AddCoupledSolidKinSpeciesAction Class Reference

#include <AddCoupledSolidKinSpeciesAction.h>

Inheritance diagram for AddCoupledSolidKinSpeciesAction:

Public Member Functions
	AddCoupledSolidKinSpeciesAction (const InputParameters &params)
virtual void	act () override

Private Attributes
const std::vector< NonlinearVariableName >	_primary_species
	Basis set of primary species. More...
const std::vector< AuxVariableName >	_secondary_species
	Secondary species added as AuxVariables. More...
std::vector< VariableName >	_solid_kinetic_species
	Secondary solid species read by the parser. More...
std::vector< std::vector< VariableName > >	_primary_species_involved
	Primary species involved in the ith kinetic reaction. More...
std::vector< std::vector< VariableName > >	_kinetic_species_involved
	Secondary solid species involved the ith primary species. More...
std::vector< std::vector< Real > >	_stos
	Stoichiometric coefficients for each primary species in each reaction. More...
std::vector< std::vector< Real > >	_weights
	Weight of each primary species in each reaction. More...
std::string	_input_reactions
	Reaction network read from input file. More...
std::vector< std::string >	_reactions
	Vector of parsed reactions. More...
unsigned int	_num_reactions
	Number of reactions. More...
const std::vector< Real >	_logk
	Log10 of equilibrium constant. More...
const std::vector< Real >	_r_area
	Specific reactive surface area, m^2/L solution. More...
const std::vector< Real >	_ref_kconst
	Reference kinetic rate constant. More...
const std::vector< Real >	_e_act
	Activation energy. More...
const Real	_gas_const
	Gas constant, (Default 8.314 J/mol/K) More...
const std::vector< Real >	_ref_temp
	Reference temperature. More...
const std::vector< VariableName >	_sys_temp
	Actual system temperature. More...

Detailed Description

Definition at line 19 of file AddCoupledSolidKinSpeciesAction.h.

Constructor & Destructor Documentation

AddCoupledSolidKinSpeciesAction()

AddCoupledSolidKinSpeciesAction::AddCoupledSolidKinSpeciesAction

(

const InputParameters &

params

)

Definition at line 53 of file AddCoupledSolidKinSpeciesAction.C.

  : Action(params),
    _primary_species(getParam<std::vector<NonlinearVariableName>>("primary_species")),
    _secondary_species(getParam<std::vector<AuxVariableName>>("secondary_species")),
    _kinetic_species_involved(_primary_species.size()),
    _weights(_primary_species.size()),
    _input_reactions(getParam<std::string>("kin_reactions")),
    _logk(getParam<std::vector<Real>>("log10_keq")),
    _r_area(getParam<std::vector<Real>>("specific_reactive_surface_area")),
    _ref_kconst(getParam<std::vector<Real>>("kinetic_rate_constant")),
    _e_act(getParam<std::vector<Real>>("activation_energy")),
    _gas_const(getParam<Real>("gas_constant")),
    _ref_temp(getParam<std::vector<Real>>("reference_temperature")),
    _sys_temp(getParam<std::vector<VariableName>>("system_temperature"))
{
  // Note: as the reaction syntax has changed, check to see if the old syntax has
  // been used and throw an informative error. The number of = signs should be one
  // more than the number of commas, while the smallest number of spaces possible is 2
  bool old_syntax = false;
  if (std::count(_input_reactions.begin(), _input_reactions.end(), '=') !=
      std::count(_input_reactions.begin(), _input_reactions.end(), ',') + 1)
    old_syntax = true;
 
  if (std::count(_input_reactions.begin(), _input_reactions.end(), ' ') < 2)
    old_syntax = true;
 
  if (old_syntax)
    mooseError("Old solid kinetic reaction syntax present.\nReactions should now be comma "
               "separated, and must have spaces between species and +/-/= operators.\n"
               "See #9972 for details");
 
  // Parse the kinetic reactions
  pcrecpp::RE re_reactions("(.+?)" // A single reaction (any character until the comma delimiter)
                           "(?:,\\s*|$)" // comma or end of string
                           ,
                           pcrecpp::RE_Options().set_extended(true));
 
  pcrecpp::RE re_terms("(\\S+)");
  pcrecpp::RE re_coeff_and_species("(?: \\(? (.*?) \\)? )" // match the leading coefficent
                                   "([A-Za-z].*)"          // match the species
                                   ,
                                   pcrecpp::RE_Options().set_extended(true));
 
  pcrecpp::StringPiece input(_input_reactions);
  pcrecpp::StringPiece single_reaction, term;
  std::string single_reaction_str;
 
  // Parse reaction network to extract each individual reaction
  while (re_reactions.FindAndConsume(&input, &single_reaction_str))
    _reactions.push_back(single_reaction_str);
 
  _num_reactions = _reactions.size();
 
  if (_num_reactions == 0)
    mooseError("No solid kinetic reaction provided!");
 
  // Start parsing each reaction
  for (unsigned int i = 0; i < _num_reactions; ++i)
  {
    single_reaction = _reactions[i];
 
    // Capture all of the terms
    std::string species, coeff_str;
    Real coeff;
    int sign = 1;
    bool secondary = false;
 
    std::vector<Real> local_stos;
    std::vector<VariableName> local_species_list;
 
    // Find every single term in this reaction (species and operators)
    while (re_terms.FindAndConsume(&single_reaction, &term))
    {
      // Separating the stoichiometric coefficients from species
      if (re_coeff_and_species.PartialMatch(term, &coeff_str, &species))
      {
        if (coeff_str.length())
          coeff = std::stod(coeff_str);
        else
          coeff = 1.0;
 
        coeff *= sign;
 
        if (secondary)
          _solid_kinetic_species.push_back(species);
        else
        {
          local_stos.push_back(coeff);
          local_species_list.push_back(species);
        }
      }
      // Finding the operators and assign value of -1.0 to "-" sign
      else if (term == "+" || term == "=" || term == "-")
      {
        if (term == "-")
        {
          sign = -1;
          term = "+";
        }
 
        if (term == "=")
          secondary = true;
      }
      else
        mooseError("Error parsing term: ", term.as_string());
    }
 
    _stos.push_back(local_stos);
    _primary_species_involved.push_back(local_species_list);
  }
 
  // Start picking out primary species and coupled primary species and assigning
  // corresponding stoichiomentric coefficients
  for (unsigned int i = 0; i < _primary_species.size(); ++i)
    for (unsigned int j = 0; j < _num_reactions; ++j)
    {
      for (unsigned int k = 0; k < _primary_species_involved[j].size(); ++k)
        if (_primary_species_involved[j][k] == _primary_species[i])
        {
          _weights[i].push_back(_stos[j][k]);
          _kinetic_species_involved[i].push_back(_solid_kinetic_species[j]);
        }
    }
 
  // Print out details of the solid kinetic reactions to the console
  _console << "Solid kinetic reactions:\n";
  for (unsigned int i = 0; i < _num_reactions; ++i)
    _console << "  Reaction " << i + 1 << ": " << _reactions[i] << "\n";
  _console << "\n";
 
  // Check that all secondary species read from the reaction network have been added
  // as AuxVariables. Note: can't sort the _solid_kinetic_species vector as it throws
  // out the species and coefficient vectors so use std::is_permutation
  if (!std::is_permutation(
          _secondary_species.begin(), _secondary_species.end(), _solid_kinetic_species.begin()))
    mooseError("All solid kinetic species must be added as secondary species");
 
  // Check that the size of property vectors is equal to the number of reactions
  if (_logk.size() != _num_reactions)
    mooseError("The number of values entered for log10_keq is not equal to the number of solid "
               "kinetic reactions");
  if (_r_area.size() != _num_reactions)
    mooseError("The number of values entered for specific_reactive_surface_area is not equal to "
               "the number of solid kinetic reactions");
  if (_ref_kconst.size() != _num_reactions)
    mooseError("The number of values entered for kinetic_rate_constant is not equal to the number "
               "of solid kinetic reactions");
  if (_e_act.size() != _num_reactions)
    mooseError("The number of values entered for activation_energy is not equal to the number of "
               "solid kinetic reactions");
  if (_ref_temp.size() != _num_reactions)
    mooseError("The number of values entered for reference_temperature is not equal to the number "
               "of solid kinetic reactions");
}

Member Function Documentation

act()

void AddCoupledSolidKinSpeciesAction::act ( )

overridevirtual

Definition at line 209 of file AddCoupledSolidKinSpeciesAction.C.

{
  if (_current_task == "add_kernel")
  {
    // Add Kernels for each primary species
    for (unsigned int i = 0; i < _primary_species.size(); ++i)
    {
      InputParameters params_kin = _factory.getValidParams("CoupledBEKinetic");
      params_kin.set<NonlinearVariableName>("variable") = _primary_species[i];
      params_kin.set<std::vector<Real>>("weight") = _weights[i];
      params_kin.set<std::vector<VariableName>>("v") = _kinetic_species_involved[i];
      _problem->addKernel("CoupledBEKinetic", _primary_species[i] + "_" + "_kin", params_kin);
    }
  }
 
  if (_current_task == "add_aux_kernel")
  {
    // Add AuxKernels for each solid kinetic species
    for (unsigned int i = 0; i < _num_reactions; ++i)
    {
      InputParameters params_kin = _factory.getValidParams("KineticDisPreConcAux");
      params_kin.set<AuxVariableName>("variable") = _solid_kinetic_species[i];
      params_kin.defaultCoupledValue("log_k", _logk[i]);
      params_kin.set<Real>("r_area") = _r_area[i];
      params_kin.set<Real>("ref_kconst") = _ref_kconst[i];
      params_kin.set<Real>("e_act") = _e_act[i];
      params_kin.set<Real>("gas_const") = _gas_const;
      params_kin.set<Real>("ref_temp") = _ref_temp[i];
      params_kin.set<std::vector<VariableName>>("sys_temp") = _sys_temp;
      params_kin.set<std::vector<Real>>("sto_v") = _stos[i];
      params_kin.set<std::vector<VariableName>>("v") = _primary_species_involved[i];
      _problem->addAuxKernel(
          "KineticDisPreConcAux", "aux_" + _solid_kinetic_species[i], params_kin);
    }
  }
}

Member Data Documentation

_e_act

const std::vector<Real> AddCoupledSolidKinSpeciesAction::_e_act

private

Activation energy.

Definition at line 54 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act(), and AddCoupledSolidKinSpeciesAction().

_gas_const

const Real AddCoupledSolidKinSpeciesAction::_gas_const

private

Gas constant, (Default 8.314 J/mol/K)

Definition at line 56 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act().

_input_reactions

std::string AddCoupledSolidKinSpeciesAction::_input_reactions

private

Reaction network read from input file.

Definition at line 42 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by AddCoupledSolidKinSpeciesAction().

_kinetic_species_involved

std::vector<std::vector<VariableName> > AddCoupledSolidKinSpeciesAction::_kinetic_species_involved

private

Secondary solid species involved the ith primary species.

Definition at line 36 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act(), and AddCoupledSolidKinSpeciesAction().

_logk

const std::vector<Real> AddCoupledSolidKinSpeciesAction::_logk

private

Log10 of equilibrium constant.

Definition at line 48 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act(), and AddCoupledSolidKinSpeciesAction().

_num_reactions

unsigned int AddCoupledSolidKinSpeciesAction::_num_reactions

private

Number of reactions.

Definition at line 46 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act(), and AddCoupledSolidKinSpeciesAction().

_primary_species

const std::vector<NonlinearVariableName> AddCoupledSolidKinSpeciesAction::_primary_species

private

Basis set of primary species.

Definition at line 28 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act(), and AddCoupledSolidKinSpeciesAction().

_primary_species_involved

std::vector<std::vector<VariableName> > AddCoupledSolidKinSpeciesAction::_primary_species_involved

private

Primary species involved in the ith kinetic reaction.

Definition at line 34 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act(), and AddCoupledSolidKinSpeciesAction().

_r_area

const std::vector<Real> AddCoupledSolidKinSpeciesAction::_r_area

private

Specific reactive surface area, m^2/L solution.

Definition at line 50 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act(), and AddCoupledSolidKinSpeciesAction().

_reactions

std::vector<std::string> AddCoupledSolidKinSpeciesAction::_reactions

private

Vector of parsed reactions.

Definition at line 44 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by AddCoupledSolidKinSpeciesAction().

_ref_kconst

const std::vector<Real> AddCoupledSolidKinSpeciesAction::_ref_kconst

private

Reference kinetic rate constant.

Definition at line 52 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act(), and AddCoupledSolidKinSpeciesAction().

_ref_temp

const std::vector<Real> AddCoupledSolidKinSpeciesAction::_ref_temp

private

Reference temperature.

Definition at line 58 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act(), and AddCoupledSolidKinSpeciesAction().

_secondary_species

const std::vector<AuxVariableName> AddCoupledSolidKinSpeciesAction::_secondary_species

private

Secondary species added as AuxVariables.

Definition at line 30 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by AddCoupledSolidKinSpeciesAction().

_solid_kinetic_species

std::vector<VariableName> AddCoupledSolidKinSpeciesAction::_solid_kinetic_species

private

Secondary solid species read by the parser.

Definition at line 32 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act(), and AddCoupledSolidKinSpeciesAction().

_stos

std::vector<std::vector<Real> > AddCoupledSolidKinSpeciesAction::_stos

private

Stoichiometric coefficients for each primary species in each reaction.

Definition at line 38 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act(), and AddCoupledSolidKinSpeciesAction().

_sys_temp

const std::vector<VariableName> AddCoupledSolidKinSpeciesAction::_sys_temp

private

Actual system temperature.

Definition at line 60 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act().

_weights

std::vector<std::vector<Real> > AddCoupledSolidKinSpeciesAction::_weights

private

Weight of each primary species in each reaction.

Definition at line 40 of file AddCoupledSolidKinSpeciesAction.h.

Referenced by act(), and AddCoupledSolidKinSpeciesAction().

---

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

• chemical_reactions/include/actions/AddCoupledSolidKinSpeciesAction.h
• chemical_reactions/src/actions/AddCoupledSolidKinSpeciesAction.C