#include <AddCoupledEqSpeciesAction.h>

Inheritance diagram for AddCoupledEqSpeciesAction:

Public Types
typedef DataFileName	DataFileParameterType

Public Member Functions
	AddCoupledEqSpeciesAction (const InputParameters &params)

virtual void	act () override

void	timedAct ()

virtual void	addRelationshipManagers (Moose::RelationshipManagerType when_type)

MooseObjectName	uniqueActionName () const

const std::string &	specificTaskName () const

const std::set< std::string > &	getAllTasks () const

void	appendTask (const std::string &task)

MooseApp &	getMooseApp () const

const std::string &	type () const

const std::string &	name () const

std::string	typeAndName () const

MooseObjectParameterName	uniqueParameterName (const std::string &parameter_name) const

MooseObjectName	uniqueName () const

const InputParameters &	parameters () const

const hit::Node *	getHitNode () const

bool	hasBase () const

const std::string &	getBase () const

const T &	getParam (const std::string &name) const

std::vector< std::pair< T1, T2 > >	getParam (const std::string &param1, const std::string &param2) const

const T *	queryParam (const std::string &name) const

const T &	getRenamedParam (const std::string &old_name, const std::string &new_name) const

T	getCheckedPointerParam (const std::string &name, const std::string &error_string="") const

bool	isParamValid (const std::string &name) const

bool	isParamSetByUser (const std::string &name) const

void	connectControllableParams (const std::string &parameter, const std::string &object_type, const std::string &object_name, const std::string &object_parameter) const

void	paramError (const std::string &param, Args... args) const

void	paramWarning (const std::string &param, Args... args) const

void	paramWarning (const std::string &param, Args... args) const

void	paramInfo (const std::string &param, Args... args) const

std::string	messagePrefix (const bool hit_prefix=true) const

std::string	errorPrefix (const std::string &) const

void	mooseError (Args &&... args) const

void	mooseDocumentedError (const std::string &repo_name, const unsigned int issue_num, Args &&... args) const

void	mooseErrorNonPrefixed (Args &&... args) const

void	mooseWarning (Args &&... args) const

void	mooseWarning (Args &&... args) const

void	mooseWarningNonPrefixed (Args &&... args) const

void	mooseWarningNonPrefixed (Args &&... args) const

void	mooseDeprecated (Args &&... args) const

void	mooseDeprecated (Args &&... args) const

void	mooseDeprecatedNoTrace (Args &&... args) const

void	mooseInfo (Args &&... args) const

void	callMooseError (std::string msg, const bool with_prefix, const hit::Node *node=nullptr, const bool show_trace=true) const

std::string	getDataFileName (const std::string &param) const

std::string	getDataFileNameByName (const std::string &relative_path) const

std::string	getDataFilePath (const std::string &relative_path) const

PerfGraph &	perfGraph ()

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

Static Public Member Functions
static InputParameters	validParams ()

static void	callMooseError (MooseApp const app, const InputParameters &params, std::string msg, const bool with_prefix, const hit::Node node, const bool show_trace=true)

Public Attributes
	usingCombinedWarningSolutionWarnings

const ConsoleStream	_console

Static Public Attributes
static const std::string	unique_action_name_param

static const std::string	type_param

static const std::string	name_param

static const std::string	unique_name_param

static const std::string	app_param

static const std::string	moose_base_param

static const std::string	kokkos_object_param

static constexpr auto	SYSTEM

static constexpr auto	NAME

Protected Member Functions
bool	addRelationshipManagers (Moose::RelationshipManagerType when_type, const InputParameters &moose_object_pars)

void	associateWithParameter (const std::string &param_name, InputParameters &params) const

void	associateWithParameter (const InputParameters &from_params, const std::string &param_name, InputParameters &params) const

const T &	getMeshProperty (const std::string &data_name, const std::string &prefix)

const T &	getMeshProperty (const std::string &data_name)

bool	hasMeshProperty (const std::string &data_name, const std::string &prefix) const

bool	hasMeshProperty (const std::string &data_name, const std::string &prefix) const

bool	hasMeshProperty (const std::string &data_name) const

bool	hasMeshProperty (const std::string &data_name) const

std::string	meshPropertyName (const std::string &data_name) const

PerfID	registerTimedSection (const std::string &section_name, const unsigned int level) const

PerfID	registerTimedSection (const std::string &section_name, const unsigned int level, const std::string &live_message, const bool print_dots=true) const

std::string	timedSectionName (const std::string &section_name) const

void	flagInvalidSolutionInternal (const InvalidSolutionID invalid_solution_id) const

InvalidSolutionID	registerInvalidSolutionInternal (const std::string &message, const bool warning) const

Static Protected Member Functions
static std::string	meshPropertyName (const std::string &data_name, const std::string &prefix)

Protected Attributes
const std::vector< NonlinearVariableName >	_primary_species
	Basis set of primary species.

const std::vector< AuxVariableName >	_secondary_species
	Secondary species added as AuxVariables.

std::vector< std::vector< Real > >	_stos
	Stoichiometric coefficients for each primary species in each reaction.

std::vector< std::vector< Real > >	_weights
	Weight of each primary species in each reaction.

std::vector< Real >	_eq_const
	Equilibrium constants for each reaction.

std::vector< VariableName >	_eq_species
	Equilibrium species.

std::set< std::string >	_aux_species
	Set of auxillary species.

std::vector< std::vector< bool > >	_primary_participation
	Participation of primary species in each reaction.

std::vector< std::vector< Real > >	_sto_u
	Stoichiometric coefficients of primary variables in each reaction.

std::vector< std::vector< std::vector< Real > > >	_sto_v
	Stoichiometric coefficients of coupled primary variables in each reaction.

std::vector< std::vector< std::vector< VariableName > > >	_coupled_v
	Coupled primary species for each reaction.

std::vector< std::vector< VariableName > >	_primary_species_involved
	Primary species involved in the ith equilibrium reaction.

std::string	_input_reactions
	Reaction network read from input file.

std::vector< std::string >	_reactions
	Vector of parsed reactions.

unsigned int	_num_reactions
	Number of reactions.

const std::vector< VariableName >	_pressure_var
	Pressure variable.

const RealVectorValue	_gravity
	Gravity (default is (0, 0, 0))

std::string	_registered_identifier

std::string	_specific_task_name

std::set< std::string >	_all_tasks

ActionWarehouse &	_awh

const std::string &	_current_task

std::shared_ptr< MooseMesh > &	_mesh

std::shared_ptr< MooseMesh > &	_displaced_mesh

std::shared_ptr< FEProblemBase > &	_problem

PerfID	_act_timer

MooseApp &	_app

Factory &	_factory

ActionFactory &	_action_factory

const std::string &	_type

const std::string &	_name

const InputParameters &	_pars

MooseApp &	_pg_moose_app

const std::string	_prefix

const Parallel::Communicator &	_communicator

Private Member Functions
bool	addRelationshipManager (Moose::RelationshipManagerType input_rm_type, const InputParameters &moose_object_pars, std::string rm_name, Moose::RelationshipManagerType rm_type, Moose::RelationshipManagerInputParameterCallback rm_input_parameter_func, Moose::RMSystemType sys_type=Moose::RMSystemType::NONE)

virtual std::string	meshPropertyPrefix (const std::string &data_name) const

const RestartableDataValue &	getMeshPropertyInternal (const std::string &data_name, const std::string &prefix) const

void	mooseErrorInternal (Args &&... args) const

Static Private Member Functions
static const hit::Node *	getHitNode (const InputParameters &params)

static std::string	messagePrefix (const InputParameters &params, const bool hit_prefix)

Private Attributes
const ParallelParamObject &	_parent

MooseApp &	_meta_data_app

const MooseObject *const	_meta_data_object

const MooseBase &	_si_moose_base

const FEProblemBase *	_si_problem

Detailed Description

Definition at line 16 of file AddCoupledEqSpeciesAction.h.

Constructor & Destructor Documentation

◆ AddCoupledEqSpeciesAction()

AddCoupledEqSpeciesAction::AddCoupledEqSpeciesAction ( const InputParameters & params )

Definition at line 41 of file AddCoupledEqSpeciesAction.C.

  : Action(params),
    _primary_species(getParam<std::vector<NonlinearVariableName>>("primary_species")),
    _secondary_species(getParam<std::vector<AuxVariableName>>("secondary_species")),
    _weights(_primary_species.size()),
    _primary_participation(_primary_species.size()),
    _sto_u(_primary_species.size()),
    _sto_v(_primary_species.size()),
    _coupled_v(_primary_species.size()),
    _input_reactions(getParam<std::string>("reactions")),
    _pressure_var(getParam<std::vector<VariableName>>("pressure")),
    _gravity(getParam<RealVectorValue>("gravity"))
{
  // Parse the aqueous equilibrium reactions
  pcrecpp::RE re_reaction(
      "(.+?)" // single reaction (any character until the equilibrium coefficient appears)
      "\\s"   // word boundary
      "("     // start capture
      "-?"    // optional minus sign
      "\\d+(?:\\.\\d*)?" // digits followed by optional decimal and more digits
      ")"                // end capture
      "\\b"              // word boundary
      "(?:,?\\s*|$)"     // optional 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;
  Real eq_coeff;
 
  // Parse reaction network to extract each individual reaction
  while (re_reaction.FindAndConsume(&input, &single_reaction_str, &eq_coeff))
  {
    _reactions.push_back(single_reaction_str);
    _eq_const.push_back(eq_coeff);
  }
 
  _num_reactions = _reactions.size();
 
  if (_num_reactions == 0)
    mooseError("No equilibrium reaction provided!");
 
  if (_pars.isParamValid("secondary_species"))
    for (unsigned int k = 0; k < _secondary_species.size(); ++k)
      _aux_species.insert(_secondary_species[k]);
 
  // 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)
          _eq_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 = "+";
        }
        else
          sign = 1;
 
        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)
  {
    _sto_u[i].resize(_num_reactions, 0.0);
    _sto_v[i].resize(_num_reactions);
    _coupled_v[i].resize(_num_reactions);
    _weights[i].resize(_num_reactions, 0.0);
 
    _primary_participation[i].resize(_num_reactions, false);
    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])
          _primary_participation[i][j] = true;
 
      if (_primary_participation[i][j])
      {
        for (unsigned int k = 0; k < _primary_species_involved[j].size(); ++k)
        {
          if (_primary_species_involved[j][k] == _primary_species[i])
          {
            _sto_u[i][j] = _stos[j][k];
            _weights[i][j] = _stos[j][k];
          }
          else
          {
            _sto_v[i][j].push_back(_stos[j][k]);
            _coupled_v[i][j].push_back(_primary_species_involved[j][k]);
          }
        }
      }
    }
  }
 
  // Print out details of the equilibrium reactions to the console
  _console << "Aqueous equilibrium reactions:\n";
  for (unsigned int i = 0; i < _num_reactions; ++i)
    _console << "  Reaction " << i + 1 << ": " << _reactions[i] << ", log10(Keq) = " << _eq_const[i]
             << "\n";
  _console << std::endl;
}

Member Function Documentation

◆ act()

void AddCoupledEqSpeciesAction::act ( )

overridevirtual

Implements Action.

Definition at line 196 of file AddCoupledEqSpeciesAction.C.

{
  if (_current_task == "add_kernel")
  {
    // Add Kernels for each primary species
    for (unsigned int i = 0; i < _primary_species.size(); ++i)
    {
      for (unsigned int j = 0; j < _num_reactions; ++j)
      {
        if (_primary_participation[i][j])
        {
          InputParameters params_sub = _factory.getValidParams("CoupledBEEquilibriumSub");
          params_sub.set<NonlinearVariableName>("variable") = _primary_species[i];
          params_sub.set<Real>("weight") = _weights[i][j];
          params_sub.defaultCoupledValue("log_k", _eq_const[j]);
          params_sub.set<Real>("sto_u") = _sto_u[i][j];
          params_sub.set<std::vector<Real>>("sto_v") = _sto_v[i][j];
          params_sub.set<std::vector<VariableName>>("v") = _coupled_v[i][j];
          _problem->addKernel("CoupledBEEquilibriumSub",
                              _primary_species[i] + "_" + _eq_species[j] + "_sub",
                              params_sub);
 
          InputParameters params_cd = _factory.getValidParams("CoupledDiffusionReactionSub");
          params_cd.set<NonlinearVariableName>("variable") = _primary_species[i];
          params_cd.set<Real>("weight") = _weights[i][j];
          params_cd.defaultCoupledValue("log_k", _eq_const[j]);
          params_cd.set<Real>("sto_u") = _sto_u[i][j];
          params_cd.set<std::vector<Real>>("sto_v") = _sto_v[i][j];
          params_cd.set<std::vector<VariableName>>("v") = _coupled_v[i][j];
          _problem->addKernel("CoupledDiffusionReactionSub",
                              _primary_species[i] + "_" + _eq_species[j] + "_cd",
                              params_cd);
 
          // If pressure is coupled, add a CoupledConvectionReactionSub Kernel as well
          if (_pars.isParamValid("pressure"))
          {
            InputParameters params_conv = _factory.getValidParams("CoupledConvectionReactionSub");
            params_conv.set<NonlinearVariableName>("variable") = _primary_species[i];
            params_conv.set<Real>("weight") = _weights[i][j];
            params_conv.defaultCoupledValue("log_k", _eq_const[j]);
            params_conv.set<Real>("sto_u") = _sto_u[i][j];
            params_conv.set<std::vector<Real>>("sto_v") = _sto_v[i][j];
            params_conv.set<std::vector<VariableName>>("v") = _coupled_v[i][j];
            params_conv.set<std::vector<VariableName>>("p") = _pressure_var;
            params_conv.set<RealVectorValue>("gravity") = _gravity;
            _problem->addKernel("CoupledConvectionReactionSub",
                                _primary_species[i] + "_" + _eq_species[j] + "_conv",
                                params_conv);
          }
        }
      }
    }
  }
 
  if (_current_task == "add_aux_kernel")
  {
    // Add AqueousEquilibriumRxnAux AuxKernels for equilibrium species
    for (unsigned int j = 0; j < _num_reactions; ++j)
    {
      if (_aux_species.find(_eq_species[j]) != _aux_species.end())
      {
        InputParameters params_eq = _factory.getValidParams("AqueousEquilibriumRxnAux");
        params_eq.set<AuxVariableName>("variable") = _eq_species[j];
        params_eq.defaultCoupledValue("log_k", _eq_const[j]);
        params_eq.set<std::vector<Real>>("sto_v") = _stos[j];
        params_eq.set<std::vector<VariableName>>("v") = _primary_species_involved[j];
        _problem->addAuxKernel("AqueousEquilibriumRxnAux", "aux_" + _eq_species[j], params_eq);
      }
    }
  }
}

◆ validParams()

InputParameters AddCoupledEqSpeciesAction::validParams ( )

static

Definition at line 26 of file AddCoupledEqSpeciesAction.C.

{
  InputParameters params = Action::validParams();
  params.addRequiredParam<std::vector<NonlinearVariableName>>(
      "primary_species", "The list of primary variables to add");
  params.addParam<std::vector<AuxVariableName>>(
      "secondary_species", "The list of aqueous equilibrium species to be output as aux variables");
  params.addParam<std::string>("reactions", "The list of aqueous equilibrium reactions");
  params.addParam<std::vector<VariableName>>("pressure", {}, "Pressure variable");
  RealVectorValue g(0, 0, 0);
  params.addParam<RealVectorValue>("gravity", g, "Gravity vector (default is (0, 0, 0))");
  params.addClassDescription("Adds coupled equilibrium Kernels and AuxKernels for primary species");
  return params;
}

Member Data Documentation

◆ _aux_species

std::set<std::string> AddCoupledEqSpeciesAction::_aux_species

protected

Set of auxillary species.

Definition at line 39 of file AddCoupledEqSpeciesAction.h.

Referenced by act(), and AddCoupledEqSpeciesAction().

◆ _coupled_v

std::vector<std::vector<std::vector<VariableName> > > AddCoupledEqSpeciesAction::_coupled_v

protected

Coupled primary species for each reaction.

Definition at line 47 of file AddCoupledEqSpeciesAction.h.

Referenced by act(), and AddCoupledEqSpeciesAction().

◆ _eq_const

std::vector<Real> AddCoupledEqSpeciesAction::_eq_const

protected

Equilibrium constants for each reaction.

Definition at line 35 of file AddCoupledEqSpeciesAction.h.

Referenced by act(), and AddCoupledEqSpeciesAction().

◆ _eq_species

std::vector<VariableName> AddCoupledEqSpeciesAction::_eq_species

protected

Equilibrium species.

Definition at line 37 of file AddCoupledEqSpeciesAction.h.

Referenced by act(), and AddCoupledEqSpeciesAction().

◆ _gravity

const RealVectorValue AddCoupledEqSpeciesAction::_gravity

protected

Gravity (default is (0, 0, 0))

Definition at line 59 of file AddCoupledEqSpeciesAction.h.

Referenced by act().

◆ _input_reactions

std::string AddCoupledEqSpeciesAction::_input_reactions

protected

Reaction network read from input file.

Definition at line 51 of file AddCoupledEqSpeciesAction.h.

Referenced by AddCoupledEqSpeciesAction().

◆ _num_reactions

unsigned int AddCoupledEqSpeciesAction::_num_reactions

protected

Number of reactions.

Definition at line 55 of file AddCoupledEqSpeciesAction.h.

Referenced by act(), and AddCoupledEqSpeciesAction().

◆ _pressure_var

const std::vector<VariableName> AddCoupledEqSpeciesAction::_pressure_var

protected

Pressure variable.

Definition at line 57 of file AddCoupledEqSpeciesAction.h.

Referenced by act().

◆ _primary_participation

std::vector<std::vector<bool> > AddCoupledEqSpeciesAction::_primary_participation

protected

Participation of primary species in each reaction.

Definition at line 41 of file AddCoupledEqSpeciesAction.h.

Referenced by act(), and AddCoupledEqSpeciesAction().

◆ _primary_species

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

protected

Basis set of primary species.

Definition at line 27 of file AddCoupledEqSpeciesAction.h.

Referenced by act(), and AddCoupledEqSpeciesAction().

◆ _primary_species_involved

std::vector<std::vector<VariableName> > AddCoupledEqSpeciesAction::_primary_species_involved

protected

Primary species involved in the ith equilibrium reaction.

Definition at line 49 of file AddCoupledEqSpeciesAction.h.

Referenced by act(), and AddCoupledEqSpeciesAction().

◆ _reactions

std::vector<std::string> AddCoupledEqSpeciesAction::_reactions

protected

Vector of parsed reactions.

Definition at line 53 of file AddCoupledEqSpeciesAction.h.

Referenced by AddCoupledEqSpeciesAction().

◆ _secondary_species

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

protected

Secondary species added as AuxVariables.

Definition at line 29 of file AddCoupledEqSpeciesAction.h.

Referenced by AddCoupledEqSpeciesAction().

◆ _sto_u

std::vector<std::vector<Real> > AddCoupledEqSpeciesAction::_sto_u

protected

Stoichiometric coefficients of primary variables in each reaction.

Definition at line 43 of file AddCoupledEqSpeciesAction.h.

Referenced by act(), and AddCoupledEqSpeciesAction().

◆ _sto_v

std::vector<std::vector<std::vector<Real> > > AddCoupledEqSpeciesAction::_sto_v

protected

Stoichiometric coefficients of coupled primary variables in each reaction.

Definition at line 45 of file AddCoupledEqSpeciesAction.h.

Referenced by act(), and AddCoupledEqSpeciesAction().

◆ _stos

std::vector<std::vector<Real> > AddCoupledEqSpeciesAction::_stos

protected

Stoichiometric coefficients for each primary species in each reaction.

Definition at line 31 of file AddCoupledEqSpeciesAction.h.

Referenced by act(), and AddCoupledEqSpeciesAction().

◆ _weights

std::vector<std::vector<Real> > AddCoupledEqSpeciesAction::_weights

protected

Weight of each primary species in each reaction.

Definition at line 33 of file AddCoupledEqSpeciesAction.h.

Referenced by act(), and AddCoupledEqSpeciesAction().

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

chemical_reactions/include/actions/AddCoupledEqSpeciesAction.h
chemical_reactions/src/actions/AddCoupledEqSpeciesAction.C

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AddCoupledEqSpeciesAction()

Member Function Documentation

◆ act()

◆ validParams()

Member Data Documentation

◆ _aux_species

◆ _coupled_v

◆ _eq_const

◆ _eq_species

◆ _gravity

◆ _input_reactions

◆ _num_reactions

◆ _pressure_var

◆ _primary_participation

◆ _primary_species

◆ _primary_species_involved

◆ _reactions

◆ _secondary_species

◆ _sto_u

◆ _sto_v

◆ _stos

◆ _weights