtomicNum );
#endif

  if( pos == end )
    return NULL;

  return *pos;
}//const Element *SandiaDecayDataBase::element( const int massNumber ) const


const Element *SandiaDecayDataBase::element( const std::string &input ) const
{

  string el;
  for( size_t i = 0; i < input.size(); ++i )
    if( isalpha( input[i] ) )
      el += tolower( input[i] );

  if( el.empty() )
    return NULL;

  const bool isSymbol = ( (el.length() <= 2)
                        || (el.length()==3 && el.substr(0,2)=="uu" ) );

  if( isSymbol )
   el[0] = toupper( el[0] );

  for( size_t i = 0; i < m_elements.size(); ++i )
  {
    const Element *testEl = m_elements[i];
    if( testEl->symbol == el || testEl->name == el )
      return testEl;
  }//for( loop over m_elements to match the current string to, i )

  return NULL;
}//const Element *element( std::string label ) const



void SandiaDecayDataBase::parseSandiaDecayXml( std::vector<char> &data,
                                               vector<const Nuclide *> &nuclides,
                                               std::vector<Nuclide> &stored_nuclides,
                                               std::vector<const Element *> &elements,
                                               std::vector<Element> &stored_elements,
                                               std::vector<Transition> &transitionStore )
{
  elements.clear();
  stored_elements.clear();

  try
  {
    using namespace ::rapidxml;

    if( data.empty() )
      throw runtime_error( "SandiaDecayDataBase: empty xml contents" );
    
    if( data.back() ) // We could null-terminate the data, but instead we'll be 
      throw runtime_error( "SandiaDecayDataBase::parseSandiaDecayXml: data must be null terminated." );
    
    xml_document<char> doc;
    doc.parse<parse_normalize_whitespace | parse_trim_whitespace>( &data.front() );

    const xml_node<char> *document_node = doc.first_node();

    nuclides.clear();
    stored_nuclides.clear();
    
    //ToDo: Right now we are pre-reserving how much memory will be allocated
    //      (doing this for cache locality), but this is brittle relative to
    //      input XML - need to time how long it would take to just loop through
    //      and count things.  (this has cost me a couple of hours to figure out
    //      once when sandia.decay.xml increased in size)
    const size_t n_transition_reserve = 4300;//actually 4278
    const size_t n_nuclide_reserve = 4100; //4085
    const size_t n_element_reserve = 119;
    
    stored_nuclides.reserve( n_nuclide_reserve );
    
#if( ENABLE_SHORT_NAME )
    bool shortnames = false;
    
    {//begin code block to check if we are using short names or not
      const xml_node<char> *node = document_node->first_node( "nuclide", 7 );
      if( !node )
      {
        node = document_node->first_node( "n", 1 );
        if( node )
          shortnames = true;
      }
      if( !node )
        throw runtime_error( "XML file appears invalid - no nuclide nodes" );
    }//end code block to check if we are using short names or not
#endif
    
#if( ENABLE_SHORT_NAME )
    for( const xml_node<char> *node = document_node->first_node( (shortnames ? "n" : "nuclide") );
        node;
        node = node->next_sibling( node->name(), node->name_size() ) )
#else
    for( const xml_node<char> *node = document_node->first_node("nuclide",7);
        node;
        node = node->next_sibling("nuclide",7) )
#endif
    {
      const rapidxml::xml_attribute<char> *revision_att = node->first_attribute( "revision", 8 );
      if( revision_att && revision_fromstr(revision_att->value()) == DeletedRevision )
        continue;
      
//#if __cplusplus > 199711L
//      stored_nuclides.emplace_back( node );  //Nuclide constructor is protected...
//#else
      stored_nuclides.push_back( Nuclide(node) );
//#endif
      
      if( stored_nuclides.size() > n_nuclide_reserve )
        throw std::runtime_error( "XML file had more nuclides than expected.  Please increase n_nuclide_reserve and recompile." );
    }//for( loop over "nuclide" nodes )

    const size_t nnuc = stored_nuclides.size();
    nuclides.resize( nnuc );
    for( size_t i = 0; i < nnuc; ++i )
      nuclides[i] = &stored_nuclides[i];
    std::sort( nuclides.begin(), nuclides.end(), &pointerLessThanBySymbol );
    
    transitionStore.clear();
    transitionStore.reserve( n_transition_reserve );
    
#if( ENABLE_SHORT_NAME )
    for( const xml_node<char> *node = document_node->first_node( (shortnames ? "t" : "transition") );
        node;
        node = node->next_sibling( node->name(), node->name_size() ) )
#else
    for( const xml_node<char> *node = document_node->first_node("transition",10);
        node;
        node = node->next_sibling("transition",10) )
#endif
    {
#if __cplusplus > 199711L
      transitionStore.emplace_back( node, nuclides );
#else
      transitionStore.push_back( Transition(node, nuclides) );
#endif
      
      if( stored_nuclides.size() > n_transition_reserve ) //could use stored_nuclides.capacity() instead of n_transition_reserve
        throw std::runtime_error( "XML file had more transistions than expected.  Please increase n_transition_reserve and recompile." );
      
      Transition *trans = &transitionStore.back();

      //XXX 20111012: the sandia.decay.xml file list transitions for isotopes with
      //    halfLife==inf, which can screw up some of the decay logic, since if
      //    the half lilfe is inf, there should be no decays, right?
      const bool use = ( (trans->parent != NULL)
                         && (trans->branchRatio > 0.0)
                         && !IsInf(trans->parent->halfLife) );

      //Perhaps the 'Transition' should insert itself into it's parent 'Nuclide' ?
      if( use )
      {
        //Could get rid of the const_cast (which might be ub?) by searching
        //  through stored_nuclides
        
        Nuclide *child = const_cast<Nuclide *>( trans->child );
        Nuclide *parent = const_cast<Nuclide *>( trans->parent );
        parent->decaysToChildren.push_back( trans );
        if( child )
          child->decaysFromParents.push_back( trans );
      }else
        transitionStore.pop_back();
    }//for( loop over "transition" nodes )

    
    vector<Element *> els; //we need non-const pointers to the Elements to add
                           //  xrays to them
    stored_elements.reserve( n_element_reserve );
    
#if( ENABLE_SHORT_NAME )
    for( xml_node<char> *node = document_node->first_node( (shortnames ? "el" : "element") );
       node;
       node = node->next_sibling( node->name(), node->name_size() ) )
#else
    for( xml_node<char> *node = document_node->first_node("element",7);
        node;
        node = node->next_sibling("element",7) )
#endif
    {
#if __cplusplus > 199711L
      stored_elements.emplace_back( node, nuclides );
#else
      stored_elements.push_back( Element( node, nuclides ) );
#endif
      
      if( stored_elements.size() > n_element_reserve ) //could use stored_elements.capacity() instead of n_element_reserve
        throw std::runtime_error( "XML file had more elements than expected.  Please increase n_element_reserve and recompile." );
    }
    
    const size_t nelements = stored_elements.size();
    els.resize( nelements );
    elements.reserve( nelements );
    
    for( size_t i = 0; i < nelements; ++i )
      els[i] = &stored_elements[i];
    std::sort( els.begin(), els.end(), &Element::lessThan );
    elements.insert( elements.end(), els.begin(), els.end() );
    
    //Check to make sure the xray data was actually in the file.
    //  This could probably be skipped to save a little time.
    //if( nelements<93 || elements[92]->xrays.empty() )
    //  throw runtime_error( filename + " did not contain elemental xray data: (" + elements[92]->symbol + ")" );
  }catch (::rapidxml::parse_error &e)
  {
    long line = static_cast<long>( std::count(&data.front(), e.where<char>(), '\n') + 1 );
    cerr << "Error parsing file on line " << line << endl;
    stored_nuclides.clear();
    nuclides.clear();
  }catch( std::exception &e )
  {
    std::cerr << "Exception " << e.what()
              << " caught when reading in SandiaDecay XML" << std::endl;
    stored_nuclides.clear();
    nuclides.clear();
  }
}//void SandiaDecayDataBase::parseSandiaDecayXml(...)


bool SandiaDecayDataBase::xmlContainedDecayXRayInfo() const
{
  return m_xmlFileContainedDecayXrays;
}
  
bool SandiaDecayDataBase::xmlContainedElementalXRayInfo() const
{
  return m_xmlFileContainedElementalXrays;
}
  
const Nuclide *SandiaDecayDataBase::nuclide( int z, int massNum, int iso ) const
{
  //This function can be optimized in the future!

  vector<const Nuclide *>::const_iterator pos;
  for( pos = m_nuclides.begin(); pos != m_nuclides.end(); ++pos )
  {
    const Nuclide *nuc = (*pos);
    if( nuc->atomicNumber==z && nuc->massNumber==massNum && nuc->isomerNumber==iso )
      return nuc;
  }

  return NULL;
}//const Nuclide *nuclide( int z, int atomicNumber ) const


const Nuclide *SandiaDecayDataBase::nuclide( const std::string &label ) const
{
  try
  {
    const string symbol = toNormalSymbolForm( label );
    // This will do a binary search to locate the nuclide with the symbol, if
    // such a nuclide exists.
    vector<const Nuclide *>::const_iterator pos = find( m_nuclides, symbol );

    if( pos == m_nuclides.end() )
      return NULL;
    return (*pos);
  }catch( std::exception & )
  {
    //cout << "Invalid: " << e.what() << endl;
  }

  return NULL;
}//const Nuclide *nuclide( const std::string &symbol ) const


const Nuclide *SandiaDecayDataBase::nuclideUnchecked(
                                                    const string &symbol ) const
{
  vector<const Nuclide *>::const_iterator pos = find( m_nuclides, symbol );

  if( pos == m_nuclides.end() )
    return NULL;

  return (*pos);
}//nuclideUnchecked(..)



//Get the nuclides corresponding to a given element
std::vector<const Nuclide *> SandiaDecayDataBase::nuclides(
                                                const Element *element ) const
{
  //  XXX - untested!

  if( !element )
    return std::vector<const Nuclide *>();

  vector<const Nuclide *>::const_iterator start = lower_bound( m_nuclides.begin(),
                                                  m_nuclides.end(),
                                                  element->symbol,
                                                  &lessThanBySymbol );
  vector<const Nuclide *>::const_iterator end = start;
  while( end != m_nuclides.end() )
  {
    string nucSym = (*end)->symbol;
    string::size_type pos = nucSym.find_first_of( "0123456789" );
    nucSym = nucSym.substr( 0, pos );

    if( nucSym != element->symbol )
      break;
    ++end;
  }//while( end != m_nuclides.end() )

  return std::vector<const Nuclide *>( start, end );
}//nuclides( const Element * )


std::vector<const Nuclide *> SandiaDecayDataBase::nuclides(
                                             const std::string &input ) const
{
  //  XXX - untested!

  string el;
  for( size_t i = 0; i < input.size(); ++i )
    if( isalpha( input[i] ) )
      el += tolower( input[i] );

  if( el.empty() )
    throw runtime_error( "SandiaDecayDataBase::nuclides( const string &):"
                         " String passed in contained no alphabetical chars" );

  const bool isSymbol = ( (el.length() <= 2)
                        || (el.length()==3 && el.substr(0,2)=="uu" ) );

  if( isSymbol )
   el[0] = toupper( el[0] );

  const Element *element = NULL;
  for( size_t i = 0; !element && (i < m_elements.size()); ++i )
  {
    const Element *testEl = m_elements[i];
    if( testEl->symbol == el || testEl->name == el )
      element = testEl;
  }//for( loop over m_elements to match the current string to, i )

  if( !element )
  {
    stringstream msg;
    msg << "SandiaDecayDataBase::nuclides( \"" << input << "\" ):"
        << " A element with name or symbol '" << el << "' couldnt be found";
    throw runtime_error( msg.str() );
  }//if( !foundSymbol )

  return nuclides( element );
}//nuclides( const std::string &element ) const




std::string SandiaDecayDataBase::toNormalSymbolForm( const std::string &symbol ) const
{
  vector<int> numbers;
  vector<string> elementSymbols;

  int meta = 0;

  const size_t len = symbol.length();

  for( size_t i = 0; i < len; )
  {
    string strStr, numStr;
    while( (i<len) && isalpha( symbol[i] ) )
      strStr += tolower( symbol[i++] );

    if( strStr.length() )
    {
      //Lets check if this text could be a meta stable state indicator
      if( (strStr.length()==1 && strStr[0]=='m')
         || (strStr.length()>=4 && strStr.substr(0,4)=="meta") )
      {
        meta = 1;
        //By requiring isdigit(symbol[i]) we are making it so integer indicating
        //  the >1 meta state must not hav any spaces beetween the "meta" or "m"
        //  and the integer.  If we didnt have the isdigit(symbol[i]) check,
        //  then having a string like "Ho166m " whould cause parse_int(...)
        //  to throw an exception because it would recieve the string " "
        if( i < len && isdigit(symbol[i]) )
        {
          const int metaLevel = parse_int( symbol.c_str()+i );
          if( metaLevel>0 && metaLevel<5 )
          {
            ++i;
            meta = metaLevel;
          }//if( it was a valid metalevel following the 'M' or 'META'
        }//if( i < len )
      }else elementSymbols.push_back( strStr );
    }//if( we found a alphabetical substring )

    while( (i<len) && isdigit( symbol[i] ) )
      numStr += symbol[i++];

    if( numStr.length() )
      numbers.push_back( parse_int( numStr.c_str() ) );

    if( numStr.empty() && strStr.empty() )
      ++i;
  }//for(...)


  int atomicMass = -1;

  //The user may have specified both the atomicNumber and atomicMass, so if
  //  there was more than one number specified (excluding the isomeric level,
  //  which should not have made it into 'numbers'), then assume the largest
  //  number is the atomicMass
  if( !numbers.empty() )
    atomicMass = *max_element( numbers.begin(), numbers.end() );


  if( elementSymbols.size()==1 )
  {
    string &el = elementSymbols[0];
    const bool isSymbol = ( (el.length() <= 2)
                          || (el.length()==3 && el.substr(0,2)=="uu" ) );

    if( isSymbol )
     el[0] = toupper( el[0] );

    bool foundSymbol = false;
    for( size_t i = 0; i < m_elements.size(); ++i )
    {
      const Element *element = m_elements[i];
      if( element->symbol == el || element->name == el )
      {
        foundSymbol = true;
        el = element->symbol;
        break;
      }//
    }//for( loop over m_elements to match the current string to, i )


    if( !foundSymbol )
    {
      stringstream msg;
      msg << "SandiaDecayDataBase::toNormalSymbolForm( \"" << symbol << "\" ):"
          << " A element with name or symbol '" << el << "' couldnt be found";
      throw runtime_error( msg.str() );
    }//if( !foundSymbol )

    char buffer[32];
    if( meta<=0 )
      snprintf( buffer, sizeof(buffer), "%s%i", el.c_str(), atomicMass );
    else if( meta==1 )
      snprintf( buffer, sizeof(buffer), "%s%im", el.c_str(), atomicMass );
    else
      snprintf( buffer, sizeof(buffer), "%s%im%i", el.c_str(), atomicMass, meta );
    
    const std::string nuffstr = buffer;
    vector<const Nuclide *>::const_iterator pos = find( m_nuclides, nuffstr );

    if( pos == m_nuclides.end() )
    {
      stringstream msg;
      msg << "SandiaDecayDataBase::toNormalSymbolForm( \"" << symbol << "\" ): "
          << el << " doesnt have an isotope with atmic mass " << atomicMass
          << " isomerNumber=" << meta;
      throw runtime_error( msg.str() );
    }//if( it was an invalid isotope mass )

    return nuffstr;
  }//if( elementSymbols.size()==1 && numbers.size()==1 )

  vector<string> candiateSymbls;

  for( size_t i = 0; i < m_elements.size(); ++i )
  {
    const Element *element = m_elements[i];
    const string &name = element->name;
    string symbol = element->symbol;
    symbol[0] = tolower( symbol[0] );

    for( size_t j = 0; j < elementSymbols.size(); ++j )
      if( (elementSymbols[j] == symbol)
          || (elementSymbols[j] == name) )
        candiateSymbls.push_back( element->symbol );
  }//for( loop over m_elements to match the current string to, i )

  if( candiateSymbls.size()!=1 )
  {
    stringstream msg;
    msg << "SandiaDecayDataBase::toNormalSymbolForm( \"" << symbol << "\" ): "
        << "Found " << candiateSymbls.size() << " candidate elements";
    throw runtime_error( msg.str() );
  }//if( candiateSymbls.size()!=1 )

  char buffer[32];
  if( meta<=0 )
    snprintf( buffer, sizeof(buffer), "%s%i", candiateSymbls[0].c_str(), atomicMass );
  else if( meta==1 )
    snprintf( buffer, sizeof(buffer), "%s%im", candiateSymbls[0].c_str(), atomicMass );
  else
    snprintf( buffer, sizeof(buffer), "%s%im%i", candiateSymbls[0].c_str(), atomicMass, meta );
  
  const std::string nuffstr = buffer;

  vector<const Nuclide *>::const_iterator pos = find( m_nuclides, nuffstr );

  if( (pos == m_nuclides.end()) )
  {
    stringstream msg;
    msg << "SandiaDecayDataBase::toNormalSymbolForm( \"" << symbol << "\" ): "
        << candiateSymbls[0] << " doesnt have an isotope with atomic mass " << atomicMass
        << " isomerNumber=" << meta;
    throw runtime_error( msg.str() );
  }//if( it was an invalid isotope mass )

  return nuffstr;
}//std::string SandiaDecayDataBase::toNormalSymbolForm( const std::string &symbol ) const



std::vector<NuclideTimeEvolution> SandiaDecayDataBase::getTimeEvolution( const Nuclide *parent,
                                                 const CalcFloatType orignal_activity  )
{
  const double n_atoms = parent->activityToNumAtoms( orignal_activity );
  vector<NuclideNumAtomsPair> parentV( 1, NuclideNumAtomsPair(parent, n_atoms) );
  return getTimeEvolution( parentV );
}//NuclideMixture getTimeEvolution(...)



std::vector<NuclideActivityPair> SandiaDecayDataBase::decay( const Nuclide *parent,
                                                             const CalcFloatType orignal_activity,
                                                             const double time_in_seconds )
{
  NuclideMixture mixture;
  mixture.addNuclideByActivity( parent, orignal_activity );
  return mixture.activity( time_in_seconds );
}//decay(...)


vector<NuclideActivityPair> SandiaDecayDataBase::decay( const vector<NuclideNumAtomsPair> &parents, const double time_in_seconds )
{
  NuclideMixture mixture;
  for( size_t i = 0; i < parents.size(); ++i )
    mixture.addNuclide( parents[i] );
  return mixture.activity( time_in_seconds );
}//vector<NuclideActivityPair> decay( const vector<NuclideNumAtomsPair> &parents, const double time_in_seconds )


vector<NuclideActivityPair> SandiaDecayDataBase::decay( const std::vector<NuclideActivityPair> &parents, const double time_in_seconds )
{
  NuclideMixture mixture;
  for( size_t i = 0; i < parents.size(); ++i )
    mixture.addNuclide( parents[i] );
  return mixture.activity( time_in_seconds );
}//vector<NuclideActivityPair> decay( const vector<NuclideActivityPair> &parents, const double time_in_seconds )





std::vector<NuclideTimeEvolution> SandiaDecayDataBase::getTimeEvolution( const std::vector<NuclideActivityPair> &parents )
{
  std::vector<NuclideNumAtomsPair> parents_by_num_atoms;
  for( size_t i =0; i < parents.size(); ++i )
  {
    const Nuclide *nuclide = parents[i].nuclide;
    const double n_atoms = nuclide->activityToNumAtoms( parents[i].activity );
    parents_by_num_atoms.push_back( NuclideNumAtomsPair(nuclide, n_atoms) );
  }

  return getTimeEvolution( parents_by_num_atoms );
}//vector<NuclideTimeEvolution> getTimeEvolution( const vector<NuclideActivityPair> & )


std::vector<NuclideTimeEvolution> SandiaDecayDataBase::getTimeEvolution( const std::vector<NuclideNumAtomsPair> &input )
{
  //This function needs serious cleanup!
  //Also, profiling done 20121010 shows that this function is what should really
  //  be optimized, which makes sense given its implementation
  
  BatemanWorkingSpace ws;
  ws.decay_coeffs.reserve( 65 );  //64 is largest in database
  ws.nuclide_path.reserve( 65 );

  //Lets make sure if the user inputed a vector with multiple entries for
  //  the same nuclide, we combine these entries
  vector<NuclideNumAtomsPair> parents;
  for( size_t i = 0; i < input.size(); ++i )
  {
    const Nuclide * const inputNuclide = input[i].nuclide;

    bool added = false;
    for( size_t p = 0; !added && (p < parents.size()); ++p )
    {
      if( parents[p].nuclide == inputNuclide ) //note: assumes both pointers from same database
      {
        added = true;
        parents[p].numAtoms += input[i].numAtoms;
      }//if( parents has this element )
    }//for( loop over current parents, p )

    if( !added )
      parents.push_back( input[i] );
  }//for( loop over input, i )

#if( DO_EMPTY_TRANSITION_FIX )
  // If an input nuclide doesnt have any children, calc_bateman_coef(...) will ignore it, so we need
  //  to take extra care to insert that nuclide into the decay coefficients.
  std::vector<NuclideNumAtomsPair> childless_parents;
#endif

  for( size_t parentNum = 0; parentNum < parents.size(); ++parentNum )
  {
    const Nuclide *parent = parents[parentNum].nuclide;
    const SandiaDecay::CalcFloatType n_original = parents[parentNum].numAtoms;
    
    const size_t num_trans = parent->decaysToChildren.size();
    for( size_t decayNum = 0; decayNum < num_trans; ++decayNum )
    {
      const Transition * const trans = parent->decaysToChildren[decayNum];
      assert( trans );
      
#if( !DO_EMPTY_TRANSITION_FIX )
      if( trans->child )
#endif
      { 
        const vector<const Transition *> decay_path( 1, trans );
        vector< vector<SandiaDecay::CalcFloatType> > coefs(1, vector<SandiaDecay::CalcFloatType>(1, n_original) );
        coefs.reserve( 128 );
        calc_bateman_coef( coefs, decay_path, ws );
      }//if( trans->child )
    }//for( loop over transition, decayNum )
    
#if( DO_EMPTY_TRANSITION_FIX )
    if( !num_trans )
      childless_parents.push_back( parents[parentNum] );
#endif
  }//for( loop over parental nucildes, parentNum )


  //Now we need to stitch the paths back together, and add up contributions
  //  to each nuclide from each decay path, but we have to be careful we
  //  dont double count contributions from identical sub paths.
  typedef vector<const Nuclide *> DecayPath;
  typedef DecayPath::const_iterator DecayPathIter;
  typedef vector< DecayPath > DecayPathVec;
  typedef DecayPathVec::const_iterator DecayPathVecIter;
  typedef map<const Nuclide *, SandiaDecay::CalcFloatType> NuclideToMagnitudeMap;
  
  // We ca either sort nuclides by value or by ptr.
  //  Doesnt really seem to matter from a time/efficiency/result standpoint
#define SORT_NUCLIDE_BY_PTR 1
#if( SORT_NUCLIDE_BY_PTR )
  typedef map<const Nuclide *, NuclideToMagnitudeMap> NuclToCoefMapMap;
  NuclToCoefMapMap nuc_to_coef_map;
#else
  typedef map<const Nuclide *, NuclideToMagnitudeMap, bool(*)(const Nuclide *,const Nuclide *) > NuclToCoefMapMap;
  NuclToCoefMapMap nuc_to_coef_map( &Nuclide::lessThanByDecay );
#endif

  DecayPathVec sub_paths_used;

  const DecayPathVec &nuclide_paths = ws.nuclide_path;
  const vector< vector< vector<SandiaDecay::CalcFloatType> > > &decay_coeffs = ws.decay_coeffs;

//  cerr << "There were " << decay_coeffs.size() << " paths found" << endl;

  for( size_t solution = 0; solution < decay_coeffs.size(); ++solution )
  {
    for( size_t i = 0; i < decay_coeffs[solution].size(); ++i )
    {
      DecayPathIter path_begin = nuclide_paths[solution].begin();
      DecayPathIter path_end   = path_begin + 1 + i;
      const DecayPath sub_path( path_begin, path_end );

      DecayPathVecIter sub_paths_begin = sub_paths_used.begin();
      DecayPathVecIter sub_paths_end   = sub_paths_used.end();

      if( find( sub_paths_begin, sub_paths_end, sub_path ) != sub_paths_end )  //20121010: This find takes up about 60% of the time of this function
        continue;

      sub_paths_used.push_back( sub_path );

      const Nuclide * const nuclide = sub_path[i];

#if( DO_EMPTY_TRANSITION_FIX )
      if( nuclide )  //Nuclides that have no transitions listed will have nullptr child
#endif
      {
        assert( sub_path.size() > i );
        NuclideToMagnitudeMap &coeff_mapp = nuc_to_coef_map[nuclide];
        
        for( size_t j = 0; j <= i; ++j )
        {
          const SandiaDecay::CalcFloatType coeff = decay_coeffs[solution][i][j];
          const Nuclide *orig_nuc = sub_path[j];
          
          if( !coeff_mapp.count( orig_nuc ) )
            coeff_mapp[orig_nuc] = 0.0;
          
          coeff_mapp[orig_nuc] += coeff;
        }//
      }//if( nuclide )
    }//for( loop over nuclides, i, that we are forming solutions for )
  }//for( loop over solution )


  std::vector<NuclideTimeEvolution> answer;

  for( NuclToCoefMapMap::const_iterator coef_map_iter = nuc_to_coef_map.begin();
      coef_map_iter != nuc_to_coef_map.end();
      ++coef_map_iter )
  {
    const Nuclide * const nuclide = coef_map_iter->first;
    answer.push_back( NuclideTimeEvolution( nuclide ) );
    NuclideTimeEvolution &evolution = answer.back();

    for( NuclideToMagnitudeMap::const_iterator coefs_iter = coef_map_iter->second.begin();
        coefs_iter != coef_map_iter->second.end();
        ++coefs_iter )
    {
      evolution.addEvolutionTerm( coefs_iter->second,  coefs_iter->first );
    }
  }//for( each nuc_to_coef_map entry )


#if( DO_EMPTY_TRANSITION_FIX )
  for( size_t i = 0; i < childless_parents.size(); ++i )
  {
    const NuclideNumAtomsPair &parent = childless_parents[i];
    
    bool found = false;
    for( size_t j = 0; j < answer.size(); ++j )
    {
      if( answer[j].nuclide == parent.nuclide )
      {
        answer[j].addEvolutionTerm( parent.numAtoms, parent.nuclide );
        found = true;
        break;
      }
    }//for( size_t j = 0; j < answer.size(); ++j )
    
    if( !found )
    {
      NuclideTimeEvolution term( parent.nuclide );
      term.addEvolutionTerm( parent.numAtoms, parent.nuclide );
      answer.push_back( term );
    }//if( !found )
  }//for( size_t i = 0; i < childless_parents.size(); ++i )
#endif

#if( SORT_NUCLIDE_BY_PTR )
  std::sort( answer.begin(), answer.end() );
#endif
  
  return answer;
}//std::vector<NuclideTimeEvolution> getTimeEvolution( std::vector<NuclideNumAtomsPair> & ) const







NuclideNumAtomsPair::NuclideNumAtomsPair( const Nuclide *_nuclide, CalcFloatType _numAtoms )
  :   nuclide( _nuclide ), numAtoms( _numAtoms )
{}



  NuclideActivityPair::NuclideActivityPair( const Nuclide *_nuclide, CalcFloatType _activity )
    : nuclide( _nuclide ), activity( _activity )
  {}


  TimeEvolutionTerm::TimeEvolutionTerm( SandiaDecay::CalcFloatType mag,  const Nuclide *nuc )
    : termCoeff( mag ), exponentialCoeff( nuc->decayConstant() )
  {}

  SandiaDecay::CalcFloatType TimeEvolutionTerm::eval( double time_in_seconds ) const
  {
    //return termCoeff * ::expq( -time_in_seconds*exponentialCoeff ); //__float128
    return termCoeff * exp( -time_in_seconds*exponentialCoeff );
  }


 EnergyRatePair::EnergyRatePair( double _numPerSecond, double _energy )
    : energy( _energy ), numPerSecond( _numPerSecond )
  {}


  bool EnergyRatePair::moreThanByNumPerSecond( const EnergyRatePair &lhs,
                                       const EnergyRatePair &rhs )
  {
      return (lhs.numPerSecond > rhs.numPerSecond);
  }

  
  bool EnergyRatePair::lessThanByEnergy( const EnergyRatePair &lhs,
                                              const EnergyRatePair &rhs )
  {
    return lhs.energy < rhs.energy;
  }

  
  bool EnergyCountPair::moreThanByCount( const EnergyCountPair &lhs,
                                     const EnergyCountPair &rhs )
  {
    return (lhs.count > rhs.count);
  }
  
  
  bool EnergyCountPair::lessThanByEnergy( const EnergyCountPair &lhs,
                               const EnergyCountPair &rhs )
  {
    return lhs.energy < rhs.energy;
  }

  
  NuclideTimeEvolution::NuclideTimeEvolution( const Nuclide *_nuclide )
     : nuclide(_nuclide){}

  SandiaDecay::CalcFloatType NuclideTimeEvolution::numAtoms( double time_in_seconds ) const
  {
    SandiaDecay::CalcFloatType n_atoms = 0.0;
    for( size_t i = 0; i < evolutionTerms.size(); ++i )
    {
      n_atoms += evolutionTerms[i].eval( time_in_seconds );
      //cout << "\tEvolutionTerms " << i << ": { termCoeff: " << evolutionTerms[i].termCoeff
      //  << ", exponentialCoeff: " << evolutionTerms[i].exponentialCoeff << " }, n_atoms=" << n_atoms << endl;
    }
    return max( SandiaDecay::CalcFloatType(0.0), n_atoms );
  }

  SandiaDecay::CalcFloatType NuclideTimeEvolution::activity( double time_in_seconds ) const
  {
    const SandiaDecay::CalcFloatType n_atoms = numAtoms( time_in_seconds );
    return nuclide->numAtomsToActivity( n_atoms );
  }

  void NuclideTimeEvolution::addEvolutionTerm( SandiaDecay::CalcFloatType mag,  const Nuclide *nuc )
  {
    evolutionTerms.push_back( TimeEvolutionTerm( mag, nuc ) );
  }

  bool NuclideTimeEvolution::operator<( const NuclideTimeEvolution &rhs ) const
  {
    //if( !nuclide || !rhs.nuclide )
    //  return nuclide < rhs.nuclide;
    
    //return ((*nuclide) < (*rhs.nuclide));
    
    return Nuclide::lessThanForOrdering( nuclide, rhs.nuclide );
  }
}//namespace SandiaDecay