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AddTimeDependentReactionSolverAction Class Reference

Action that sets up a time-dependent equilibrium reaction solver. More...

#include <AddTimeDependentReactionSolverAction.h>

Inheritance diagram for AddTimeDependentReactionSolverAction:
[legend]

Public Types

typedef DataFileName DataFileParameterType
 

Public Member Functions

 AddTimeDependentReactionSolverAction (const InputParameters &parameters)
 
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
 
virtual const std::string & name () const
 
std::string typeAndName () const
 
std::string errorPrefix (const std::string &error_type) const
 
void callMooseError (std::string msg, const bool with_prefix) const
 
MooseObjectParameterName uniqueParameterName (const std::string &parameter_name) const
 
const InputParameters & parameters () const
 
MooseObjectName uniqueName () 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 &nm) const
 
void paramError (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
 
void connectControllableParams (const std::string &parameter, const std::string &object_type, const std::string &object_name, const std::string &object_parameter) const
 
void mooseError (Args &&... args) const
 
void mooseErrorNonPrefixed (Args &&... args) const
 
void mooseDocumentedError (const std::string &repo_name, const unsigned int issue_num, Args &&... args) const
 
void mooseWarning (Args &&... args) const
 
void mooseWarningNonPrefixed (Args &&... args) const
 
void mooseDeprecated (Args &&... args) const
 
void mooseInfo (Args &&... args) 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 ()
 

Public Attributes

const ConsoleStream _console
 

Static Public Attributes

static constexpr auto SYSTEM
 
static constexpr auto NAME
 

Protected Member Functions

void addAuxSpecies (const std::string &var_name, const std::string &species_name, const std::string &unit)
 Adds AuxVariable and AuxKernel that will record species concentrations. More...
 
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
 

Static Protected Member Functions

static std::string meshPropertyName (const std::string &data_name, const std::string &prefix)
 

Protected Attributes

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
 
const std::string _type
 
const std::string _name
 
const InputParameters & _pars
 
Factory & _factory
 
ActionFactory & _action_factory
 
MooseApp & _pg_moose_app
 
const std::string _prefix
 
const Parallel::Communicator & _communicator
 

Detailed Description

Action that sets up a time-dependent equilibrium reaction solver.

Definition at line 17 of file AddTimeDependentReactionSolverAction.h.

Constructor & Destructor Documentation

◆ AddTimeDependentReactionSolverAction()

AddTimeDependentReactionSolverAction::AddTimeDependentReactionSolverAction ( const InputParameters &  parameters)

Definition at line 39 of file AddTimeDependentReactionSolverAction.C.

41  : AddGeochemistrySolverAction(params)
42 {
43 }
AddGeochemistrySolverAction::AddGeochemistrySolverAction
AddGeochemistrySolverAction(const InputParameters &parameters)
Definition: AddGeochemistrySolverAction.C:134

Member Function Documentation

◆ act()

void AddTimeDependentReactionSolverAction::act ( )
overridevirtual

Reimplemented from AddGeochemistrySolverAction.

Definition at line 46 of file AddTimeDependentReactionSolverAction.C.

47 {
48  // create Output and Aux objects
49  AddGeochemistrySolverAction::act();
50 
51  // Set up an arbitrary mesh
52  if (_current_task == "setup_mesh")
53  {
54  const std::string class_name = "GeneratedMesh";
55  InputParameters params = _factory.getValidParams(class_name);
56  params.set<MooseEnum>("dim") = "1";
57  _mesh = _factory.create<MooseMesh>(class_name, "mesh", params);
58  }
59  // Initialize the arbitrary mesh
60  else if (_current_task == "init_mesh")
61  {
62  _mesh->init();
63  }
64  // Create a "solve=false" FEProblem, if appropriate
65  else if (_current_task == "create_problem")
66  {
67  const std::string class_name = "FEProblem";
68  InputParameters params = _factory.getValidParams(class_name);
69  params.set<MooseMesh *>("mesh") = _mesh.get();
70  params.set<bool>("use_nonlinear") = true;
71  params.set<bool>("solve") = getParam<bool>("include_moose_solve");
72  _problem = _factory.create<FEProblemBase>(class_name, "Problem", params);
73  _problem->setKernelCoverageCheck(getParam<bool>("include_moose_solve")
74  ? FEProblemBase::CoverageCheckMode::TRUE
75  : FEProblemBase::CoverageCheckMode::FALSE);
76  }
77  else if (_current_task == "add_geochemistry_reactor")
78  {
79  const std::string class_name = "GeochemistryTimeDependentReactor";
80  auto params = _factory.getValidParams(class_name);
81  // Only pass parameters that were supplied to this action
82  if (isParamValid("block"))
83  params.set<std::vector<SubdomainName>>("block") =
84  getParam<std::vector<SubdomainName>>("block");
85  if (isParamValid("boundary"))
86  params.set<std::vector<BoundaryName>>("boundary") =
87  getParam<std::vector<BoundaryName>>("boundary");
88  params.set<UserObjectName>("model_definition") = getParam<UserObjectName>("model_definition");
89  if (isParamValid("swap_out_of_basis"))
90  params.set<std::vector<std::string>>("swap_out_of_basis") =
91  getParam<std::vector<std::string>>("swap_out_of_basis");
92  if (isParamValid("swap_into_basis"))
93  params.set<std::vector<std::string>>("swap_into_basis") =
94  getParam<std::vector<std::string>>("swap_into_basis");
95  params.set<MultiMooseEnum>("constraint_meaning") =
96  getParam<MultiMooseEnum>("constraint_meaning");
97  params.set<std::vector<std::string>>("constraint_species") =
98  getParam<std::vector<std::string>>("constraint_species");
99  params.set<std::vector<Real>>("constraint_value") =
100  getParam<std::vector<Real>>("constraint_value");
101  params.set<MultiMooseEnum>("constraint_unit") = getParam<MultiMooseEnum>("constraint_unit");
102  params.set<Real>("max_ionic_strength") = getParam<Real>("max_ionic_strength");
103  params.set<unsigned>("extra_iterations_to_make_consistent") =
104  getParam<unsigned>("extra_iterations_to_make_consistent");
105  params.applySpecificParameters(parameters(), {"temperature"});
106  params.applySpecificParameters(parameters(), {"cold_temperature"});
107  params.set<unsigned>("heating_increments") = getParam<unsigned>("heating_increments");
108  params.set<Real>("stoichiometry_tolerance") = getParam<Real>("stoichiometry_tolerance");
109  params.set<std::string>("charge_balance_species") =
110  getParam<std::string>("charge_balance_species");
111  if (isParamValid("prevent_precipitation"))
112  params.set<std::vector<std::string>>("prevent_precipitation") =
113  getParam<std::vector<std::string>>("prevent_precipitation");
114  params.set<Real>("abs_tol") = getParam<Real>("abs_tol");
115  params.set<Real>("rel_tol") = getParam<Real>("rel_tol");
116  params.set<Real>("min_initial_molality") = getParam<Real>("min_initial_molality");
117  params.set<unsigned>("max_iter") = getParam<unsigned>("max_iter");
118  params.set<Real>("max_initial_residual") = getParam<Real>("max_initial_residual");
119  params.set<Real>("swap_threshold") = getParam<Real>("swap_threshold");
120  params.set<unsigned>("max_swaps_allowed") = getParam<unsigned>("max_swaps_allowed");
121  params.set<unsigned>("ramp_max_ionic_strength_initial") =
122  getParam<unsigned>("ramp_max_ionic_strength_initial");
123  params.set<unsigned>("ramp_max_ionic_strength_subsequent") =
124  getParam<unsigned>("ramp_max_ionic_strength_subsequent");
125  params.set<bool>("ionic_str_using_basis_only") = getParam<bool>("ionic_str_using_basis_only");
126  params.set<bool>("stoichiometric_ionic_str_using_Cl_only") =
127  getParam<bool>("stoichiometric_ionic_str_using_Cl_only");
128  params.set<Real>("close_system_at_time") = getParam<Real>("close_system_at_time");
129  if (isParamValid("remove_fixed_activity_name"))
130  params.set<std::vector<std::string>>("remove_fixed_activity_name") =
131  getParam<std::vector<std::string>>("remove_fixed_activity_name");
132  if (isParamValid("remove_fixed_activity_time"))
133  params.set<std::vector<Real>>("remove_fixed_activity_time") =
134  getParam<std::vector<Real>>("remove_fixed_activity_time");
135  if (isParamValid("source_species_names"))
136  params.set<std::vector<std::string>>("source_species_names") =
137  getParam<std::vector<std::string>>("source_species_names");
138  if (isParamValid("source_species_rates"))
139  params.applySpecificParameters(parameters(), {"source_species_rates"});
140  if (isParamValid("controlled_activity_name"))
141  params.set<std::vector<std::string>>("controlled_activity_name") =
142  getParam<std::vector<std::string>>("controlled_activity_name");
143  if (isParamValid("controlled_activity_value"))
144  params.applySpecificParameters(parameters(), {"controlled_activity_value"});
145  params.applySpecificParameters(parameters(), {"mode"});
146  params.set<Real>("initial_temperature") = getParam<Real>("initial_temperature");
147  params.set<bool>("evaluate_kinetic_rates_always") =
148  getParam<bool>("evaluate_kinetic_rates_always");
149  if (isParamValid("kinetic_species_name"))
150  params.set<std::vector<std::string>>("kinetic_species_name") =
151  getParam<std::vector<std::string>>("kinetic_species_name");
152  if (isParamValid("kinetic_species_initial_value"))
153  params.set<std::vector<Real>>("kinetic_species_initial_value") =
154  getParam<std::vector<Real>>("kinetic_species_initial_value");
155  if (isParamValid("kinetic_species_unit"))
156  params.set<MultiMooseEnum>("kinetic_species_unit") =
157  getParam<MultiMooseEnum>("kinetic_species_unit");
158  params.set<ExecFlagEnum>("execute_on") = {EXEC_TIMESTEP_END};
159  _problem->addUserObject(
160  class_name, getParam<UserObjectName>("geochemistry_reactor_name"), params);
161  }
162 }
MooseMesh
InputParameters::applySpecificParameters
void applySpecificParameters(const InputParameters &common, const std::vector< std::string > &include, bool allow_private=false)
InputParameters::set
T & set(const std::string &name, bool quiet_mode=false)
Factory::create
std::shared_ptr< MooseObject > create(const std::string &obj_name, const std::string &name, const InputParameters &parameters, THREAD_ID tid=0, bool print_deprecated=true)
Factory::getValidParams
InputParameters getValidParams(const std::string &name) const
EXEC_TIMESTEP_END
const ExecFlagType EXEC_TIMESTEP_END
Action::isParamValid
bool isParamValid(const std::string &name) const
Action::_factory
Factory & _factory
Action::getParam
const T & getParam(const std::string &name) const
Action::_current_task
const std::string & _current_task
Action::_mesh
std::shared_ptr< MooseMesh > & _mesh
Real
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
Action::_problem
std::shared_ptr< FEProblemBase > & _problem
Action::parameters
const InputParameters & parameters() const

◆ addAuxSpecies()

void AddGeochemistrySolverAction::addAuxSpecies ( const std::string &  var_name,
const std::string &  species_name,
const std::string &  unit 
)
protectedinherited

Adds AuxVariable and AuxKernel that will record species concentrations.

Parameters
var_nameAuxVariable name
species_nameSpecies name
unitUnit choice: defined in GeochemistryQuantityAux

Definition at line 255 of file AddGeochemistrySolverAction.C.

Referenced by AddGeochemistrySolverAction::act().

258 {
259  // add AuxVariable
260  auto var_params = _factory.getValidParams("MooseVariable");
261  _problem->addAuxVariable("MooseVariable", var_name, var_params);
262  // add AuxKernel
263  const std::string class_name = "GeochemistryQuantityAux";
264  auto params = _factory.getValidParams(class_name);
265  params.set<std::string>("species") = species_name;
266  params.set<MooseEnum>("quantity") = quantity;
267  params.set<UserObjectName>("reactor") = getParam<UserObjectName>("geochemistry_reactor_name");
268  params.set<AuxVariableName>("variable") = var_name;
269  params.set<ExecFlagEnum>("execute_on") = EXEC_TIMESTEP_END;
270  _problem->addAuxKernel(class_name, var_name, params);
271 }
InputParameters::set
T & set(const std::string &name, bool quiet_mode=false)
Factory::getValidParams
InputParameters getValidParams(const std::string &name) const
Action::_factory
Factory & _factory
Action::_problem
std::shared_ptr< FEProblemBase > & _problem

◆ validParams()

InputParameters AddTimeDependentReactionSolverAction::validParams ( )
static

Definition at line 27 of file AddTimeDependentReactionSolverAction.C.

28 {
29  InputParameters params = AddGeochemistrySolverAction::validParams();
30  params += GeochemistryTimeDependentReactor::sharedParams();
31  params.addClassDescription(
32  "Action that sets up a time-dependent equilibrium reaction solver. This creates creates a "
33  "time-dependent geochemistry solver, and adds AuxVariables corresonding to the molalities, "
34  "etc");
35 
36  return params;
37 }
AddGeochemistrySolverAction::validParams
static InputParameters validParams()
Definition: AddGeochemistrySolverAction.C:25
GeochemistryTimeDependentReactor::sharedParams
static InputParameters sharedParams()
params that are shared with AddTimeDependentReactionSolverAction
Definition: GeochemistryTimeDependentReactor.C:15
InputParameters::addClassDescription
void addClassDescription(const std::string &doc_string)
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