Mark new nucleation sites for refinement. More...

#include <DiscreteNucleationMarker.h>

Inheritance diagram for DiscreteNucleationMarker:

Public Types
enum	MarkerValue

typedef DataFileName	DataFileParameterType

Public Member Functions
	DiscreteNucleationMarker (const InputParameters &parameters)

virtual void	computeMarker ()

bool	isActive () const

virtual void	markerSetup ()

virtual const std::set< std::string > &	getRequestedItems () override

virtual const std::set< std::string > &	getSuppliedItems () override

virtual bool	enabled () const

std::shared_ptr< MooseObject >	getSharedPtr ()

std::shared_ptr< const MooseObject >	getSharedPtr () const

bool	isKokkosObject () const

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

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

unsigned int	numBlocks () const

virtual const std::set< SubdomainID > &	blockIDs () const

unsigned int	blocksMaxDimension () const

bool	hasBlocks (const SubdomainName &name) const

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

bool	hasBlocks (const std::set< SubdomainName > &names) const

bool	hasBlocks (SubdomainID id) const

bool	hasBlocks (const std::vector< SubdomainID > &ids) const

bool	hasBlocks (const std::set< SubdomainID > &ids) const

bool	isBlockSubset (const std::set< SubdomainID > &ids) const

bool	isBlockSubset (const std::vector< SubdomainID > &ids) const

bool	hasBlockMaterialProperty (const std::string &prop_name)

const std::set< SubdomainID > &	meshBlockIDs () const

virtual bool	blockRestricted () const

virtual void	checkVariable (const MooseVariableFieldBase &variable) const

virtual void	initialSetup ()

virtual void	timestepSetup ()

virtual void	jacobianSetup ()

virtual void	residualSetup ()

virtual void	subdomainSetup ()

virtual void	customSetup (const ExecFlagType &)

const ExecFlagEnum &	getExecuteOnEnum () const

const std::set< MooseVariableFieldBase * > &	getMooseVariableDependencies () const

std::set< MooseVariableFieldBase * >	checkAllVariables (const DofObjectType &dof_object, const std::set< MooseVariableFieldBase * > &vars_to_omit={})

virtual std::set< MooseVariableFieldBase * >	checkVariables (const libMesh::Node &node, const std::set< MooseVariableFieldBase * > &vars_to_check)

std::set< MooseVariableFieldBase * >	checkVariables (const libMesh::Elem &element, const std::set< MooseVariableFieldBase * > &vars_to_check)

void	addMooseVariableDependency (MooseVariableFieldBase *var)

void	addMooseVariableDependency (const std::vector< MooseVariableFieldBase * > &vars)

UserObjectName	getUserObjectName (const std::string &param_name) const

const T &	getUserObject (const std::string &param_name, bool is_dependency=true) const

const T &	getUserObjectByName (const UserObjectName &object_name, bool is_dependency=true) const

const UserObjectBase &	getUserObjectBase (const std::string &param_name, bool is_dependency=true) const

const UserObjectBase &	getUserObjectBaseByName (const UserObjectName &object_name, bool is_dependency=true) const

bool	isDefaultPostprocessorValue (const std::string &param_name, const unsigned int index=0) const

bool	hasPostprocessor (const std::string &param_name, const unsigned int index=0) const

bool	hasPostprocessorByName (const PostprocessorName &name) const

std::size_t	coupledPostprocessors (const std::string &param_name) const

const PostprocessorName &	getPostprocessorName (const std::string &param_name, const unsigned int index=0) const

virtual void	meshChanged ()

void	buildOutputHideVariableList (std::set< std::string > variable_names)

const std::set< OutputName > &	getOutputs ()

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

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

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

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

bool	hasUserObjectByName (const UserObjectName &object_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

const PostprocessorValue &	getPostprocessorValue (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValue (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOld (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOld (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOlder (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOlder (const std::string &param_name, const unsigned int index=0) const

virtual const PostprocessorValue &	getPostprocessorValueByName (const PostprocessorName &name) const

virtual const PostprocessorValue &	getPostprocessorValueByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOldByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOldByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOlderByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOlderByName (const PostprocessorName &name) 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)

static MooseEnum	markerStates ()

static void	sort (typename std::vector< T > &vector)

static void	sortDFS (typename std::vector< T > &vector)

static void	cyclicDependencyError (CyclicDependencyException< T2 > &e, const std::string &header, NameFunc &&name_func)

static void	cyclicDependencyError (CyclicDependencyException< T2 > &e, const std::string &header)

Public Attributes
	DONT_MARK

	COARSEN

	DO_NOTHING

	REFINE

	usingCombinedWarningSolutionWarnings

const ConsoleStream	_console

Static Public Attributes
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

Protected Member Functions
virtual MarkerValue	computeElementMarker () override

ErrorVector &	getErrorVector (std::string indicator)

const MooseArray< Real > &	getMarkerValue (std::string name)

void	flagInvalidSolutionInternal (const InvalidSolutionID invalid_solution_id) const

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

virtual bool	hasBlockMaterialPropertyHelper (const std::string &prop_name)

void	initializeBlockRestrictable (const MooseObject *moose_object)

void	initializeKokkosBlockRestrictable ()

Moose::CoordinateSystemType	getBlockCoordSystem ()

KOKKOS_FUNCTION dof_id_type	numKokkosBlockElements () const

KOKKOS_FUNCTION dof_id_type	numKokkosBlockNodes () const

KOKKOS_FUNCTION dof_id_type	numKokkosBlockSides () const

KOKKOS_FUNCTION ContiguousElementID	kokkosBlockElementID (Moose::Kokkos::ThreadID tid) const

KOKKOS_FUNCTION ContiguousElementID	kokkosBlockNodeID (Moose::Kokkos::ThreadID tid) const

KOKKOS_FUNCTION auto	kokkosBlockElementSideID (Moose::Kokkos::ThreadID tid) const

virtual void	addUserObjectDependencyHelper (const UserObjectBase &) const

T &	declareRestartableData (const std::string &data_name, Args &&... args)

ManagedValue< T >	declareManagedRestartableDataWithContext (const std::string &data_name, void *context, Args &&... args)

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

T &	declareRestartableDataWithContext (const std::string &data_name, void *context, Args &&... args)

T &	declareRecoverableData (const std::string &data_name, Args &&... args)

T &	declareRestartableDataWithObjectName (const std::string &data_name, const std::string &object_name, Args &&... args)

T &	declareRestartableDataWithObjectNameWithContext (const std::string &data_name, const std::string &object_name, void *context, Args &&... args)

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

virtual void	addPostprocessorDependencyHelper (const PostprocessorName &) const

Protected Attributes
const DiscreteNucleationMap &	_map
	UserObject providing a map of currently active nuclei.

const MooseVariableFieldBase *const	_periodic_var
	variable to use for minPeriodicDistance calls (i.e. use the periodicity of this variable)

const DiscreteNucleationInserterBase &	_inserter
	UserObject that manages nucleus insertin and deletion.

const Real	_int_width
	Nucleus interface width.

const DiscreteNucleationInserterBase::NucleusList &	_nucleus_list
	list of nuclei maintained bu the inserter object

SubProblem &	_subproblem

FEProblemBase &	_fe_problem

Adaptivity &	_adaptivity

SystemBase &	_sys

THREAD_ID	_tid

Assembly &	_assembly

MooseVariable &	_field_var

const Elem *const &	_current_elem

MooseMesh &	_mesh

std::set< std::string >	_depend

std::set< std::string >	_supplied

const bool &	_enabled

MooseApp &	_app

Factory &	_factory

ActionFactory &	_action_factory

const std::string &	_type

const std::string &	_name

const InputParameters &	_pars

const MaterialData *	_blk_material_data

const ExecFlagEnum &	_execute_enum

const ExecFlagType &	_current_execute_flag

MooseApp &	_restartable_app

const std::string	_restartable_system_name

const THREAD_ID	_restartable_tid

const bool	_restartable_read_only

FEProblemBase &	_mci_feproblem

const Parallel::Communicator &	_communicator

Private Member Functions
std::set< MooseVariableFieldBase * >	checkVariablesHelper (const DofObjectType &dof_object, const std::set< MooseVariableFieldBase * > &vars_to_check)

const UserObjectBase &	getUserObjectFromFEProblem (const UserObjectName &object_name, const THREAD_ID tid=0) const

const T &	castUserObject (const UserObjectBase &uo_base, const std::string &param_name="") const

void	mooseObjectError (const std::string &param_name, std::stringstream &oss) const

const std::string &	userObjectType (const UserObjectBase &uo) const

const std::string &	userObjectName (const UserObjectBase &uo) const

RestartableDataValue &	registerRestartableDataOnApp (std::unique_ptr< RestartableDataValue > data, THREAD_ID tid) const

void	registerRestartableNameWithFilterOnApp (const std::string &name, Moose::RESTARTABLE_FILTER filter)

RestartableData< T > &	declareRestartableDataHelper (const std::string &data_name, void *context, Args &&... args) const

const PostprocessorName &	getPostprocessorNameInternal (const std::string &param_name, const unsigned int index, const bool allow_default_value=true) const

bool	isDefaultPostprocessorValueByName (const PostprocessorName &name) const

PostprocessorValue	getDefaultPostprocessorValueByName (const PostprocessorName &name) const

void	checkParam (const std::string &param_name, const unsigned int index=std::numeric_limits< unsigned int >::max()) const

bool	postprocessorsAdded () const

const PostprocessorValue &	getPostprocessorValueInternal (const std::string &param_name, unsigned int index, std::size_t t_index) const

const PostprocessorValue &	getPostprocessorValueInternal (const std::string &param_name, unsigned int index, std::size_t t_index) const

const PostprocessorValue &	getPostprocessorValueByNameInternal (const PostprocessorName &name, std::size_t t_index) const

const PostprocessorValue &	getPostprocessorValueByNameInternal (const PostprocessorName &name, std::size_t t_index) 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

const MooseBase &	_si_moose_base

const FEProblemBase *	_si_problem

std::set< SubdomainID >	_blk_ids

std::vector< SubdomainID >	_vec_ids

std::vector< SubdomainName >	_blocks

const bool	_blk_dual_restrictable

FEProblemBase *	_blk_feproblem

const MooseMesh *	_blk_mesh

const std::set< BoundaryID >	_empty_boundary_ids

const std::set< BoundaryID > &	_boundary_ids

THREAD_ID	_blk_tid

const std::string &	_blk_name

unsigned int	_blk_dim

const MooseObject *	_moose_object

Moose::Kokkos::Array< ContiguousElementID >	_kokkos_element_ids

Moose::Kokkos::Array< ContiguousNodeID >	_kokkos_node_ids

Moose::Kokkos::Array< Moose::Kokkos::Pair< ContiguousElementID, unsigned int > >	_kokkos_element_side_ids

ExecFlagEnum	_empty_execute_enum

std::set< MooseVariableFieldBase * >	_moose_variable_dependencies

std::vector< libMesh::dof_id_type >	_dof_indices

const MooseObject &	_uoi_moose_object

const FEProblemBase &	_uoi_feproblem

const THREAD_ID	_uoi_tid

const RestartableDataMapName	_metaname

std::string	_restartable_name

const MooseObject &	_ppi_moose_object

const InputParameters &	_ppi_params

const FEProblemBase &	_ppi_feproblem

std::map< PostprocessorName, std::unique_ptr< PostprocessorValue > >	_default_values

MooseApp &	_oi_moose_app

OutputWarehouse &	_oi_output_warehouse

std::set< OutputName >	_oi_outputs

Detailed Description

Mark new nucleation sites for refinement.

Definition at line 20 of file DiscreteNucleationMarker.h.

Constructor & Destructor Documentation

◆ DiscreteNucleationMarker()

DiscreteNucleationMarker::DiscreteNucleationMarker ( const InputParameters & parameters )

Definition at line 24 of file DiscreteNucleationMarker.C.

  : Marker(parameters),
    _map(getUserObject<DiscreteNucleationMap>("map")),
    _periodic_var(_map.getPeriodicVar()),
    _inserter(_map.getInserter()),
    _int_width(_map.getWidth()),
    _nucleus_list(_inserter.getNucleusList())
{
}

Member Function Documentation

◆ computeElementMarker()

Marker::MarkerValue DiscreteNucleationMarker::computeElementMarker ( )

overrideprotectedvirtual

Implements Marker.

Definition at line 35 of file DiscreteNucleationMarker.C.

{
  const RealVectorValue centroid = _current_elem->vertex_average();
  const Real size = 0.5 * _current_elem->hmax();
 
  // check if the surface of a nucleus might touch the element
  for (unsigned i = 0; i < _nucleus_list.size(); ++i)
  {
    // get the radius of the current nucleus
    const Real radius = _nucleus_list[i].radius;
 
    // use a non-periodic or periodic distance
    const Real r =
        _periodic_var ? _mesh.minPeriodicDistance(*_periodic_var, centroid, _nucleus_list[i].center)
                      : (centroid - _nucleus_list[i].center).norm();
    if (r < radius + size && r > radius - size && size > _int_width)
      return REFINE;
  }
 
  // We return don't mark to allow coarsening when used in a ComboMarker
  return DONT_MARK;
}

◆ validParams()

InputParameters DiscreteNucleationMarker::validParams ( )

static

Definition at line 16 of file DiscreteNucleationMarker.C.

{
  InputParameters params = Marker::validParams();
  params.addClassDescription("Mark new nucleation sites for refinement");
  params.addRequiredParam<UserObjectName>("map", "DiscreteNucleationMap user object");
  return params;
}

Member Data Documentation

◆ _inserter

const DiscreteNucleationInserterBase& DiscreteNucleationMarker::_inserter

protected

UserObject that manages nucleus insertin and deletion.

Definition at line 37 of file DiscreteNucleationMarker.h.

◆ _int_width

const Real DiscreteNucleationMarker::_int_width

protected

Nucleus interface width.

Definition at line 40 of file DiscreteNucleationMarker.h.

Referenced by computeElementMarker().

◆ _map

const DiscreteNucleationMap& DiscreteNucleationMarker::_map

protected

UserObject providing a map of currently active nuclei.

Definition at line 31 of file DiscreteNucleationMarker.h.

◆ _nucleus_list

const DiscreteNucleationInserterBase::NucleusList& DiscreteNucleationMarker::_nucleus_list

protected

list of nuclei maintained bu the inserter object

Definition at line 43 of file DiscreteNucleationMarker.h.

Referenced by computeElementMarker().

◆ _periodic_var

const MooseVariableFieldBase* const DiscreteNucleationMarker::_periodic_var

protected

variable to use for minPeriodicDistance calls (i.e. use the periodicity of this variable)

Definition at line 34 of file DiscreteNucleationMarker.h.

Referenced by computeElementMarker().

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

phase_field/include/markers/DiscreteNucleationMarker.h
phase_field/src/markers/DiscreteNucleationMarker.C

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DiscreteNucleationMarker()

Member Function Documentation

◆ computeElementMarker()

◆ validParams()

Member Data Documentation

◆ _inserter

◆ _int_width

◆ _map

◆ _nucleus_list

◆ _periodic_var