parser.cc

/* 
Beam Delivery Simulation (BDSIM) Copyright (C) Royal Holloway, 
University of London 2001 - 2024.
 
This file is part of BDSIM.
 
BDSIM is free software: you can redistribute it and/or modify 
it under the terms of the GNU General Public License as published 
by the Free Software Foundation version 3 of the License.
 
BDSIM 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 General Public License for more details.
 
You should have received a copy of the GNU General Public License
along with BDSIM.  If not, see <http://www.gnu.org/licenses/>.
*/
#include "parser.h"
 
#include <algorithm>
#include <cmath>
#include <iostream>
#include <list>
#include <set>
#include <string>
#include <vector>
 
// for getpwuid: http://linux.die.net/man/3/getpwuid
#include <unistd.h>
#include <sys/types.h>
#include <pwd.h>
 
#include "array.h"
#include "sym_table.h"
 
namespace {
  // helper method
  // replace algorithm of all substring instances
  // from http://stackoverflow.com/questions/2896600/how-to-replace-all-occurrences-of-a-character-in-string
  void replaceAll(std::string& source, const std::string& from, const std::string& to)
  {
    std::string newString;
    newString.reserve( source.length() );  // avoids a few memory allocations
    
    std::string::size_type lastPos = 0;
    std::string::size_type findPos;
    
    while( std::string::npos != ( findPos = source.find( from, lastPos )))
      {
        newString.append( source, lastPos, findPos - lastPos );
        newString += to;
        lastPos = findPos + from.length();
      }
 
    // Care for the rest after last occurrence
    newString += source.substr( lastPos );
    
    source.swap( newString );
  }
}
 
namespace GMAD {
  // Explicitly make the templates we need here
  template void Parser::Add<Atom, FastList<Atom> >();
  template void Parser::Add<Aperture, FastList<Aperture> >();
  template void Parser::Add<BLMPlacement, FastList<BLMPlacement> >();
  template void Parser::Add<CavityModel, FastList<CavityModel> >();
  template void Parser::Add<Crystal, FastList<Crystal> >();
  template void Parser::Add<Field, FastList<Field> >();
  template void Parser::Add<Material, FastList<Material> >();
  template void Parser::Add<Modulator, FastList<Modulator> >();
  template void Parser::Add<NewColour, FastList<NewColour> >();
  template void Parser::Add<PhysicsBiasing, FastList<PhysicsBiasing> >();
  template void Parser::Add<Placement, FastList<Placement> >();
  template void Parser::Add<Query, FastList<Query> >();
  template void Parser::Add<Region, FastList<Region> >();
  template void Parser::Add<SamplerPlacement, FastList<SamplerPlacement> >();
  template void Parser::Add<Scorer, FastList<Scorer> >();
  template void Parser::Add<ScorerMesh, FastList<ScorerMesh> >();
  template void Parser::Add<Tunnel, FastList<Tunnel> >();
 
  template void Parser::Add<Atom, FastList<Atom> >(bool unique, const std::string& className);
  template void Parser::Add<Aperture, FastList<Aperture> >(bool unique, const std::string& className);
  template void Parser::Add<BLMPlacement, FastList<BLMPlacement> >(bool unique, const std::string& className);
  template void Parser::Add<CavityModel, FastList<CavityModel> >(bool unique, const std::string& className);
  template void Parser::Add<CoolingChannel, FastList<CoolingChannel> >(bool unique, const std::string& className);
  template void Parser::Add<Crystal, FastList<Crystal> >(bool unique, const std::string& className);
  template void Parser::Add<Field, FastList<Field> >(bool unique, const std::string& className);
  template void Parser::Add<ScorerMesh, FastList<ScorerMesh> >(bool unique, const std::string& className);
  template void Parser::Add<Material, FastList<Material> >(bool unique, const std::string& className);
  template void Parser::Add<Modulator, FastList<Modulator> >(bool unique, const std::string& className);
  template void Parser::Add<NewColour, FastList<NewColour> >(bool unique, const std::string& className);
  template void Parser::Add<PhysicsBiasing, FastList<PhysicsBiasing> >(bool unique, const std::string& className);
  //template void Parser::Add<Placement, FastList<Placement> >(bool unique, const std::string& className);
  template void Parser::Add<Query, FastList<Query> >(bool unique, const std::string& className);
  template void Parser::Add<Region, FastList<Region> >(bool unique, const std::string& className);
  template void Parser::Add<SamplerPlacement, FastList<SamplerPlacement> >(bool unique, const std::string& className);
  template void Parser::Add<Scorer, FastList<Scorer> >(bool unique, const std::string& className);
  template void Parser::Add<Tunnel, FastList<Tunnel> >(bool unique, const std::string& className);
  template void Parser::Add<Laser, FastList<Laser> >(bool unique, const std::string& className);
}
 
using namespace GMAD;
 
namespace GMAD {
  extern std::string yyfilename;
}
 
extern int yyparse();
extern FILE *yyin;
 
Parser* Parser::instance = nullptr;
 
Parser::Parser() {
 
}
 
Parser* Parser::Instance()
{
  if (!instance)
    {
      std::cerr << "Parser has not been initialized!" << std::endl;
      exit(1);
    }
  return instance;
}
 
Parser* Parser::Instance(const std::string& name)
{
  if(instance)
    {
      std::cerr << "Warning parser was already initialized!" << std::endl;
      delete instance;
    }
  instance = new Parser(name);
  return instance;
}
 
Parser::~Parser()
{
  beamline_list.erase();
  // delete allocated lines
  for (auto element : allocated_lines)
    {delete element;}
  
  instance = nullptr;
}
 
Parser::Parser(std::string name)
{
  instance = this;
#ifdef BDSDEBUG
  std::cout << "gmad_parser> opening file" << std::endl;
#endif
  // replace all ~ symbols with home directory to allow for that
  // note $HOME is not necessarily equivalent to ~
  // see http://linux.die.net/man/3/getpwuid
  std::string tilde("~");
  std::string home(getpwuid(getuid())->pw_dir);
 
  replaceAll(name,tilde,home);
  
  FILE *f = fopen(name.c_str(),"r");
 
  if(f==nullptr)
    {
      std::cerr << "gmad_parser> Can't open input file " << name << std::endl;
      exit(1);
    }
  // set global string for parser
  yyfilename = std::string(name);
 
  Initialise();
  
  std::cout.precision(10); // set output precision to 10 decimals
 
  ParseFile(f);
}
 
void Parser::ParseFile(FILE *f)
{
  yyin=f; 
 
#ifdef BDSDEBUG
  std::cout << "gmad_parser> beginning to parse file" << std::endl;
#endif
 
  while(!feof(yyin))
    {yyparse();}
  
  expand_sequences();
#ifdef BDSDEBUG
  std::cout << "gmad_parser> finished to parsing file" << std::endl;
#endif
  // clear temporary stuff
#ifdef BDSDEBUG
  std::cout << "gmad_parser> clearing temporary lists" << std::endl;
#endif
  element_list.clear();
  tmp_list.clear();
  symtab_map.clear();
  for(auto it : var_list)
    {delete it;}
 
#ifdef BDSDEBUG
  std::cout << "gmad_parser> finished" << std::endl;
#endif
 
  fclose(f);
}
 
void Parser::Initialise()
{
  const int reserved = 1;
  // embedded arithmetical functions
  add_func("sqrt",std::sqrt);
  add_func("cos",std::cos);
  add_func("sin",std::sin);
  add_func("exp",std::exp);
  add_func("log",std::log);
  add_func("tan",std::tan);
  add_func("asin",std::asin);
  add_func("acos",std::acos);
  add_func("atan",std::atan);
  add_func("abs",std::abs);
 
  add_var("pi",     4.0*std::atan(1),reserved);
  add_var("twopi",  8.0*std::atan(1),reserved);
  add_var("halfpi", 2.0*std::atan(1),reserved);
 
  add_var("PeV",1e6, reserved);
  add_var("TeV",1e3, reserved);
  add_var("GeV",1.0 ,reserved);
  add_var("MeV",1e-3,reserved);
  add_var("keV",1e-6,reserved);
  add_var("KeV",1e-6,reserved); // for compatibility
  add_var("eV" ,1e-9,reserved);
 
  add_var("PJ", 1e12,  reserved);
  add_var("GJ", 1e9,   reserved);
  add_var("MJ", 1e6,   reserved);
  add_var("kJ", 1e3,   reserved);
  add_var("J",  1,     reserved);
  add_var("mJ", 1e-3,  reserved);
  add_var("uJ", 1e-6,  reserved);
  add_var("nJ", 1e-9,  reserved);
  add_var("pJ", 1e-12, reserved);
 
  add_var("mV",1e-3,reserved);
  add_var("V" ,1.0, reserved);
  add_var("kV",1e+3,reserved);
  add_var("MV",1e+6,reserved);
  add_var("GV",1e+9,reserved);
 
  add_var("Tesla",1.0,reserved);
  add_var("T",    1.0,reserved);
 
  add_var("km" ,1e3 ,reserved);
  add_var("m"  ,1.0 ,reserved);
  add_var("cm" ,1e-2,reserved);
  add_var("mm" ,1e-3,reserved);
  add_var("um" ,1e-6,reserved);
  add_var("mum",1e-6,reserved);
  add_var("nm" ,1e-9,reserved);
  add_var("ang",1e-10,reserved);
  add_var("pm" ,1e-12,reserved);
 
  add_var("s"  ,1.0  ,reserved);
  add_var("ms" ,1.e-3,reserved);
  add_var("us" ,1.e-6,reserved);
  add_var("ns" ,1.e-9,reserved);
  add_var("ps" ,1.e-12,reserved);
 
  add_var("Hz" ,1.0,  reserved);
  add_var("kHz",1e+3, reserved);
  add_var("MHz",1e+6, reserved);
  add_var("GHz",1e+9, reserved);
  add_var("THz",1e+12,reserved);
 
  add_var("rad" ,1.0, reserved);
  add_var("mrad",1e-3,reserved);
  add_var("urad",1e-6,reserved);
  add_var("nrad",1e-9,reserved);
 
  add_var("degrees",std::atan(1)/45,reserved);
 
  add_var("clight",2.99792458e+8,reserved);
 
  add_var("kg_per_cubic_m", 1e-3, reserved);
  add_var("g_per_cubic_m", 1e-6, reserved);
  add_var("g_per_cubic_cm", 1, reserved);
 
  add_var("pascal", 1/101324.99987983676, reserved);
  add_var("bar", 1/1.0132499987983676, reserved);
  add_var("torr", 0.00131579, reserved);
  add_var("atmosphere", 1, reserved);
 
  params.flush();
}
 
void Parser::quit()
{
  std::cout << "parsing complete..." << std::endl;
  exit(0);
}
 
void Parser::write_table(std::string* name, ElementType type, bool isLine)
{
  Element e;
  e.set(params,*name,type);
  if (isLine)
    {
      e.lst = new std::list<Element>(tmp_list);
      allocated_lines.push_back(e.lst);
      // clean list
      tmp_list.clear();
      sequences.push_back(*name); // append to all sequence definitions
    }
  
  // insert element with uniqueness requirement
  element_list.push_back(e,true);
}
 
void Parser::expand_sequences()
{
  for (const auto& name : sequences)
    {
      FastList<Element>* newLine = new FastList<Element>();
      expand_line(*newLine, name);
      expandedSequences[name] = newLine;
    }
}
 
void Parser::expand_line(const std::string& name,
                         const std::string& start,
                         const std::string& end)
{
  expand_line(beamline_list, name, start, end);
}
 
void Parser::expand_line(FastList<Element>& target,
                         const std::string& name,
                         const std::string& start,
                         const std::string& end)
{
  const Element& line = find_element(name);
  if(line.type != ElementType::_LINE && line.type != ElementType::_REV_LINE )
    {
      std::cerr << "Error with use command: \"" << name << "\" is not a line" << std::endl;
      exit(1);
    }
  
  // delete the previous beamline  
  target.clear();
  
  // expand the desired beamline
  Element e;
  e.type = line.type;
  e.name = name;
  e.l = 0;
  e.lst = nullptr;
  
  target.push_back(e);
 
#ifdef BDSDEBUG 
  std::cout << "expanding line " << name << ", range = " << start << end << std::endl;
#endif
  if (!line.lst)
    {return;} //list empty
    
  // first expand the whole range 
  std::list<Element>::iterator sit = line.lst->begin();
  std::list<Element>::iterator eit = line.lst->end();
  
  // copy the list into the resulting list
  switch(line.type)
    {
      case ElementType::_LINE:
        {target.insert(target.end(),sit,eit); break;}
      case ElementType::_REV_LINE:
        {target.insert(target.end(),line.lst->rbegin(),line.lst->rend()); break;}
      default:
        {target.insert(target.end(),sit,eit); break;}
    }
  // bool to check if beamline is fully expanded
  bool is_expanded = false;
  
  // parse starting from the second element until the list is expanded
  int iteration = 0;
    while (!is_expanded)
    {
      is_expanded = true;
      // start at second element
      std::list<Element>::iterator it = ++target.begin();
      for (; it!=target.end(); ++it)
        {
          Element& element = *it; // alias
          const ElementType& type = element.type;
#ifdef BDSDEBUG 
          std::cout << element.name << " , " << type << std::endl;
#endif
          // if list - expand further
          if (type != ElementType::_LINE && type != ElementType::_REV_LINE)
            {continue;}
          is_expanded = false;
          // lookup the line in main list
          std::list<Element>::const_iterator tmpit = element_list.find(element.name);
          std::list<Element>::const_iterator iterEnd = element_list.end();
          if ( (tmpit != iterEnd) && ( (*tmpit).lst != nullptr) )
            { // sublist found and not empty
              const Element& list = *tmpit; // alias
#ifdef BDSDEBUG
              std::cout << "inserting sequence for " << element.name << " - " << list.name << " ...";
#endif
              if (type == ElementType::_LINE)
                {target.insert(it,list.lst->begin(),list.lst->end());}
              else if (type == ElementType::_REV_LINE)
                {
                  //iterate over list and invert any sublines contained within. SPM
                  std::list<Element> tmpList;
                  tmpList.insert(tmpList.end(),list.lst->begin(),list.lst->end());
                  for (std::list<Element>::iterator itLineInverter = tmpList.begin();
                       itLineInverter != tmpList.end(); ++itLineInverter)
                    {
                      if ( (*itLineInverter).type == ElementType::_LINE)
                        {(*itLineInverter).type = ElementType::_REV_LINE;}
                      else if ((*itLineInverter).type == ElementType::_REV_LINE)
                        {(*itLineInverter).type = ElementType::_LINE;}
                    }
                  target.insert(it,tmpList.rbegin(),tmpList.rend());
                }
#ifdef BDSDEBUG
              std::cout << "inserted" << std::endl;
#endif
              // delete the list pointer
              target.erase(it--);
            }
          else if ( tmpit != iterEnd )
            { // entry points to a scalar element type -
              //transfer properties from the main list
#ifdef BDSDEBUG 
              std::cout << "keeping element..." << element.name << std::endl;
#endif
              // copy properties
              element = (*tmpit);
              
#ifdef BDSDEBUG 
              std::cout << "done" << std::endl;
#endif
            }
          else
            { // element of undefined type
              std::cerr << "Error : Expanding line \"" << name << "\" : element \"" << element.name
                        << "\" has not been defined! " << std::endl;
              exit(1);
            }
        }
      iteration++;
      if ( iteration > MAX_EXPAND_ITERATIONS )
        {
          std::cerr << "Error : Line expansion of '" << name << "' seems to loop, " << std::endl
                    << "possible recursive line definition, quitting" << std::endl;
          exit(1);
        }
    }// while
    
  // leave only the desired range
  //
  // rule - from first occurrence of 'start' till first 'end' coming after 'start'
  
  if ( !start.empty()) // determine the start element
    {
      std::list<Element>::const_iterator startIt = target.find(std::string(start));
      
      if(startIt!=target.end())
        {target.erase(target.begin(),startIt);}
    }
  
  if ( !end.empty()) // determine the end element
    {
      std::list<Element>::const_iterator endIt = target.find(std::string(end));
      
      if(endIt!=target.end())
        {target.erase(++endIt,target.end());}
    }
  
  // insert the tunnel if present
  
  std::list<Element>::iterator itTunnel = element_list.find("tunnel");
  if (itTunnel!=element_list.end())
    {target.push_back(*itTunnel);}
}
 
const FastList<Element>& Parser::get_sequence(const std::string& name)
{
  // search for previously queried beamlines
  const auto search = expandedSequences.find(name);
  if (search != expandedSequences.end())
    {return *(search->second);}
  else
    {std::cerr << "parser> no such sequence \"" << name << "\"" << std::endl; exit(1);} 
}
 
void Parser::set_sampler(const std::string& name,
                         int                count,
                         ElementType        type,
                         const std::string& samplerType,
                         double             samplerRadius,
                         int                particleSetID)
{
  // if count equal to -2 add to all elements regardless of name
  // typically used for output elements like samplers
  // skip first element and add one at the end
  if (count == -2)
    {
      for (auto it = beamline_list.begin(); it != beamline_list.end(); ++it)
        {// skip LINEs
          if((*it).type == ElementType::_LINE || (*it).type == ElementType::_REV_LINE)
            {continue;}
          // if type not equal to NONE and elements have to match type 
          if (type != ElementType::_NONE && type != (*it).type)
            {continue;}
          
          (*it).setSamplerInfo(samplerType,(*it).name,samplerRadius,particleSetID);
        }
    } 
  else if (count == -1) // if count equal to -1 add sampler to all element instances
    {
      auto itPair = beamline_list.equal_range(name);
      if (itPair.first == itPair.second)
        {
          std::string msg = "parser> SetSampler> current beamline doesn't contain element \"" + name + "\"";
          yyerror2(msg.c_str());
        }
      for (auto it = itPair.first; it != itPair.second; ++it)
        {
          // if sampler is attached to a marker, really attach it to the previous element with the name of marker
          auto elementIt = (it->second);
          std::string samplerName = elementIt->name;
          if ((*elementIt).type == ElementType::_MARKER)
            {
              // need to find real element before
              // but careful not to go beyond first element also!
              while ((*elementIt).isSpecial())
                {
                  elementIt--;
                  // have to break first before continue since in while loop
                  if (elementIt == beamline_list.begin())
                    {break;}
                }
          
              if (elementIt==beamline_list.begin())
                {
                  std::cout << "parser> SetSampler> WARNING: no element before marker " << name << ", no sampler added" << std::endl;
                  continue;
                }
            }
          (*elementIt).setSamplerInfo(samplerType,samplerName,samplerRadius,particleSetID);
        }
    }
  else
    {
      auto it = beamline_list.find(name,count);
      if (it==beamline_list.end())
        {
          std::string msg = "parser> SetSampler> current beamline doesn't contain element \"" + name + "\" with number " + std::to_string(count);
          yyerror2(msg.c_str());
        }
      // if sampler is attached to a marker, really attach it to the previous element with the name of marker
      std::string samplerName = (*it).name;
      if ((*it).type == ElementType::_MARKER)
        {
          // need to find real element before
          // but careful not to go beyond first element also!
          while ((*it).isSpecial())
            {
              it--;
              if (it == beamline_list.begin())
                {
                  std::cout << "parser> SetSampler> WARNING: no element before marker " << name << ", no sampler added" << std::endl;
                  return;
                }
            }
        }
      (*it).setSamplerInfo(samplerType,samplerName,samplerRadius,particleSetID);
    }
}
 
int Parser::add_sampler_partIDSet(std::list<int>* samplerPartIDListIn)
{
  if (!samplerPartIDListIn)
    {return -1;}
  std::set<int> partIDs = std::set<int>(std::begin(*samplerPartIDListIn), std::end(*samplerPartIDListIn));
  auto alreadyExists = samplerFilters.count(partIDs);
  if (alreadyExists > 0)
    {return setToSamplerFilterID[partIDs];}
  else
    {
      int particleSetID = (int) samplerFilterIDToSet.size();
      samplerFilterIDToSet[particleSetID] = partIDs;
      setToSamplerFilterID[partIDs] = particleSetID;
      samplerFilters.insert(partIDs);
      return particleSetID;
    }
}
 
void Parser::add_sampler(const std::string& name, int count, ElementType type, std::string samplerType, std::list<int>* samplerPartIDListIn)
{
#ifdef BDSDEBUG 
  std::cout << "inserting sampler " << name;
  if (count>=0)
    {std::cout << "[" << count << "]";}
  std::cout << std::endl;
#endif
  int particleSetID = add_sampler_partIDSet(samplerPartIDListIn);
  set_sampler(name,count,type,samplerType,0,particleSetID);
}
 
Element& Parser::find_element(const std::string& element_name)
{
  std::list<Element>::iterator it = element_list.find(element_name);
  std::list<Element>::const_iterator iterEnd = element_list.end();
 
  if(it == iterEnd)
    {
      std::cerr << "parser.h> Error: element (type) \"" << element_name
                << "\" has not been defined." << std::endl;
      exit(1);
    }
  return (*it);
}
 
const Element& Parser::find_element(const std::string& element_name)const
{
  auto search = element_list.find(element_name);
  if (search == element_list.end())
    {
      std::cerr << "parser.h> Error: unknown element \"" << element_name << "\"." << std::endl; 
      exit(1);
    }
  return (*search);
}
 
const Element* Parser::find_placement_element_safe(const std::string& element_name) const
{
  const Element* result = nullptr;
  auto search = placement_elements.find(element_name);
  if (search != placement_elements.end())
    {
      const GMAD::Element& ele = *search;
      result = &ele;
    }
  return result;
}
 
const Element* Parser::find_element_safe(const std::string& element_name) const
{
  const Element* result = nullptr;
  auto search = element_list.find(element_name);
  if (search != element_list.end())
    {
      const GMAD::Element& ele = *search;
      result = &ele;
    }
  return result;
}
 
double Parser::property_lookup(const std::string& element_name, const std::string& property_name)const
{
  const Element& element = find_element(element_name);
  return element.property_lookup(property_name);
}
 
void Parser::add_element_temp(const std::string& name, int number, bool pushfront, ElementType linetype)
{
#ifdef BDSDEBUG
  std::cout << "matched sequence element, " << name;
  if (number > 1)
    {std::cout << " * " << number;}
  std::cout << std::endl;
#endif
  // add to temporary element sequence
  Element e;
  e.name = name;
  e.type = linetype;
  e.lst = nullptr;
  if (pushfront)
    {
      for (int i = 0; i < number; i++)
        {tmp_list.push_front(e);}
    }
  else
    {
      for (int i = 0; i < number; i++)
        {tmp_list.push_back(e);}
    }
}
 
int Parser::copy_element_to_params(const std::string& elementName)
{
  int type;
#ifdef BDSDEBUG
  std::cout << "newinstance : VARIABLE -- " << elementName << std::endl;
#endif
  const Element& element = find_element(elementName);
 
  // inherit properties from the base type
  type = static_cast<int>(element.type);
  params.inherit_properties(element);
 
  return type;
}
 
void Parser::add_func(std::string name, double (*func)(double))
{
  Symtab *sp=symtab_map.symcreate(name);
  sp->Set(func);
}
 
void Parser::add_var(std::string name, double value, int is_reserved)
{
  Symtab* sp = symtab_map.symcreate(name);
  sp->Set(value,is_reserved);
}
 
bool Parser::InvalidSymbolName(const std::string& s, std::string& errorReason)
{
  bool result = false;
  if (options.NameExists(s))
    {result = true; errorReason = "The variable name \"" + s + "\" is an option name and cannot be used as a variable name";}
  return result;
}
 
Symtab * Parser::symcreate(const std::string& s)
{
  return symtab_map.symcreate(s);
}
 
Symtab * Parser::symlook(const std::string& s)
{
  return symtab_map.symlook(s);
}
void Parser::Store(double value)
{
  tmparray.push_front(value);
}
 
void Parser::Store(const std::string& name)
{
  tmpstring.push_front(name);
}
 
void Parser::FillArray(Array* array)
{
  array->Copy(tmparray);
  tmparray.clear();
}
 
void Parser::FillString(Array* array)
{
  array->Copy(tmpstring);
  tmpstring.clear();
}
 
void Parser::ClearParams()
{
  params.flush();
  samplerFilters.clear();
}
 
void Parser::Overwrite(const std::string& objectName)
{
  // find object and set values
 
  // possible object types are:
  // element, atom, colour, crystal, coolingchannel, field, laser, material, physicsbiasing, placement,
  // query, region, tunnel, cavitymodel, samplerplacement, aperture, scorer, scorermesh, blm
  bool extended = false;
  auto element_it = element_list.find(objectName);
  if (element_it != element_list.end())
    {
      ExtendObject(*element_it);
      extended = true;
    }
  else
    {
      auto it = xsecbias_list.find(objectName);
      if (it != xsecbias_list.end() )
        {
          ExtendObject(*it);
          extended = true;
        }
    }
  // vectors
  if (!extended) {
    if (      (extended = FindAndExtend<Atom>       (objectName)) ) {}
    else if ( (extended = FindAndExtend<NewColour>  (objectName)) ) {}
    else if ( (extended = FindAndExtend<Crystal>    (objectName)) ) {}
    else if ( (extended = FindAndExtend<CoolingChannel> (objectName)) ) {}
    else if ( (extended = FindAndExtend<Field>      (objectName)) ) {}
    else if ( (extended = FindAndExtend<Material>   (objectName)) ) {}
    else if ( (extended = FindAndExtend<Placement>  (objectName)) ) {}
    else if ( (extended = FindAndExtend<Query>      (objectName)) ) {}
    else if ( (extended = FindAndExtend<Region>     (objectName)) ) {}
    else if ( (extended = FindAndExtend<Tunnel>     (objectName)) ) {}
    else if ( (extended = FindAndExtend<CavityModel>(objectName)) ) {}
    else if ( (extended = FindAndExtend<SamplerPlacement>(objectName)) ) {}
    else if ( (extended = FindAndExtend<Scorer>     (objectName)) ) {}
    else if ( (extended = FindAndExtend<ScorerMesh> (objectName)) ) {}
    else if ( (extended = FindAndExtend<Aperture>   (objectName)) ) {}
    else if ( (extended = FindAndExtend<BLMPlacement> (objectName)) ) {}
    else if ( (extended = FindAndExtend<Modulator>  (objectName)) ) {}
    else if ( (extended = FindAndExtend<Laser>      (objectName)) ) {}
  }
 
  if (!extended)
    {
      std::cerr << "parser.h> Error: object \"" << objectName
                << "\" has not been defined and can't be extended." << std::endl;
      exit(1);
    }
 
  // clear maps
  extendedNumbers.clear();
  extendedStrings.clear();
  extendedVectors.clear();
}
 
template <class C>
bool Parser::FindAndExtend(const std::string& objectName)
{
  GMAD::FastList<C>& fl = GetList<C>();
  auto search = fl.find(objectName);
  if (search != fl.end())
    {
      ExtendObject(*search);
      return true;
    }
  return false;
}
 
template<class C>
void Parser::ExtendObject(C& object)
{
  for (auto& option : extendedNumbers)
    {object.set_value(option.first, option.second);}
  for (auto& option : extendedStrings)
    {object.set_value(option.first, option.second);}
  for (auto& option : extendedVectors)
    {object.set_value(option.first, option.second);}
}
 
void Parser::AddVariable(std::string* name)
{
  var_list.push_back(name);
}
 
void Parser::PrintBeamline()const
{
  beamline_list.print();
}
 
void Parser::PrintElements()const
{
  element_list.print();
}
 
void Parser::PrintOptions()const
{
  options.print();
}
 
bool Parser::TryPrintingObject(const std::string& objectName) const
{
  // We just don't know the type of the object, only the name, so we must
  // search each member vector. Try to optimise by returning once done.
  // This is a cpu-heavy solution vs a memory-heavy one that would have to
  // keep a duplicate copy of all objects for printing.
  
  const std::string& on = objectName; // shortcut
 
  // we use a lambda to compare against obj.name instead of obj itself
  auto searchAtom = std::find_if(atom_list.begin(), atom_list.end(), [&on](const Atom& obj) {return obj.name == on;});
  if (searchAtom != atom_list.end())
    {searchAtom->print(); return true;}
  auto searchNewColour = std::find_if(colour_list.begin(), colour_list.end(), [&on](const NewColour& obj) {return obj.name == on;});
  if (searchNewColour != colour_list.end())
    {searchNewColour->print(); return true;}
  auto searchCrystal = std::find_if(crystal_list.begin(), crystal_list.end(), [&on](const Crystal& obj) {return obj.name == on;});
  if (searchCrystal != crystal_list.end())
    {searchCrystal->print(); return true;}
  auto searchCoolingChannel = std::find_if(coolingchannel_list.begin(), coolingchannel_list.end(), [&on](const CoolingChannel& obj) {return obj.name == on;});
  if (searchCoolingChannel != coolingchannel_list.end())
    {searchCoolingChannel->print(); return true;}
  auto searchField = std::find_if(field_list.begin(), field_list.end(), [&on](const Field& obj) {return obj.name == on;});
  if (searchField != field_list.end())
    {searchField->print(); return true;}
  auto searchLaser = std::find_if(laser_list.begin(), laser_list.end(), [&on](const Laser& obj) {return obj.name == on;});
  if (searchLaser != laser_list.end())
    {searchLaser->print(); return true;}
  auto searchMaterial = std::find_if(material_list.begin(), material_list.end(), [&on](const Material& obj) {return obj.name == on;});
  if (searchMaterial != material_list.end())
    {searchMaterial->print(); return true;}
  auto searchQuery = std::find_if(query_list.begin(), query_list.end(), [&on](const Query& obj) {return obj.name == on;});
  if (searchQuery != query_list.end())
    {searchQuery->print(); return true;}
  auto searchRegion = std::find_if(region_list.begin(), region_list.end(), [&on](const Region& obj) {return obj.name == on;});
  if (searchRegion != region_list.end())
    {searchRegion->print(); return true;}
  auto searchTunnel = std::find_if(tunnel_list.begin(), tunnel_list.end(), [&on](const Tunnel& obj) {return obj.name == on;});
  if (searchTunnel != tunnel_list.end())
    {searchTunnel->print(); return true;}
  auto searchXsecbias = std::find_if(xsecbias_list.begin(), xsecbias_list.end(), [&on](const PhysicsBiasing& obj) {return obj.name == on;});
  if (searchXsecbias != xsecbias_list.end())
    {searchXsecbias->print(); return true;}
  auto searchPlacement = std::find_if(placement_list.begin(), placement_list.end(), [&on](const Placement& obj) {return obj.name == on;});
  if (searchPlacement != placement_list.end())
    {searchPlacement->print(); return true;}
  auto searchCavityModel = std::find_if(cavitymodel_list.begin(), cavitymodel_list.end(), [&on](const CavityModel& obj) {return obj.name == on;});
  if (searchCavityModel != cavitymodel_list.end())
    {searchCavityModel->print(); return true;}
  auto searchSamplerPlacement = std::find_if(samplerplacement_list.begin(), samplerplacement_list.end(), [&on](const SamplerPlacement& obj) {return obj.name == on;});
  if (searchSamplerPlacement != samplerplacement_list.end())
    {searchSamplerPlacement->print(); return true;}
  auto searchScorer = std::find_if(scorer_list.begin(), scorer_list.end(), [&on](const Scorer& obj) {return obj.name == on;});
  if (searchScorer != scorer_list.end())
  {searchScorer->print(); return true;}
  auto searchScorerMesh = std::find_if(scorermesh_list.begin(), scorermesh_list.end(), [&on](const ScorerMesh& obj) {return obj.name == on;});
  if (searchScorerMesh != scorermesh_list.end())
    {searchScorerMesh->print(); return true;}
  auto searchAperture = std::find_if(aperture_list.begin(), aperture_list.end(), [&on](const Aperture& obj) {return obj.name == on;});
  if (searchAperture != aperture_list.end())
    {searchAperture->print(); return true;}
  auto searchBLMPlacement = std::find_if(blm_list.begin(), blm_list.end(), [&on](const BLMPlacement& obj) {return obj.name == on;});
  if (searchBLMPlacement != blm_list.end())
    {searchBLMPlacement->print(); return true;}
  auto searchModulator = std::find_if(modulator_list.begin(), modulator_list.end(), [&on](const Modulator& obj) {return obj.name == on;});
  if (searchModulator != modulator_list.end())
    {searchModulator->print(); return true;}
  
  return false;
}
 
const FastList<Element>& Parser::GetBeamline()const
{
  return beamline_list;
}
 
//template specialisation
// put explicitly in namespace since g++ complains
namespace GMAD {
 
  template<> Aperture& Parser::GetGlobal() {return aperture;}
  template<> Aperture* Parser::GetGlobalPtr(){return &aperture;}
  template<> FastList<Aperture>& Parser::GetList<Aperture>() {return aperture_list;}
 
  template<> Atom& Parser::GetGlobal(){return atom;}
  template<> Atom* Parser::GetGlobalPtr(){return &atom;}
  template<> FastList<Atom>& Parser::GetList<Atom>(){return atom_list;}
 
  template<> Beam& Parser::GetGlobal(){return beam;}
  template<> Beam* Parser::GetGlobalPtr(){return &beam;}
 
  template<> BLMPlacement& Parser::GetGlobal() {return blm;}
  template<> BLMPlacement* Parser::GetGlobalPtr() {return &blm;}
  template<> FastList<BLMPlacement>& Parser::GetList<BLMPlacement>() {return blm_list;}
 
  template<> CavityModel& Parser::GetGlobal(){return cavitymodel;}
  template<> CavityModel* Parser::GetGlobalPtr(){return &cavitymodel;}
  template<> FastList<CavityModel>& Parser::GetList<CavityModel>(){return cavitymodel_list;}
 
  template<> NewColour& Parser::GetGlobal(){return colour;}
  template<> NewColour* Parser::GetGlobalPtr(){return &colour;}
  template<> FastList<NewColour>& Parser::GetList<NewColour>(){return colour_list;}
 
  template<> CoolingChannel& Parser::GetGlobal(){return coolingchannel;}
  template<> CoolingChannel* Parser::GetGlobalPtr(){return &coolingchannel;}
  template<> FastList<CoolingChannel>& Parser::GetList<CoolingChannel>(){return coolingchannel_list;}
 
  template<> Crystal& Parser::GetGlobal(){return crystal;}
  template<> Crystal* Parser::GetGlobalPtr(){return &crystal;}
  template<> FastList<Crystal>& Parser::GetList<Crystal>(){return crystal_list;}
 
  template<> Field& Parser::GetGlobal(){return field;}
  template<> Field* Parser::GetGlobalPtr(){return &field;}
  template<> FastList<Field>& Parser::GetList<Field>(){return field_list;}
 
 
  template<> Material& Parser::GetGlobal(){return material;}
  template<> Material* Parser::GetGlobalPtr(){return &material;}
  template<> FastList<Material>& Parser::GetList<Material>(){return material_list;}
 
  template<> Laser& Parser::GetGlobal(){return laser;}
  template<> Laser* Parser::GetGlobalPtr(){return &laser;}
  template<> FastList<Laser>& Parser::GetList<Laser>(){return laser_list;}
 
  template<> Modulator& Parser::GetGlobal() {return modulator;}
  template<> Modulator* Parser::GetGlobalPtr() {return &modulator;}
  template<> FastList<Modulator>& Parser::GetList<Modulator>() {return modulator_list;}
 
  template<> Options& Parser::GetGlobal(){return options;}
  template<> Options* Parser::GetGlobalPtr(){return &options;}
 
  template<> Parameters& Parser::GetGlobal(){return params;}
  template<> Parameters* Parser::GetGlobalPtr(){return &params;}
 
  template<> PhysicsBiasing& Parser::GetGlobal(){return xsecbias;}
  template<> PhysicsBiasing* Parser::GetGlobalPtr(){return &xsecbias;}
  template<> FastList<PhysicsBiasing>& Parser::GetList<PhysicsBiasing, FastList<PhysicsBiasing>>(){return xsecbias_list;}
 
  template<> Placement& Parser::GetGlobal(){return placement;}
  template<> Placement* Parser::GetGlobalPtr(){return &placement;}
  template<> FastList<Placement>& Parser::GetList<Placement>(){return placement_list;}
 
  template<> Query& Parser::GetGlobal(){return query;}
  template<> Query* Parser::GetGlobalPtr(){return &query;}
  template<> FastList<Query>& Parser::GetList<Query>(){return query_list;}
 
  template<> Region& Parser::GetGlobal(){return region;}
  template<> Region* Parser::GetGlobalPtr(){return &region;}
  template<> FastList<Region>& Parser::GetList<Region>(){return region_list;}
 
  template<> SamplerPlacement& Parser::GetGlobal(){return samplerplacement;}
  template<> SamplerPlacement* Parser::GetGlobalPtr(){return &samplerplacement;}
  template<> FastList<SamplerPlacement>& Parser::GetList<SamplerPlacement>() {return samplerplacement_list;}
 
  template<> Scorer& Parser::GetGlobal(){return scorer;}
  template<> Scorer* Parser::GetGlobalPtr(){return &scorer;}
  template<> FastList<Scorer>& Parser::GetList<Scorer>() {return scorer_list;}
 
  template<> ScorerMesh& Parser::GetGlobal(){return scorermesh;}
  template<> ScorerMesh* Parser::GetGlobalPtr(){return &scorermesh;}
  template<> FastList<ScorerMesh>& Parser::GetList<ScorerMesh>() {return scorermesh_list;}
 
  template<> Tunnel& Parser::GetGlobal(){return tunnel;}
  template<> Tunnel* Parser::GetGlobalPtr(){return &tunnel;}
  template<> FastList<Tunnel>& Parser::GetList<Tunnel>(){return tunnel_list;}
 
 
  template<>
  void Parser::ExtendValue(const std::string& property, double value)
  {extendedNumbers[property]=value;}
 
  template<>
  void Parser::ExtendValue(const std::string& property, std::string value)
  {extendedStrings[property]=value;}
 
  template<>
  void Parser::ExtendValue(const std::string& property, Array* value)
  {extendedVectors[property]=value;}
  
  template <class C, class Container>
  void Parser::Add()
  {
    // copy from global
    C& global = GetGlobal<C>();
    C inst(global);
    // reset global
    global.clear();
#ifdef BDSDEBUG
    inst.print();
#endif
    GetList<C, Container>().push_back(inst);
  }
  
  template <class C, class Container>
  void Parser::Add(bool unique, const std::string& className)
  {
    // copy from global
    C& global = GetGlobal<C>();
    C inst(global);
    // reset global
    global.clear();
#ifdef BDSDEBUG
    inst.print();
#endif
    GetList<C, Container>().push_back(inst, unique, className);
  }
  
  template <>
  void Parser::Add<Placement, FastList<Placement>>(bool unique, const std::string& className)
  {
    // copy from global
    Placement& global = GetGlobal<Placement>();
    Placement inst(global);
    // reset global
    global.clear();
#ifdef BDSDEBUG
    inst.print();
#endif
    GetList<Placement, FastList<Placement>>().push_back(inst, unique, className);
    // if an element definition is used for a placement, keep a separate copy of it
    if (!inst.bdsimElement.empty())
      {
        const Element* elDef = find_element_safe(inst.bdsimElement);
        if (!elDef)
          {
            std::cerr << "The bdsimElement referred to in \"" << inst.name << "\" (\""
                      << inst.bdsimElement << "\") cannot be found and should be defined"
                      << " before this placement" << std::endl;
            exit(1);
          }
        placement_elements.push_back(Element(*elDef));
      }
  }
}