Creates all the objects needed to solve a reaction network of chemical reactions at equilibrium in an aqueous medium with a finite element continuous Galerkin discretization. More...

#include <AqueousReactionsEquilibriumPhysics.h>

Inheritance diagram for AqueousReactionsEquilibriumPhysics:

[legend]

Public Types
typedef DataFileName	DataFileParameterType

Public Member Functions
	AqueousReactionsEquilibriumPhysics (const InputParameters &parameters)

void	addComponent (const ActionComponent &component) override

virtual InputParameters	getAdditionalRMParams () const

virtual void	act () override final

virtual void	actOnAdditionalTasks ()

void	addBlocks (const std::vector< SubdomainName > &blocks)

void	addBlocksById (const std::vector< SubdomainID > &block_ids)

const std::vector< SubdomainName > &	blocks () const

bool	checkBlockRestrictionIdentical (const std::string &object_name, const std::vector< SubdomainName > &blocks, const bool error_if_not_identical=true) const

bool	hasBlocks (const std::vector< SubdomainName > &blocks) const

const T *	getCoupledPhysics (const PhysicsName &phys_name, const bool allow_fail=false) const

const std::vector< T * >	getCoupledPhysics (const bool allow_fail=false) const

unsigned int	dimension () const

const ActionComponent &	getActionComponent (const ComponentName &comp_name) const

void	checkComponentType (const ActionComponent &component) const

const std::vector< VariableName > &	solverVariableNames () const

const std::vector< VariableName > &	auxVariableNames () const

virtual std::vector< UserObjectName >	getSuppliedUserObjects () const

void	timedAct ()

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 ()

void	assertParamDefined (const std::string &libmesh_dbg_var(param)) const

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
virtual void	addAuxiliaryKernels () override

virtual void	addFEKernels () override

void	assertParamDefined (const std::string &param) const

bool	isTransient () const

Factory &	getFactory ()

Factory &	getFactory () const

virtual FEProblemBase &	getProblem ()

virtual const FEProblemBase &	getProblem () const

void	prepareCopyVariablesFromMesh () const

void	copyVariablesFromMesh (const std::vector< VariableName > &variables_to_copy, bool are_nonlinear=true)

std::string	prefix () const

void	addUserObject (const std::string &uo_type, const std::string &uo_name, InputParameters &params)

void	saveSolverVariableName (const VariableName &var_name)

void	saveAuxVariableName (const VariableName &var_name)

bool	variableExists (const VariableName &var_name, bool error_if_aux) const

bool	solverVariableExists (const VariableName &var_name) const

const SolverSystemName &	getSolverSystem (unsigned int variable_index) const

const SolverSystemName &	getSolverSystem (const VariableName &variable_name) const

void	addRequiredPhysicsTask (const std::string &task)

void	assignBlocks (InputParameters &params, const std::vector< SubdomainName > &blocks) const

bool	allMeshBlocks (const std::vector< SubdomainName > &blocks) const

bool	allMeshBlocks (const std::set< SubdomainName > &blocks) const

std::set< SubdomainID >	getSubdomainIDs (const std::set< SubdomainName > &blocks) const

std::vector< std::string >	getSubdomainNamesAndIDs (const std::set< SubdomainID > &blocks) const

void	addPetscPairsToPetscOptions (const std::vector< std::pair< MooseEnumItem, std::string > > &petsc_pair_options)

bool	isVariableFV (const VariableName &var_name) const

bool	isVariableScalar (const VariableName &var_name) const

bool	shouldCreateVariable (const VariableName &var_name, const std::vector< SubdomainName > &blocks, const bool error_if_aux)

bool	shouldCreateIC (const VariableName &var_name, const std::vector< SubdomainName > &blocks, const bool ic_is_default_ic, const bool error_if_already_defined) const

bool	shouldCreateTimeDerivative (const VariableName &var_name, const std::vector< SubdomainName > &blocks, const bool error_if_already_defined) const

void	reportPotentiallyMissedParameters (const std::vector< std::string > &param_names, const std::string &object_type, const std::string &object_name="") const

virtual void	checkIntegrity () const

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

void	checkParamsBothSetOrNotSet (const std::string &param1, const std::string &param2) const

void	checkSecondParamSetOnlyIfFirstOneTrue (const std::string &param1, const std::string &param2) const

void	checkSecondParamSetOnlyIfFirstOneSet (const std::string &param1, const std::string &param2) const

void	checkSecondParamNotSetIfFirstOneSet (const std::string &param1, const std::string &param2) const

void	checkVectorParamsSameLength (const std::string &param1, const std::string &param2) const

void	checkVectorParamAndMultiMooseEnumLength (const std::string &param1, const std::string &param2) const

void	checkTwoDVectorParamsSameLength (const std::string &param1, const std::string &param2) const

void	checkVectorParamsNoOverlap (const std::vector< std::string > &param_vecs) const

void	checkTwoDVectorParamsNoRespectiveOverlap (const std::vector< std::string > &param_vecs) const

void	checkTwoDVectorParamInnerSameLengthAsOneDVector (const std::string &param1, const std::string &param2) const

void	checkTwoDVectorParamMultiMooseEnumSameLength (const std::string &param1, const std::string &param2, const bool error_for_param2) const

void	checkVectorParamNotEmpty (const std::string &param1) const

void	checkVectorParamsSameLengthIfSet (const std::string &param1, const std::string &param2, const bool ignore_empty_default_param2=false) const

void	checkVectorParamLengthSameAsCombinedOthers (const std::string &param1, const std::string &param2, const std::string &param3) const

void	checkBlockwiseConsistency (const std::string &block_param_name, const std::vector< std::string > &parameter_names) const

bool	parameterConsistent (const InputParameters &other_param, const std::string &param_name) const

void	warnInconsistent (const InputParameters &parameters, const std::string &param_name) const

void	errorDependentParameter (const std::string &param1, const std::string &value_not_set, const std::vector< std::string > &dependent_params) const

void	errorInconsistentDependentParameter (const std::string &param1, const std::string &value_set, const std::vector< std::string > &dependent_params) const

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

Protected Attributes
std::vector< std::vector< Real > >	_stos
	Stoichiometric coefficients for each primary species (outer indexing) in each reaction.

std::vector< std::vector< Real > >	_sto_u
	Stoichiometric coefficients of primary/solver variables (outer indexing) in each reaction.

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

std::vector< std::vector< Real > >	_weights
	Weight of each primary species (outer indexing) in each reaction.

std::vector< Real >	_log_eq_const
	log10(Equilibrium constants) for each reaction

std::vector< VariableName >	_eq_species
	Equilibrium species: only one per reaction. This is a restriction of this implementation.

std::vector< std::vector< bool > >	_primary_participation
	Vector of vectors, indexed by (i, j), of whether primary solver species 'i' is present in reaction 'j'.

std::vector< std::vector< std::vector< VariableName > > >	_coupled_v
	Coupled primary species for each reaction (outer indexing is primary species, then reactions then innermost is the species in the reaction)

std::vector< std::vector< VariableName > >	_solver_species_involved
	Primary species involved in the ith equilibrium reaction (outer indexing)

const std::vector< VariableName > &	_pressure_var
	Name of the pressure variable.

const RealVectorValue	_gravity
	Gravity vector.

const std::vector< VariableName > &	_solver_species
	Name of the species variables to solve for in the reaction network.

const unsigned int	_num_solver_species
	Number of species to solve for.

const std::vector< AuxVariableName > &	_aux_species
	Name of the species variables that can be computed without additional solves, simply auxkernels.

const unsigned int	_num_aux_species
	Number of auxiliary species.

std::vector< std::string >	_reactions_input
	Reaction network as a vector of lines for pretty output.

const std::vector< ReactionNetworkUtils::Reaction >	_reactions
	Reaction network after being parsed in initializePhysics()

const unsigned int	_num_reactions
	Number of reactions involved in the network.

std::vector< SolverSystemName >	_system_names

std::vector< unsigned int >	_system_numbers

const bool	_verbose

const MooseEnum &	_preconditioning

std::vector< SubdomainName >	_blocks

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
virtual void	addSolverVariables () override
	Add solver variables (currently coded for CGFE)

virtual void	addAuxiliaryVariables () override
	Add nodal auxiliary variables.

virtual void	addPreconditioning () override
	Add default preconditioning options (not implemented at this time)

virtual void	addInitialConditions () override
	Add initial conditions for the solver variable (auxiliary not implemented)

virtual void	addRelationshipManagers (Moose::RelationshipManagerType input_rm_type) override

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

virtual void	addRelationshipManagers (Moose::RelationshipManagerType when_type)

void	initializePhysics ()

virtual void	initializePhysicsAdditional ()

virtual void	checkIntegrityEarly () const

virtual void	addFVKernels ()

virtual void	addFVInterpolationMethods ()

virtual void	addNodalKernels ()

virtual void	addDiracKernels ()

virtual void	addDGKernels ()

virtual void	addScalarKernels ()

virtual void	addInterfaceKernels ()

virtual void	addFVInterfaceKernels ()

virtual void	addFEBCs ()

virtual void	addFVBCs ()

virtual void	addNodalBCs ()

virtual void	addPeriodicBCs ()

virtual void	addFunctions ()

virtual void	addMaterials ()

virtual void	addFunctorMaterials ()

virtual void	addUserObjects ()

virtual void	addCorrectors ()

virtual void	addMultiApps ()

virtual void	addTransfers ()

virtual void	addPostprocessors ()

virtual void	addVectorPostprocessors ()

virtual void	addReporters ()

virtual void	addOutputs ()

virtual void	addExecutioner ()

virtual void	addExecutors ()

void	checkRequiredTasks () const

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

const T &	forwardGetParam (const std::string &param_name) const

const InputParameters &	forwardParameters () const

bool	forwardIsParamSetByUser (const std::string &param_name) const

bool	forwardIsParamValid (const std::string &param_name) const

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

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

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

const std::string &	forwardType () const

virtual const std::string &	forwardName () const

const std::vector< SubdomainName > &	forwardBlocks () 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
MooseEnum	_is_transient

std::vector< VariableName >	_solver_var_names

std::vector< VariableName >	_aux_var_names

unsigned int	_dim

std::set< std::string >	_required_tasks

const ParallelParamObject &	_parent

MooseApp &	_meta_data_app

const MooseObject *const	_meta_data_object

const MooseBase &	_si_moose_base

const FEProblemBase *	_si_problem

const PhysicsBase *const	_customer_class

Detailed Description

Creates all the objects needed to solve a reaction network of chemical reactions at equilibrium in an aqueous medium with a finite element continuous Galerkin discretization.

Definition at line 18 of file AqueousReactionsEquilibriumPhysics.h.

Constructor & Destructor Documentation

◆ AqueousReactionsEquilibriumPhysics()

AqueousReactionsEquilibriumPhysics::AqueousReactionsEquilibriumPhysics ( const InputParameters & parameters )

Definition at line 49 of file AqueousReactionsEquilibriumPhysics.C.

  : ReactionNetworkPhysicsBase(parameters),
    _sto_u(_num_solver_species),
    _sto_v(_num_solver_species),
    _weights(_num_solver_species),
    _primary_participation(_num_solver_species),
    _coupled_v(_num_solver_species),
    _pressure_var(getParam<std::vector<VariableName>>("pressure"))
{
  // Further parse the reactions
  // Keeping the data in these vectors of vectors as an intermediate processing step
  for (const auto i : index_range(_reactions))
  {
    const auto & reaction = _reactions[i];
    _solver_species_involved.push_back(reaction.getReactantSpecies());
    _stos.push_back(reaction.getStoichiometricCoefficients());
 
    // There are only one equilibrium species. We look at the output species
    const auto & products = reaction.getProductSpecies();
    if (products.size() != 1)
      mooseError("Reaction:\n" + _reactions_input[i] +
                 "\n has more than one product species (on the RHS). This Physics only supports "
                 "one product species per reaction");
    _eq_species.push_back(products[0]);
 
    // If user passed log_K use that, else use K
    if (reaction.hasMetaData<Real>("log10_K"))
      _log_eq_const.push_back(std::stod(reaction.getMetaData("log10_K")));
    else if (reaction.hasMetaData<Real>("K"))
      _log_eq_const.push_back(std::log10(std::stod(reaction.getMetaData("K"))));
    else if (reaction.hasMetaData("K") || reaction.hasMetaData("log10_K"))
      paramError("reactions",
                 "Equilibrium constant species in square brackets must be specified as a float, "
                 "not a name");
    else
      paramError("reactions",
                 "Reaction: '" + _reactions_input[i] +
                     "'\n is missing an equilibrium constant [K=] or its logarithm [log10_K=] in "
                     "its metadata");
  }
 
  // For each primary/solver species, we examine the reactions to get the coefficients
  // and various constants
  for (unsigned int i = 0; i < _solver_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)
    {
      // Set the booleans for involvement in a reaction
      for (unsigned int k = 0; k < _solver_species_involved[j].size(); ++k)
        if (_solver_species_involved[j][k] == _solver_species[i])
          _primary_participation[i][j] = true;
 
      if (_primary_participation[i][j])
      {
        for (unsigned int k = 0; k < _solver_species_involved[j].size(); ++k)
        {
          // Re-sort the coefficients into a more convenient format
          if (_solver_species_involved[j][k] == _solver_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(_solver_species_involved[j][k]);
          }
        }
      }
    }
  }
 
  // Parameter checks
  checkSecondParamSetOnlyIfFirstOneTrue("add_darcy_advection_term", "pressure");
  checkSecondParamSetOnlyIfFirstOneTrue("add_darcy_advection_term", "gravity");
}

Member Function Documentation

◆ addAuxiliaryKernels()

void AqueousReactionsEquilibriumPhysics::addAuxiliaryKernels ( )

overrideprotectedvirtual

Reimplemented from PhysicsBase.

Definition at line 196 of file AqueousReactionsEquilibriumPhysics.C.

{
  // Add AqueousEquilibriumRxnAux AuxKernels for equilibrium species
  for (const auto j : make_range(_num_reactions))
  {
    // Add these aux-kernels only for the aux species involved in the reaction
    // we should not be adding them twice, since only 1 eq_species per reaction
    if (std::find(_aux_species.begin(), _aux_species.end(), _eq_species[j]) != _aux_species.end())
    {
      InputParameters params_eq = _factory.getValidParams("AqueousEquilibriumRxnAux");
      assignBlocks(params_eq, _blocks);
      params_eq.set<AuxVariableName>("variable") = _eq_species[j];
      params_eq.defaultCoupledValue("log_k", _log_eq_const[j]);
      mooseAssert(_stos[j].size() >= _solver_species_involved[j].size(),
                  "Coefs are for solver + auxiliary");
      std::vector<Real> stos_primary(_stos[j].begin(),
                                     _stos[j].begin() + _solver_species_involved[j].size());
      params_eq.set<std::vector<Real>>("sto_v") = stos_primary;
      params_eq.set<std::vector<VariableName>>("v") = _solver_species_involved[j];
      getProblem().addAuxKernel("AqueousEquilibriumRxnAux", "aux_" + _eq_species[j], params_eq);
    }
  }
}

◆ addAuxiliaryVariables()

void ReactionNetworkPhysicsBase::addAuxiliaryVariables ( )

overrideprivatevirtualinherited

Add nodal auxiliary variables.

Reimplemented from PhysicsBase.

Definition at line 105 of file ReactionNetworkPhysicsBase.C.

{
  for (const auto i : index_range(_aux_species))
  {
    const auto & var_name = _aux_species[i];
    // If the variable was added outside the Physics
    if (variableExists(var_name, /*error_if_aux*/ false))
    {
      reportPotentiallyMissedParameters({"variable_order"}, "MooseVariable", var_name);
      continue;
    }
 
    const std::string variable_type = "MooseVariable";
    InputParameters params = getFactory().getValidParams(variable_type);
    params.set<MooseEnum>("order") = getParam<MooseEnum>("variable_order");
    assignBlocks(params, _blocks);
    getProblem().addAuxVariable(variable_type, var_name, params);
  }
}

◆ addComponent()

void ReactionNetworkPhysicsBase::addComponent ( const ActionComponent & component )

overridevirtualinherited

Reimplemented from PhysicsBase.

Definition at line 133 of file ReactionNetworkPhysicsBase.C.

{
  for (const auto & block : component.blocks())
    _blocks.push_back(block);
}

◆ addFEKernels()

void AqueousReactionsEquilibriumPhysics::addFEKernels ( )

overrideprotectedvirtual

Reimplemented from PhysicsBase.

Definition at line 134 of file AqueousReactionsEquilibriumPhysics.C.

{
  // Add Kernels for each primary species
  // Note that the equations are on a per-species basis!
  // So equations are organized differently than reactions
  for (const auto i : index_range(_solver_species))
  {
    for (const auto j : make_range(_num_reactions))
    {
      if (_primary_participation[i][j])
      {
        {
          InputParameters params_sub = _factory.getValidParams("CoupledBEEquilibriumSub");
          assignBlocks(params_sub, _blocks);
          params_sub.set<NonlinearVariableName>("variable") = _solver_species[i];
          params_sub.set<Real>("weight") = _weights[i][j];
          params_sub.defaultCoupledValue("log_k", _log_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",
                              _solver_species[i] + "_" + _eq_species[j] + "_sub",
                              params_sub);
        }
 
        {
          InputParameters params_cd = _factory.getValidParams("CoupledDiffusionReactionSub");
          assignBlocks(params_cd, _blocks);
          params_cd.set<NonlinearVariableName>("variable") = _solver_species[i];
          params_cd.set<Real>("weight") = _weights[i][j];
          params_cd.defaultCoupledValue("log_k", _log_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",
                              _solver_species[i] + "_" + _eq_species[j] + "_cd",
                              params_cd);
        }
 
        // If pressure is coupled, add a CoupledConvectionReactionSub Kernel as well
        if (getParam<bool>("add_darcy_advection_term") && isParamValid("pressure"))
        {
          InputParameters params_conv = _factory.getValidParams("CoupledConvectionReactionSub");
          assignBlocks(params_conv, _blocks);
          params_conv.set<NonlinearVariableName>("variable") = _solver_species[i];
          params_conv.set<Real>("weight") = _weights[i][j];
          params_conv.defaultCoupledValue("log_k", _log_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") = getParam<RealVectorValue>("gravity");
          _problem->addKernel("CoupledConvectionReactionSub",
                              _solver_species[i] + "_" + _eq_species[j] + "_conv",
                              params_conv);
        }
      }
    }
  }
}

◆ addInitialConditions()

void ReactionNetworkPhysicsBase::addInitialConditions ( )

overrideprivatevirtualinherited

Add initial conditions for the solver variable (auxiliary not implemented)

Reimplemented from PhysicsBase.

Definition at line 140 of file ReactionNetworkPhysicsBase.C.

{
  InputParameters params = getFactory().getValidParams("FunctorIC");
  assignBlocks(params, _blocks);
  std::vector<MooseFunctorName> empty_functor_vector;
  const auto & initial_functors =
      isParamValid("initial_conditions")
          ? getParam<std::vector<MooseFunctorName>>("initial_conditions")
          : empty_functor_vector;
 
  for (const auto i : index_range(_solver_species))
  {
    const auto & var_name = _solver_species[i];
    // always obey the user specification of initial conditions
    // Base class does not have a default but derived classes could set one
    if (isParamValid("initial_conditions") &&
        shouldCreateIC(var_name,
                       _blocks,
                       /*whether IC is a default*/ !isParamSetByUser("initial_conditions"),
                       /*error if already an IC*/ true))
    {
      params.set<VariableName>("variable") = var_name;
      params.set<MooseFunctorName>("functor") = initial_functors[i];
      getProblem().addInitialCondition("FunctorIC", prefix() + var_name + "_ic", params);
    }
  }
}

◆ addPreconditioning()

void ReactionNetworkPhysicsBase::addPreconditioning ( )

overrideprivatevirtualinherited

Add default preconditioning options (not implemented at this time)

Reimplemented from PhysicsBase.

Definition at line 126 of file ReactionNetworkPhysicsBase.C.

{
  // TODO: identify fully independent or sequential groups in the reaction network
  // Solve using a segregated approach in the order of the sequence
}

◆ addSolverVariables()

void ReactionNetworkPhysicsBase::addSolverVariables ( )

overrideprivatevirtualinherited

Add solver variables (currently coded for CGFE)

Reimplemented from PhysicsBase.

Definition at line 77 of file ReactionNetworkPhysicsBase.C.

{
  for (const auto i : index_range(_solver_species))
  {
    const auto & var_name = _solver_species[i];
    // If the variable was added outside the Physics
    if (variableExists(var_name, /*error_if_aux*/ true))
    {
      reportPotentiallyMissedParameters(
          {"variable_order", "system_names", "equation_scaling"}, "MooseVariable", var_name);
      continue;
    }
 
    const std::string variable_type = "MooseVariable";
    InputParameters params = getFactory().getValidParams(variable_type);
    params.set<MooseEnum>("order") = getParam<MooseEnum>("variable_order");
    if (isParamValid("equation_scaling"))
      // all our variables have a single component
      params.set<std::vector<Real>>("scaling") = {
          getParam<std::vector<Real>>("equation_scaling")[i]};
    assignBlocks(params, _blocks);
    params.set<SolverSystemName>("solver_sys") = getSolverSystem(var_name);
 
    getProblem().addVariable(variable_type, var_name, params);
  }
}

◆ validParams()

InputParameters AqueousReactionsEquilibriumPhysics::validParams ( )

static

Definition at line 19 of file AqueousReactionsEquilibriumPhysics.C.

{
  InputParameters params = ReactionNetworkPhysicsBase::validParams();
  params.addClassDescription("Forms the equations for the chemical reaction networks in a fluid"
                             " medium using a continuous Galerkin finite element discretization.");
 
  // Rename parameters to match the previously existing actions for AqueousEquilibrium
  // ReactionNetwork
  params.renameParam("solver_variables", "primary_species", "The list of primary species to add");
  params.renameParam(
      "auxiliary_variables", "secondary_species", "The list of secondary species to add");
  params.renameParam(
      "variable_order", "order", "Order of both the primary and secondary species variables");
  params.renameParam("equation_scaling", "scaling", "");
  params.setDocString("reactions", "The list of equilibrium reactions occuring in the fluid");
 
  // To preserve the legacy option to perform Darcy-advection with AqueousEquilibrium
  // ReactionNetwork
  params.addParam<bool>("add_darcy_advection_term",
                        false,
                        "Whether to add an advection term using the Darcy equation to compute the "
                        "advecting velocity");
  params.addParam<std::vector<VariableName>>(
      "pressure", {}, "Pressure variable (for Darcy advection)");
  params.addParam<RealVectorValue>(
      "gravity", RealVectorValue(0, 0, -9.81), "Gravity vector (for Darcy advection)");
 
  return params;
}

Member Data Documentation

◆ _aux_species

const std::vector<AuxVariableName>& ReactionNetworkPhysicsBase::_aux_species

protectedinherited

Name of the species variables that can be computed without additional solves, simply auxkernels.

Definition at line 43 of file ReactionNetworkPhysicsBase.h.

Referenced by addAuxiliaryKernels(), ReactionNetworkPhysicsBase::addAuxiliaryVariables(), and ReactionNetworkPhysicsBase::ReactionNetworkPhysicsBase().

◆ _coupled_v

std::vector<std::vector<std::vector<VariableName> > > AqueousReactionsEquilibriumPhysics::_coupled_v

protected

Coupled primary species for each reaction (outer indexing is primary species, then reactions then innermost is the species in the reaction)

Definition at line 45 of file AqueousReactionsEquilibriumPhysics.h.

Referenced by addFEKernels(), and AqueousReactionsEquilibriumPhysics().

◆ _eq_species

std::vector<VariableName> AqueousReactionsEquilibriumPhysics::_eq_species

protected

Equilibrium species: only one per reaction. This is a restriction of this implementation.

Definition at line 40 of file AqueousReactionsEquilibriumPhysics.h.

Referenced by addAuxiliaryKernels(), addFEKernels(), and AqueousReactionsEquilibriumPhysics().

◆ _gravity

const RealVectorValue AqueousReactionsEquilibriumPhysics::_gravity

protected

Gravity vector.

Definition at line 52 of file AqueousReactionsEquilibriumPhysics.h.

◆ _log_eq_const

std::vector<Real> AqueousReactionsEquilibriumPhysics::_log_eq_const

protected

log10(Equilibrium constants) for each reaction

Definition at line 38 of file AqueousReactionsEquilibriumPhysics.h.

Referenced by addAuxiliaryKernels(), addFEKernels(), and AqueousReactionsEquilibriumPhysics().

◆ _num_aux_species

const unsigned int ReactionNetworkPhysicsBase::_num_aux_species

protectedinherited

Number of auxiliary species.

Definition at line 45 of file ReactionNetworkPhysicsBase.h.

◆ _num_reactions

const unsigned int ReactionNetworkPhysicsBase::_num_reactions

protectedinherited

Number of reactions involved in the network.

Definition at line 51 of file ReactionNetworkPhysicsBase.h.

Referenced by addAuxiliaryKernels(), addFEKernels(), AqueousReactionsEquilibriumPhysics(), and ReactionNetworkPhysicsBase::ReactionNetworkPhysicsBase().

◆ _num_solver_species

const unsigned int ReactionNetworkPhysicsBase::_num_solver_species

protectedinherited

Number of species to solve for.

Definition at line 41 of file ReactionNetworkPhysicsBase.h.

◆ _pressure_var

const std::vector<VariableName>& AqueousReactionsEquilibriumPhysics::_pressure_var

protected

Name of the pressure variable.

Definition at line 50 of file AqueousReactionsEquilibriumPhysics.h.

Referenced by addFEKernels().

◆ _primary_participation

std::vector<std::vector<bool> > AqueousReactionsEquilibriumPhysics::_primary_participation

protected

Vector of vectors, indexed by (i, j), of whether primary solver species 'i' is present in reaction 'j'.

Definition at line 42 of file AqueousReactionsEquilibriumPhysics.h.

Referenced by addFEKernels(), and AqueousReactionsEquilibriumPhysics().

◆ _reactions

const std::vector<ReactionNetworkUtils::Reaction> ReactionNetworkPhysicsBase::_reactions

protectedinherited

Reaction network after being parsed in initializePhysics()

Definition at line 49 of file ReactionNetworkPhysicsBase.h.

Referenced by AqueousReactionsEquilibriumPhysics().

◆ _reactions_input

std::vector<std::string> ReactionNetworkPhysicsBase::_reactions_input

protectedinherited

Reaction network as a vector of lines for pretty output.

Definition at line 47 of file ReactionNetworkPhysicsBase.h.

Referenced by AqueousReactionsEquilibriumPhysics(), and ReactionNetworkPhysicsBase::ReactionNetworkPhysicsBase().

◆ _solver_species

const std::vector<VariableName>& ReactionNetworkPhysicsBase::_solver_species

protectedinherited

Name of the species variables to solve for in the reaction network.

Definition at line 39 of file ReactionNetworkPhysicsBase.h.

Referenced by addFEKernels(), ReactionNetworkPhysicsBase::addInitialConditions(), ReactionNetworkPhysicsBase::addSolverVariables(), AqueousReactionsEquilibriumPhysics(), and ReactionNetworkPhysicsBase::ReactionNetworkPhysicsBase().

◆ _solver_species_involved

std::vector<std::vector<VariableName> > AqueousReactionsEquilibriumPhysics::_solver_species_involved

protected

Primary species involved in the ith equilibrium reaction (outer indexing)

Definition at line 47 of file AqueousReactionsEquilibriumPhysics.h.

Referenced by addAuxiliaryKernels(), and AqueousReactionsEquilibriumPhysics().

◆ _sto_u

std::vector<std::vector<Real> > AqueousReactionsEquilibriumPhysics::_sto_u

protected

Stoichiometric coefficients of primary/solver variables (outer indexing) in each reaction.

Definition at line 32 of file AqueousReactionsEquilibriumPhysics.h.

Referenced by addFEKernels(), and AqueousReactionsEquilibriumPhysics().

◆ _sto_v

std::vector<std::vector<std::vector<Real> > > AqueousReactionsEquilibriumPhysics::_sto_v

protected

Stoichiometric coefficients of coupled primary variables (outer indexing) in each reaction.

Definition at line 34 of file AqueousReactionsEquilibriumPhysics.h.

Referenced by addFEKernels(), and AqueousReactionsEquilibriumPhysics().

◆ _stos

std::vector<std::vector<Real> > AqueousReactionsEquilibriumPhysics::_stos

protected

Stoichiometric coefficients for each primary species (outer indexing) in each reaction.

Definition at line 30 of file AqueousReactionsEquilibriumPhysics.h.

Referenced by addAuxiliaryKernels(), and AqueousReactionsEquilibriumPhysics().

◆ _weights

std::vector<std::vector<Real> > AqueousReactionsEquilibriumPhysics::_weights

protected

Weight of each primary species (outer indexing) in each reaction.

Definition at line 36 of file AqueousReactionsEquilibriumPhysics.h.

Referenced by addFEKernels(), and AqueousReactionsEquilibriumPhysics().

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

chemical_reactions/include/physics/AqueousReactionsEquilibriumPhysics.h
chemical_reactions/src/physics/AqueousReactionsEquilibriumPhysics.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

◆ AqueousReactionsEquilibriumPhysics()

Member Function Documentation

◆ addAuxiliaryKernels()

◆ addAuxiliaryVariables()

◆ addComponent()

◆ addFEKernels()

◆ addInitialConditions()

◆ addPreconditioning()

◆ addSolverVariables()

◆ validParams()

Member Data Documentation

◆ _aux_species

◆ _coupled_v

◆ _eq_species

◆ _gravity

◆ _log_eq_const

◆ _num_aux_species

◆ _num_reactions

◆ _num_solver_species

◆ _pressure_var

◆ _primary_participation

◆ _reactions

◆ _reactions_input

◆ _solver_species

◆ _solver_species_involved

◆ _sto_u

◆ _sto_v

◆ _stos

◆ _weights