ReactionNetworkUtils::Reaction Struct Reference

#include <ReactionNetworkUtils.h>

Public Member Functions
std::vector< VariableName >	getSpecies () const
	Get all species involved in the reaction.
std::vector< VariableName >	getUniqueSpecies () const
	Get all unique species involved in the reaction Note: a species will only appear once even if both a reactant and a product.
std::vector< Real >	getStoichiometricCoefficients () const
	Get the stoeichiometric coefficients for each species in the reaction The sign used matches the sign in the reaction equation.
std::map< VariableName, Real >	getUniqueStoichiometricCoefficients () const
	Get the stoeichiometric coefficients for each unique species in the reaction Note: if a species is both a reactant and a product, the coefficient will be the difference between its product and reactor coefficients Note: this means all coefficients for reactants that are not products are negative, unlike in getStoichiometricCoefficients()
std::vector< VariableName >	getReactantSpecies () const
	Get all reactant species involved in the reaction (on LHS)
std::vector< VariableName >	getUniqueReactantSpecies () const
	Get all unique reactant species involved in the reaction (on LHS)
std::vector< std::string >	getProductSpecies () const
	Get all product species involved in the reaction (on RHS)
std::vector< std::string >	getUniqueProductSpecies () const
	Get all unique product species involved in the reaction (on RHS)
template<typename T >
bool	hasMetaData (const std::string &key) const
	Whether the reaction has the metadata with the given type.
bool	hasMetaData (const std::string &key) const
	Whether the reaction has the metadata.
const std::string &	getMetaData (const std::string &key) const
	Get the metadata from the reaction.
template<>
bool	hasMetaData (const std::string &key) const

Public Attributes
TermList	reactants
TermList	products
Metadata	metadata

Detailed Description

Definition at line 44 of file ReactionNetworkUtils.h.

Member Function Documentation

getMetaData()

const std::string & ReactionNetworkUtils::Reaction::getMetaData

(

const std::string &

key

)

const

Get the metadata from the reaction.

Definition at line 327 of file ReactionNetworkUtils.C.

{
  // Get a better error
  if (hasMetaData(key))
    return libmesh_map_find(metadata, key);
  else
    mooseError("MetaData item '" + key + "' was not found in reaction:\n" +
               Moose::stringify(*this));
}

getProductSpecies()

std::vector< std::string > ReactionNetworkUtils::Reaction::getProductSpecies

(

)

const

Get all product species involved in the reaction (on RHS)

Definition at line 283 of file ReactionNetworkUtils.C.

{
  std::vector<std::string> species;
  for (const auto & term : products)
    species.push_back(term.species + term.state.value_or("") + term.charge.value_or(""));
  return species;
}

getReactantSpecies()

std::vector< VariableName > ReactionNetworkUtils::Reaction::getReactantSpecies

(

)

const

Get all reactant species involved in the reaction (on LHS)

Definition at line 260 of file ReactionNetworkUtils.C.

{
  std::vector<VariableName> species;
  for (const auto & term : reactants)
    species.push_back(term.species + term.state.value_or("") + term.charge.value_or(""));
  return species;
}

getSpecies()

std::vector< VariableName > ReactionNetworkUtils::Reaction::getSpecies

(

)

const

Get all species involved in the reaction.

Definition at line 201 of file ReactionNetworkUtils.C.

{
  std::vector<VariableName> species;
  for (const auto & term : reactants)
    species.push_back(term.species + term.state.value_or("") + term.charge.value_or(""));
  for (const auto & term : products)
    species.push_back(term.species + term.state.value_or("") + term.charge.value_or(""));
  return species;
}

getStoichiometricCoefficients()

std::vector< Real > ReactionNetworkUtils::Reaction::getStoichiometricCoefficients

(

)

const

Get the stoeichiometric coefficients for each species in the reaction The sign used matches the sign in the reaction equation.

Definition at line 232 of file ReactionNetworkUtils.C.

{
  std::vector<Real> coeffs;
  for (const auto & term : reactants)
    coeffs.push_back(term.coefficient);
  for (const auto & term : products)
    coeffs.push_back(term.coefficient);
  return coeffs;
}

getUniqueProductSpecies()

std::vector< std::string > ReactionNetworkUtils::Reaction::getUniqueProductSpecies

(

)

const

Get all unique product species involved in the reaction (on RHS)

Definition at line 292 of file ReactionNetworkUtils.C.

{
  std::vector<std::string> species;
  std::set<Term> terms_gathered;
  for (const auto & term : products)
    if (terms_gathered.find(term) == terms_gathered.end())
    {
      species.push_back(term.species + term.state.value_or("") + term.charge.value_or(""));
      terms_gathered.insert(term);
    }
  return species;
}

getUniqueReactantSpecies()

std::vector< VariableName > ReactionNetworkUtils::Reaction::getUniqueReactantSpecies

(

)

const

Get all unique reactant species involved in the reaction (on LHS)

Definition at line 269 of file ReactionNetworkUtils.C.

{
  std::vector<VariableName> species;
  std::set<Term> terms_gathered;
  for (const auto & term : reactants)
    if (terms_gathered.find(term) == terms_gathered.end())
    {
      species.push_back(term.species + term.state.value_or("") + term.charge.value_or(""));
      terms_gathered.insert(term);
    }
  return species;
}

getUniqueSpecies()

std::vector< VariableName > ReactionNetworkUtils::Reaction::getUniqueSpecies

(

)

const

Get all unique species involved in the reaction Note: a species will only appear once even if both a reactant and a product.

Definition at line 212 of file ReactionNetworkUtils.C.

{
  std::vector<VariableName> species;
  std::set<Term> terms_gathered;
  for (const auto & term : reactants)
    if (terms_gathered.find(term) == terms_gathered.end())
    {
      species.push_back(term.species + term.state.value_or("") + term.charge.value_or(""));
      terms_gathered.insert(term);
    }
  for (const auto & term : products)
    if (terms_gathered.find(term) == terms_gathered.end())
    {
      species.push_back(term.species + term.state.value_or("") + term.charge.value_or(""));
      terms_gathered.insert(term);
    }
  return species;
}

getUniqueStoichiometricCoefficients()

std::map< VariableName, Real > ReactionNetworkUtils::Reaction::getUniqueStoichiometricCoefficients

(

)

const

Get the stoeichiometric coefficients for each unique species in the reaction Note: if a species is both a reactant and a product, the coefficient will be the difference between its product and reactor coefficients Note: this means all coefficients for reactants that are not products are negative, unlike in getStoichiometricCoefficients()

Definition at line 243 of file ReactionNetworkUtils.C.

{
  std::map<VariableName, Real> terms_gathered;
  for (const auto & term : reactants)
  {
    const auto term_str = term.species + term.state.value_or("") + term.charge.value_or("");
    terms_gathered[term_str] -= term.coefficient;
  }
  for (const auto & term : products)
  {
    const auto term_str = term.species + term.state.value_or("") + term.charge.value_or("");
    terms_gathered[term_str] += term.coefficient;
  }
  return terms_gathered;
}

hasMetaData() [1/3]

template<typename T >

bool ReactionNetworkUtils::Reaction::hasMetaData

(

const std::string &

key

)

const

Whether the reaction has the metadata with the given type.

Definition at line 314 of file ReactionNetworkUtils.C.

{
  mooseError("Has metadata not implemented for type " + MooseUtils::prettyCppType<T>());
  return false;
}

Referenced by getMetaData().

hasMetaData() [2/3]

bool ReactionNetworkUtils::Reaction::hasMetaData

(

const std::string &

key

)

const

Whether the reaction has the metadata.

Definition at line 321 of file ReactionNetworkUtils.C.

{
  return metadata.count(key);
}

hasMetaData() [3/3]

template<>

bool ReactionNetworkUtils::Reaction::hasMetaData

(

const std::string &

key

)

const

Definition at line 306 of file ReactionNetworkUtils.C.

{
  return metadata.count(key) && MooseUtils::isFloat(libmesh_map_find(metadata, key));
}

Member Data Documentation

metadata

Metadata ReactionNetworkUtils::Reaction::metadata

Definition at line 48 of file ReactionNetworkUtils.h.

Referenced by getMetaData(), hasMetaData(), ReactionNetworkUtils::parseReactionNetwork(), and Moose::stringify().

products

TermList ReactionNetworkUtils::Reaction::products

Definition at line 47 of file ReactionNetworkUtils.h.

Referenced by getProductSpecies(), getSpecies(), getStoichiometricCoefficients(), getUniqueProductSpecies(), getUniqueSpecies(), getUniqueStoichiometricCoefficients(), ReactionNetworkUtils::parseReactionNetwork(), and Moose::stringify().

reactants

TermList ReactionNetworkUtils::Reaction::reactants

Definition at line 46 of file ReactionNetworkUtils.h.

Referenced by getReactantSpecies(), getSpecies(), getStoichiometricCoefficients(), getUniqueReactantSpecies(), getUniqueSpecies(), getUniqueStoichiometricCoefficients(), ReactionNetworkUtils::parseReactionNetwork(), and Moose::stringify().

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The documentation for this struct was generated from the following files:

• chemical_reactions/include/utils/ReactionNetworkUtils.h
• chemical_reactions/src/utils/ReactionNetworkUtils.C