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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 | List of all members
ReactionNetworkPhysicsBase Class Reference

Base class to host all common parameters and attributes of Physics actions to solve equations for multiple species involved in chemical reactions. More...

#include <ReactionNetworkPhysicsBase.h>

Inheritance diagram for ReactionNetworkPhysicsBase:
[legend]

Public Types

typedef DataFileName DataFileParameterType
 

Public Member Functions

 ReactionNetworkPhysicsBase (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

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

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 addFEKernels ()
 
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 addAuxiliaryKernels ()
 
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

Base class to host all common parameters and attributes of Physics actions to solve equations for multiple species involved in chemical reactions.

For example, reaction kinetics, but also, equilibrium.

Definition at line 28 of file ReactionNetworkPhysicsBase.h.

Constructor & Destructor Documentation

◆ ReactionNetworkPhysicsBase()

ReactionNetworkPhysicsBase::ReactionNetworkPhysicsBase ( const InputParameters &  parameters)

Definition at line 39 of file ReactionNetworkPhysicsBase.C.

40 : PhysicsBase(parameters),
41 _solver_species(getParam<std::vector<VariableName>>("solver_variables")),
42 _num_solver_species(_solver_species.size()),
43 _aux_species(getParam<std::vector<AuxVariableName>>("auxiliary_variables")),
44 _num_aux_species(_aux_species.size()),
45 _reactions(
46 ReactionNetworkUtils::parseReactionNetwork(getParam<std::string>("reactions"), _verbose)),
47 _num_reactions(_reactions.size())
48{
49 // Keep track of variables
50 for (const auto & var_name : _solver_species)
51 saveSolverVariableName(var_name);
52 for (const auto & var_name : _aux_species)
53 saveAuxVariableName(var_name);
54
55 // Parameter checking
56 if (isParamValid("initial_conditions"))
57 checkVectorParamsSameLength<VariableName, MooseFunctorName>("solver_variables",
58 "initial_conditions");
59 if (isParamValid("equation_scaling"))
60 checkVectorParamsSameLength<VariableName, Real>("solver_variables", "equation_scaling");
61
62 addRequiredPhysicsTask("add_ic");
63 addRequiredPhysicsTask("add_variable");
64 addRequiredPhysicsTask("add_aux_variable");
65 addRequiredPhysicsTask("init_physics");
66
67 // Parse the lines in the reaction
68 std::stringstream reactions_param(getParam<std::string>("reactions"));
69 std::string line;
70 while (std::getline(reactions_param, line, '\n'))
71 _reactions_input.push_back(line);
72 mooseAssert(_num_reactions == _reactions_input.size(),
73 "Should be the same size. Extra line break in the reaction network?");
74}
PhysicsBase::parameters
const InputParameters & parameters() const
PhysicsBase::getParam
const T & getParam(const std::string &name) const
PhysicsBase::isParamValid
bool isParamValid(const std::string &name) const
PhysicsBase::saveSolverVariableName
void saveSolverVariableName(const VariableName &var_name)
PhysicsBase::saveAuxVariableName
void saveAuxVariableName(const VariableName &var_name)
PhysicsBase::_verbose
const bool _verbose
PhysicsBase::addRequiredPhysicsTask
void addRequiredPhysicsTask(const std::string &task)
ReactionNetworkPhysicsBase::_reactions
const std::vector< ReactionNetworkUtils::Reaction > _reactions
Reaction network after being parsed in initializePhysics()
Definition ReactionNetworkPhysicsBase.h:49
ReactionNetworkPhysicsBase::_num_aux_species
const unsigned int _num_aux_species
Number of auxiliary species.
Definition ReactionNetworkPhysicsBase.h:45
ReactionNetworkPhysicsBase::_reactions_input
std::vector< std::string > _reactions_input
Reaction network as a vector of lines for pretty output.
Definition ReactionNetworkPhysicsBase.h:47
ReactionNetworkPhysicsBase::_num_solver_species
const unsigned int _num_solver_species
Number of species to solve for.
Definition ReactionNetworkPhysicsBase.h:41
ReactionNetworkPhysicsBase::_aux_species
const std::vector< AuxVariableName > & _aux_species
Name of the species variables that can be computed without additional solves, simply auxkernels.
Definition ReactionNetworkPhysicsBase.h:43
ReactionNetworkPhysicsBase::_num_reactions
const unsigned int _num_reactions
Number of reactions involved in the network.
Definition ReactionNetworkPhysicsBase.h:51
ReactionNetworkPhysicsBase::_solver_species
const std::vector< VariableName > & _solver_species
Name of the species variables to solve for in the reaction network.
Definition ReactionNetworkPhysicsBase.h:39
ReactionNetworkUtils::parseReactionNetwork
std::vector< Reaction > parseReactionNetwork(const std::string &reaction_network_string, bool output_to_cout)
Parses the reaction network from a string form to a vector a Reaction.
Definition ReactionNetworkUtils.C:23

Member Function Documentation

◆ addAuxiliaryVariables()

void ReactionNetworkPhysicsBase::addAuxiliaryVariables ( )
overrideprivatevirtual

Add nodal auxiliary variables.

Reimplemented from PhysicsBase.

Definition at line 105 of file ReactionNetworkPhysicsBase.C.

106{
107 for (const auto i : index_range(_aux_species))
108 {
109 const auto & var_name = _aux_species[i];
110 // If the variable was added outside the Physics
111 if (variableExists(var_name, /*error_if_aux*/ false))
112 {
113 reportPotentiallyMissedParameters({"variable_order"}, "MooseVariable", var_name);
114 continue;
115 }
116
117 const std::string variable_type = "MooseVariable";
118 InputParameters params = getFactory().getValidParams(variable_type);
119 params.set<MooseEnum>("order") = getParam<MooseEnum>("variable_order");
120 assignBlocks(params, _blocks);
121 getProblem().addAuxVariable(variable_type, var_name, params);
122 }
123}
FEProblemBase::addAuxVariable
virtual void addAuxVariable(const std::string &var_type, const std::string &var_name, InputParameters &params)
Factory::getValidParams
InputParameters getValidParams(const std::string &name) const
InputParameters::set
T & set(const std::string &name, bool quiet_mode=false)
PhysicsBase::getProblem
virtual FEProblemBase & getProblem()
PhysicsBase::getFactory
Factory & getFactory()
PhysicsBase::assignBlocks
void assignBlocks(InputParameters &params, const std::vector< SubdomainName > &blocks) const
PhysicsBase::reportPotentiallyMissedParameters
void reportPotentiallyMissedParameters(const std::vector< std::string > &param_names, const std::string &object_type, const std::string &object_name="") const
PhysicsBase::variableExists
bool variableExists(const VariableName &var_name, bool error_if_aux) const
PhysicsBase::_blocks
std::vector< SubdomainName > _blocks
libMesh::index_range
auto index_range(const T &sizable)

◆ addComponent()

void ReactionNetworkPhysicsBase::addComponent ( const ActionComponent &  component)
overridevirtual

Reimplemented from PhysicsBase.

Definition at line 133 of file ReactionNetworkPhysicsBase.C.

134{
135 for (const auto & block : component.blocks())
136 _blocks.push_back(block);
137}
PhysicsBase::blocks
const std::vector< SubdomainName > & blocks() const
RankTwoScalarTools::component
T component(const RankTwoTensorTempl< T > &r2tensor, unsigned int i, unsigned int j)
Definition RankTwoScalarTools.h:67

◆ addInitialConditions()

void ReactionNetworkPhysicsBase::addInitialConditions ( )
overrideprivatevirtual

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

Reimplemented from PhysicsBase.

Definition at line 140 of file ReactionNetworkPhysicsBase.C.

141{
142 InputParameters params = getFactory().getValidParams("FunctorIC");
143 assignBlocks(params, _blocks);
144 std::vector<MooseFunctorName> empty_functor_vector;
145 const auto & initial_functors =
146 isParamValid("initial_conditions")
147 ? getParam<std::vector<MooseFunctorName>>("initial_conditions")
148 : empty_functor_vector;
149
150 for (const auto i : index_range(_solver_species))
151 {
152 const auto & var_name = _solver_species[i];
153 // always obey the user specification of initial conditions
154 // Base class does not have a default but derived classes could set one
155 if (isParamValid("initial_conditions") &&
156 shouldCreateIC(var_name,
157 _blocks,
158 /*whether IC is a default*/ !isParamSetByUser("initial_conditions"),
159 /*error if already an IC*/ true))
160 {
161 params.set<VariableName>("variable") = var_name;
162 params.set<MooseFunctorName>("functor") = initial_functors[i];
163 getProblem().addInitialCondition("FunctorIC", prefix() + var_name + "_ic", params);
164 }
165 }
166}
FEProblemBase::addInitialCondition
virtual void addInitialCondition(const std::string &ic_name, const std::string &name, InputParameters &parameters)
PhysicsBase::isParamSetByUser
bool isParamSetByUser(const std::string &name) const
PhysicsBase::shouldCreateIC
bool shouldCreateIC(const VariableName &var_name, const std::vector< SubdomainName > &blocks, const bool ic_is_default_ic, const bool error_if_already_defined) const
PhysicsBase::prefix
std::string prefix() const

◆ addPreconditioning()

void ReactionNetworkPhysicsBase::addPreconditioning ( )
overrideprivatevirtual

Add default preconditioning options (not implemented at this time)

Reimplemented from PhysicsBase.

Definition at line 126 of file ReactionNetworkPhysicsBase.C.

127{
128 // TODO: identify fully independent or sequential groups in the reaction network
129 // Solve using a segregated approach in the order of the sequence
130}

◆ addSolverVariables()

void ReactionNetworkPhysicsBase::addSolverVariables ( )
overrideprivatevirtual

Add solver variables (currently coded for CGFE)

Reimplemented from PhysicsBase.

Definition at line 77 of file ReactionNetworkPhysicsBase.C.

78{
79 for (const auto i : index_range(_solver_species))
80 {
81 const auto & var_name = _solver_species[i];
82 // If the variable was added outside the Physics
83 if (variableExists(var_name, /*error_if_aux*/ true))
84 {
85 reportPotentiallyMissedParameters(
86 {"variable_order", "system_names", "equation_scaling"}, "MooseVariable", var_name);
87 continue;
88 }
89
90 const std::string variable_type = "MooseVariable";
91 InputParameters params = getFactory().getValidParams(variable_type);
92 params.set<MooseEnum>("order") = getParam<MooseEnum>("variable_order");
93 if (isParamValid("equation_scaling"))
94 // all our variables have a single component
95 params.set<std::vector<Real>>("scaling") = {
96 getParam<std::vector<Real>>("equation_scaling")[i]};
97 assignBlocks(params, _blocks);
98 params.set<SolverSystemName>("solver_sys") = getSolverSystem(var_name);
99
100 getProblem().addVariable(variable_type, var_name, params);
101 }
102}
FEProblemBase::addVariable
virtual void addVariable(const std::string &var_type, const std::string &var_name, InputParameters &params)
PhysicsBase::getSolverSystem
const SolverSystemName & getSolverSystem(unsigned int variable_index) const

◆ validParams()

InputParameters ReactionNetworkPhysicsBase::validParams ( )
static

Definition at line 14 of file ReactionNetworkPhysicsBase.C.

15{
16 InputParameters params = PhysicsBase::validParams();
17 params.addClassDescription("Base class to create a reaction network Physics from.");
18
19 // Variables parameters
20 params.addRequiredParam<std::vector<VariableName>>("solver_variables", "Species to solve for");
21 params.addRequiredParam<std::vector<AuxVariableName>>(
22 "auxiliary_variables",
23 "Additional species to output the concentration of, which do not require an additional "
24 "equation to obtain");
25 params.transferParam<MooseEnum>(MooseVariableBase::validParams(), "order", "variable_order");
26 params.addParam<std::vector<Real>>("equation_scaling",
27 "Scaling factor to apply to each equation");
28
29 // Initial conditions
30 params.addParam<std::vector<MooseFunctorName>>("initial_conditions",
31 "Initial conditions for the species to solve for");
32
33 // Reaction network
34 params.addParam<std::string>("reactions", "The list of chemical reactions");
35
36 return params;
37}
InputParameters::addRequiredParam
void addRequiredParam(const std::string &name, const std::string &doc_string)
InputParameters::transferParam
void transferParam(const InputParameters &source_param, const std::string &name, const std::string &new_name="", const std::string &new_description="")
InputParameters::addParam
void addParam(const std::string &name, const std::initializer_list< typename T::value_type > &value, const std::string &doc_string)
InputParameters::addClassDescription
void addClassDescription(const std::string &doc_string)
MooseVariableBase::validParams
static InputParameters validParams()
PhysicsBase::validParams
static InputParameters validParams()

Referenced by AqueousReactionsEquilibriumPhysics::validParams().

Member Data Documentation

◆ _aux_species

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

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

Definition at line 43 of file ReactionNetworkPhysicsBase.h.

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

◆ _num_aux_species

const unsigned int ReactionNetworkPhysicsBase::_num_aux_species
protected

Number of auxiliary species.

Definition at line 45 of file ReactionNetworkPhysicsBase.h.

◆ _num_reactions

const unsigned int ReactionNetworkPhysicsBase::_num_reactions
protected

Number of reactions involved in the network.

Definition at line 51 of file ReactionNetworkPhysicsBase.h.

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

◆ _num_solver_species

const unsigned int ReactionNetworkPhysicsBase::_num_solver_species
protected

Number of species to solve for.

Definition at line 41 of file ReactionNetworkPhysicsBase.h.

◆ _reactions

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

Reaction network after being parsed in initializePhysics()

Definition at line 49 of file ReactionNetworkPhysicsBase.h.

Referenced by AqueousReactionsEquilibriumPhysics::AqueousReactionsEquilibriumPhysics().

◆ _reactions_input

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

Reaction network as a vector of lines for pretty output.

Definition at line 47 of file ReactionNetworkPhysicsBase.h.

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

◆ _solver_species

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

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

Definition at line 39 of file ReactionNetworkPhysicsBase.h.

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

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