doxygen/html/SpeciesFactory_8h_source.html

//* This file is a part of PRISM: Plasma Reaction Input SysteM,

//* A library for parcing chemical reaction networks for plasma chemistry

//* https://github.com/NCSU-ComPS-Group/prism

//*

//* Licensed under MIT, please see LICENSE for details

//* https://opensource.org/license/mit

//*

//* Copyright 2024, North Carolina State University

//* ALL RIGHTS RESERVED

//*

#pragma once

#include <map>

#include <string>

#include <unordered_map>


#include "yaml-cpp/yaml.h"


#include "Species.h"

#include "PrismConstants.h"


namespace prism

{

class Reaction;

class SpeciesSummaryWriterBase;


class SpeciesFactory

{

#ifndef TESTING

private:

#else

public:

#endif

  static SpeciesFactory & instance();

  void clear();

  // if we are in testing mode we'll give other people access to these

  // otherwise we want them to be private

  void collectCustomSpecies(const YAML::Node & network);

  void collectLumpedSpecies(const YAML::Node & network);

  void collectLatexOverrides(const YAML::Node & network);

  void collectConstantSpecies(const YAML::Node & network);

  double getMass(const std::string & name) const;

#ifdef TESTING

private:

#endif

  friend class NetworkParser;

  friend class SubSpecies;

  friend class Reaction;


  const std::string getLatexOverride(const std::string & name) const;


  std::weak_ptr<Species> getSpecies(const std::string & name);

  // /**

  //  *

  //  */

  const std::vector<std::shared_ptr<Species>> & species() const { return _species; }

  const std::vector<std::shared_ptr<const Species>> & transientSpecies() const

  {

    return _transient_species;

  }


  const std::vector<std::string> & speciesNames() const { return _species_names; }

  std::weak_ptr<Species> getLumpedSpecies(std::weak_ptr<Species> s);

  void indexSpecies();


  void addRateBasedReaction(std::shared_ptr<const Reaction> r);

  void addXSecBasedReaction(std::shared_ptr<const Reaction> r);


  SpeciesFactory();

  // Private copy constructor and assignment operator to prevent cloning

  SpeciesFactory(const SpeciesFactory &) = delete;

  SpeciesFactory & operator=(const SpeciesFactory &) = delete;

  // Private instance of the singleton

  static SpeciesFactory * _instance;


  void writeSpeciesSummary(const std::string & file,

                           SpeciesSummaryWriterBase & writer,

                           const std::vector<std::shared_ptr<Reaction>> & rate_based,

                           const std::vector<std::shared_ptr<Reaction>> & xsec_based) const;

  std::vector<std::shared_ptr<Species>> _species;

  std::unordered_map<std::string, SpeciesId> _species_indicies;

  std::vector<std::string> _species_names;

  std::vector<std::shared_ptr<const Species>> _transient_species;

  std::map<std::string, std::string> _lumped_map;

  std::set<std::string> _constant_species;

  std::unordered_map<std::string, std::string> _latex_overrides;

  std::unordered_map<std::string, double> _default_masses = {{"hnu", 0.0},

                                                             {"M", 1},

                                                             {"e", 5.4857990943E-4},

                                                             {"E", 5.4857990943E-4},

                                                             {"H", 1.00794},

                                                             {"D", 2.014102},

                                                             {"T", 3.01604928},

                                                             {"He", 4.002602},

                                                             {"Li", 6.941},

                                                             {"Be", 9.012182},

                                                             {"B", 10.811},

                                                             {"C", 12.0107},

                                                             {"N", 14.0067},

                                                             {"O", 15.9994},

                                                             {"F", 18.9984032},

                                                             {"Ne", 20.1797},

                                                             {"Na", 22.98976928},

                                                             {"Mg", 24.3050},

                                                             {"Al", 26.9815386},

                                                             {"Si", 28.0855},

                                                             {"P", 30.973762},

                                                             {"S", 32.065},

                                                             {"Cl", 35.453},

                                                             {"Ar", 39.948},

                                                             {"K", 39.0983},

                                                             {"Ca", 40.078},

                                                             {"Sc", 44.955912},

                                                             {"Ti", 47.867},

                                                             {"V", 50.9415},

                                                             {"Cr", 51.9961},

                                                             {"Mn", 54.938045},

                                                             {"Fe", 55.845},

                                                             {"Co", 58.933195},

                                                             {"Ni", 58.6934},

                                                             {"Cu", 63.546},

                                                             {"Zn", 65.409},

                                                             {"Ga", 69.723},

                                                             {"Ge", 72.64},

                                                             {"As", 74.92160},

                                                             {"Se", 78.96},

                                                             {"Br", 79.904},

                                                             {"Kr", 83.798},

                                                             {"Rb", 85.4678},

                                                             {"Sr", 87.62},

                                                             {"Y", 88.90585},

                                                             {"Zr", 91.224},

                                                             {"Nb", 92.90638},

                                                             {"Mo", 95.94},

                                                             {"Tc", 98},

                                                             {"Ru", 101.07},

                                                             {"Rh", 102.90550},

                                                             {"Pd", 106.42},

                                                             {"Ag", 107.8682},

                                                             {"Cd", 112.411},

                                                             {"In", 114.818},

                                                             {"Sn", 118.710},

                                                             {"Sb", 121.760},

                                                             {"Te", 126.90447},

                                                             {"I", 126.90447},

                                                             {"Xe", 131.293},

                                                             {"Cs", 132.9054519},

                                                             {"Ba", 137.327},

                                                             {"La", 138.90547},

                                                             {"Hf", 178.89},

                                                             {"Ta", 180.94788},

                                                             {"W", 183.84},

                                                             {"Re", 186.207},

                                                             {"Os", 190.23},

                                                             {"Ir", 192.217},

                                                             {"Pt", 195.084},

                                                             {"Au", 196.966569},

                                                             {"Hg", 200.59},

                                                             {"Ti", 204.3833},

                                                             {"Pb", 207.2},

                                                             {"Bi", 208.98040},

                                                             {"Po", 209},

                                                             {"At", 210},

                                                             {"Rn", 222},

                                                             {"Fr", 223},

                                                             {"Ra", 226},

                                                             {"Ac", 227},

                                                             {"Rf", 267},

                                                             {"Db", 268.12567},

                                                             {"Sg", 271.13393},

                                                             {"Bh", 272.13826},

                                                             {"Hs", 270.13429},

                                                             {"Mt", 276.15159},

                                                             {"Ds", 281.16451},

                                                             {"Rg", 280.16514},

                                                             {"Cn", 285.17712},

                                                             // Lanthoids

                                                             {"Ce", 140.116},

                                                             {"Pr", 140.90765},

                                                             {"Nd", 144.242},

                                                             {"Pm", 145},

                                                             {"Sm", 150.36},

                                                             {"Eu", 151.964},

                                                             {"Gs", 157.25},

                                                             {"Tb", 158.92535},

                                                             {"Dy", 162.500},

                                                             {"Ho", 164.93032},

                                                             {"Er", 167.259},

                                                             {"Tm", 168.93421},

                                                             {"Yb", 173.04},

                                                             {"Lu", 174.967},

                                                             // Actinoids

                                                             {"Th", 232.02806},

                                                             {"Pa", 231.03588},

                                                             {"U", 238.02891},

                                                             {"Np", 237},

                                                             {"Pu", 244},

                                                             {"Am", 241.0568293},

                                                             {"Cm", 243.0613893},

                                                             {"Bk", 247.0703073},

                                                             {"Cf", 249.0748539},

                                                             {"Es", 252.082980},

                                                             {"Fm", 257.0951061},

                                                             {"Md", 28.0984315},

                                                             {"No", 259.10103},

                                                             {"Lr", 262.10961}};

  std::unordered_map<std::string, double> _base_masses = _default_masses;

};


}

prism::Reaction
Stores all of the data needed to perform calculations with a specific reaction.
Definition Reaction.h:73

prism::SpeciesFactory::NetworkParser
friend class NetworkParser
friend class so the parser can call several private methods
Definition SpeciesFactory.h:58

prism::SpeciesSummaryWriterBase
Definition SpeciesSummaryWriterBase.h:27