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GrainTracker Class Reference

#include <GrainTracker.h>

Inheritance diagram for GrainTracker:
[legend]

Classes

struct  CacheValues
 
struct  PartialFeatureData
 

Public Types

enum  RemapCacheMode { RemapCacheMode::FILL, RemapCacheMode::USE, RemapCacheMode::BYPASS }
 
enum  FieldType {
  FieldType::UNIQUE_REGION, FieldType::VARIABLE_COLORING, FieldType::GHOSTED_ENTITIES, FieldType::HALOS,
  FieldType::CENTROID, FieldType::ACTIVE_BOUNDS
}
 
enum  Status : unsigned char { Status::CLEAR = 0x0, Status::MARKED = 0x1, Status::DIRTY = 0x2, Status::INACTIVE = 0x4 }
 This enumeration is used to indicate status of the grains in the _unique_grains data structure. More...
 

Public Member Functions

 GrainTracker (const InputParameters &parameters)
 
virtual ~GrainTracker ()
 
virtual void meshChanged () override
 
virtual void initialize () override
 
virtual void execute () override
 
virtual void finalize () override
 
virtual std::size_t getTotalFeatureCount () const override
 Returns the total feature count (active and inactive ids, useful for sizing vectors) More...
 
virtual Real getEntityValue (dof_id_type node_id, FieldType field_type, std::size_t var_index=0) const override
 
virtual const std::vector< unsigned int > & getVarToFeatureVector (dof_id_type elem_id) const override
 Returns a list of active unique feature ids for a particular element. More...
 
virtual unsigned int getFeatureVar (unsigned int feature_id) const override
 Returns the variable representing the passed in feature. More...
 
virtual std::size_t getNumberActiveGrains () const override
 Returns the number of active grains current stored in the GrainTracker. More...
 
virtual Point getGrainCentroid (unsigned int grain_id) const override
 Returns the centroid for the given grain number. More...
 
virtual bool doesFeatureIntersectBoundary (unsigned int feature_id) const override
 Returns a Boolean indicating whether this feature intersects any boundary. More...
 
virtual std::vector< unsigned int > getNewGrainIDs () const override
 This method returns all of the new ids generated in an invocation of the GrainTracker. More...
 
virtual void initialSetup () override
 
virtual Real getValue () override
 
std::size_t getNumberActiveFeatures () const
 Return the number of active features. More...
 
virtual Point featureCentroid (unsigned int feature_id) const
 Returns the centroid of the designated feature (only suppored without periodic boundaries) More...
 
std::size_t numCoupledVars () const
 Returns the number of coupled varaibles. More...
 
const std::vector< MooseVariable * > & getCoupledVars () const
 Returns a const vector to the coupled variable pointers. More...
 
const std::vector< MooseVariableFEBase * > & getFECoupledVars () const
 Returns a const vector to the coupled MooseVariableFEBase pointers. More...
 
bool isElemental () const
 
const std::vector< FeatureData > & getFeatures () const
 Return a constant reference to the vector of all discovered features. More...
 

Static Public Attributes

static const std::size_t invalid_size_t = std::numeric_limits<std::size_t>::max()
 
static const unsigned int invalid_id = std::numeric_limits<unsigned int>::max()
 

Protected Member Functions

virtual void updateFieldInfo () override
 This method is used to populate any of the data structures used for storing field data (nodal or elemental). More...
 
virtual Real getThreshold (std::size_t current_index) const override
 Return the starting comparison threshold to use when inspecting an entity during the flood stage. More...
 
void prepopulateState (const FeatureFloodCount &ffc_object)
 This method extracts the necessary state from the passed in object necessary to continue tracking grains. More...
 
void communicateHaloMap ()
 
void assignGrains ()
 When the tracking phase starts (_t_step == _tracking_step) it assigns a unique id to every FeatureData object found by the FeatureFloodCount object. More...
 
void trackGrains ()
 On subsequent time_steps, incoming FeatureData objects are compared to previous time_step information to track grains between time steps. More...
 
virtual void newGrainCreated (unsigned int new_grain_id)
 This method is called when a new grain is detected. More...
 
void remapGrains ()
 This method is called after trackGrains to remap grains that are too close to each other. More...
 
void broadcastAndUpdateGrainData ()
 Broadcast essential Grain information to all processors. More...
 
void computeMinDistancesFromGrain (FeatureData &grain, std::vector< std::list< GrainDistance >> &min_distances)
 Populates and sorts a min_distances vector with the minimum distances to all grains in the simulation for a given grain. More...
 
bool attemptGrainRenumber (FeatureData &grain, unsigned int depth, unsigned int max_depth)
 This is the recursive part of the remapping algorithm. More...
 
void swapSolutionValues (FeatureData &grain, std::size_t new_var_index, std::vector< std::map< Node *, CacheValues >> &cache, RemapCacheMode cache_mode)
 A routine for moving all of the solution values from a given grain to a new variable number. More...
 
void swapSolutionValuesHelper (Node *curr_node, std::size_t curr_var_index, std::size_t new_var_index, std::vector< std::map< Node *, CacheValues >> &cache, RemapCacheMode cache_mode)
 Helper method for actually performing the swaps. More...
 
Real boundingRegionDistance (std::vector< MeshTools::BoundingBox > &bboxes1, std::vector< MeshTools::BoundingBox > &bboxes2) const
 This method returns the minimum periodic distance between two vectors of bounding boxes. More...
 
Real centroidRegionDistance (std::vector< MeshTools::BoundingBox > &bboxes1, std::vector< MeshTools::BoundingBox > &bboxes2) const
 This method returns the minimum periodic distance between the centroids of two vectors of bounding boxes. More...
 
unsigned int getNextUniqueID ()
 Retrieve the next unique grain number if a new grain is detected during trackGrains. More...
 
template<typename T >
bool isBoundaryEntity (const T *entity) const
 Returns a Boolean indicating whether the entity is on one of the desired boundaries. More...
 
bool flood (const DofObject *dof_object, std::size_t current_index)
 This method will check if the current entity is above the supplied threshold and "mark" it. More...
 
virtual Real getConnectingThreshold (std::size_t current_index) const
 Return the "connecting" comparison threshold to use when inspecting an entity during the flood stage. More...
 
bool compareValueWithThreshold (Real entity_value, Real threshold) const
 This method is used to determine whether the current entity value is part of a feature or not. More...
 
virtual bool isNewFeatureOrConnectedRegion (const DofObject *dof_object, std::size_t &current_index, FeatureData *&feature, Status &status, unsigned int &new_id)
 Method called during the recursive flood routine that should return whether or not the current entity is part of the current feature (if one is being explored), or if it's the start of a new feature. More...
 
void expandPointHalos ()
 This method takes all of the partial features and expands the local, ghosted, and halo sets around those regions to account for the diffuse interface. More...
 
void expandEdgeHalos (unsigned int num_layers_to_expand)
 This method expands the existing halo set by some width determined by the passed in value. More...
 
template<typename T >
void visitNeighborsHelper (const T *curr_entity, std::vector< const T *> neighbor_entities, FeatureData *feature, bool expand_halos_only, bool topological_neighbor, bool disjoint_only)
 The actual logic for visiting neighbors is abstracted out here. More...
 
void prepareDataForTransfer ()
 This routine uses the local flooded data to build up the local feature data structures (_feature_sets). More...
 
void serialize (std::string &serialized_buffer, unsigned int var_num=invalid_id)
 This routines packs the _partial_feature_sets data into a structure suitable for parallel communication operations. More...
 
void deserialize (std::vector< std::string > &serialized_buffers, unsigned int var_num=invalid_id)
 This routine takes the vector of byte buffers (one for each processor), deserializes them into a series of FeatureSet objects, and appends them to the _feature_sets data structure. More...
 
virtual void mergeSets ()
 This routine is called on the master rank only and stitches together the partial feature pieces seen on any processor. More...
 
virtual bool areFeaturesMergeable (const FeatureData &f1, const FeatureData &f2) const
 Method for determining whether two features are mergeable. More...
 
void communicateAndMerge ()
 This routine handles all of the serialization, communication and deserialization of the data structures containing FeatureData objects. More...
 
void sortAndLabel ()
 Sort and assign ids to features based on their position in the container after sorting. More...
 
void scatterAndUpdateRanks ()
 Calls buildLocalToGlobalIndices to build the individual local to global indicies for each rank and scatters that information to all ranks. More...
 
virtual void buildLocalToGlobalIndices (std::vector< std::size_t > &local_to_global_all, std::vector< int > &counts) const
 This routine populates a stacked vector of local to global indices per rank and the associated count vector for scattering the vector to the ranks. More...
 
void buildFeatureIdToLocalIndices (unsigned int max_id)
 This method builds a lookup map for retrieving the right local feature (by index) given a global index or id. More...
 
virtual void clearDataStructures ()
 Helper routine for clearing up data structures during initialize and prior to parallel communication. More...
 
void appendPeriodicNeighborNodes (FeatureData &feature) const
 This routine adds the periodic node information to our data structure prior to packing the data this makes those periodic neighbors appear much like ghosted nodes in a multiprocessor setting. More...
 
void updateRegionOffsets ()
 This routine updates the _region_offsets variable which is useful for quickly determining the proper global number for a feature when using multimap mode. More...
 
void visitNodalNeighbors (const Node *node, FeatureData *feature, bool expand_halos_only)
 These two routines are utility routines used by the flood routine and by derived classes for visiting neighbors. More...
 
void visitElementalNeighbors (const Elem *elem, FeatureData *feature, bool expand_halos_only, bool disjoint_only)
 

Static Protected Member Functions

template<class InputIterator >
static bool setsIntersect (InputIterator first1, InputIterator last1, InputIterator first2, InputIterator last2)
 This method detects whether two sets intersect without building a result set. More...
 

Protected Attributes

const int _tracking_step
 The timestep to begin tracking grains. More...
 
const unsigned short _halo_level
 The thickness of the halo surrounding each grain. More...
 
const unsigned short _max_remap_recursion_depth
 Depth of renumbering recursion (a depth of zero means no recursion) More...
 
const unsigned short _n_reserve_ops
 The number of reserved order parameters. More...
 
const std::size_t _reserve_op_index
 The cutoff index where if variable index >= this number, no remapping TO that variable will occur. More...
 
const Real _reserve_op_threshold
 The threshold above (or below) where a grain may be found on a reserve op field. More...
 
const bool _remap
 Inidicates whether remapping should be done or not (remapping is independent of tracking) More...
 
const bool _tolerate_failure
 Indicates whether we should continue after a remap failure (will result in non-physical results) More...
 
NonlinearSystemBase & _nl
 A reference to the nonlinear system (used for retrieving solution vectors) More...
 
std::vector< FeatureData > _feature_sets_old
 This data structure holds the map of unique grains from the previous time step. More...
 
const PolycrystalUserObjectBase_poly_ic_uo
 An optional IC UserObject which can provide initial data structures to this object. More...
 
const short _verbosity_level
 Verbosity level controlling the amount of information printed to the console. More...
 
bool & _first_time
 Boolean to indicate the first time this object executes. More...
 
const bool _error_on_grain_creation
 Boolean to terminate with an error if a new grain is created during the simulation. More...
 
std::vector< MooseVariableFEBase * > _fe_vars
 The vector of coupled in variables. More...
 
std::vector< MooseVariable * > _vars
 The vector of coupled in variables cast to MooseVariable. More...
 
const DofMap & _dof_map
 Reference to the dof_map containing the coupled variables. More...
 
const Real _threshold
 The threshold above (or below) where an entity may begin a new region (feature) More...
 
Real _step_threshold
 
const Real _connecting_threshold
 The threshold above (or below) which neighboring entities are flooded (where regions can be extended but not started) More...
 
Real _step_connecting_threshold
 
MooseMesh & _mesh
 A reference to the mesh. More...
 
unsigned long _var_number
 This variable is used to build the periodic node map. More...
 
const bool _single_map_mode
 This variable is used to indicate whether or not multiple maps are used during flooding. More...
 
const bool _condense_map_info
 
const bool _global_numbering
 This variable is used to indicate whether or not we identify features with unique numbers on multiple maps. More...
 
const bool _var_index_mode
 This variable is used to indicate whether the maps will contain unique region information or just the variable numbers owning those regions. More...
 
const bool _compute_halo_maps
 Indicates whether or not to communicate halo map information with all ranks. More...
 
const bool _compute_var_to_feature_map
 Indicates whether or not the var to feature map is populated. More...
 
const bool _use_less_than_threshold_comparison
 Use less-than when comparing values against the threshold value. More...
 
const std::size_t _n_vars
 
const std::size_t _maps_size
 Convenience variable holding the size of all the datastructures size by the number of maps. More...
 
const processor_id_type _n_procs
 Convenience variable holding the number of processors in this simulation. More...
 
std::vector< std::set< dof_id_type > > _entities_visited
 This variable keeps track of which nodes have been visited during execution. More...
 
std::vector< std::map< dof_id_type, int > > _var_index_maps
 This map keeps track of which variables own which nodes. More...
 
std::vector< std::vector< const Elem * > > _nodes_to_elem_map
 The data structure used to find neighboring elements give a node ID. More...
 
std::vector< unsigned int > _feature_counts_per_map
 The number of features seen by this object per map. More...
 
unsigned int _feature_count
 The number of features seen by this object (same as summing _feature_counts_per_map) More...
 
std::vector< std::list< FeatureData > > _partial_feature_sets
 The data structure used to hold partial and communicated feature data, during the discovery and merging phases. More...
 
std::vector< FeatureData > & _feature_sets
 The data structure used to hold the globally unique features. More...
 
std::vector< FeatureData > _volatile_feature_sets
 Derived objects (e.g. More...
 
std::vector< std::map< dof_id_type, int > > _feature_maps
 The feature maps contain the raw flooded node information and eventually the unique grain numbers. More...
 
std::vector< std::size_t > _local_to_global_feature_map
 The vector recording the local to global feature indices. More...
 
std::vector< std::size_t > _feature_id_to_local_index
 The vector recording the grain_id to local index (several indices will contain invalid_size_t) More...
 
PeriodicBoundaries * _pbs
 A pointer to the periodic boundary constraints object. More...
 
std::unique_ptr< PointLocatorBase > _point_locator
 
const PostprocessorValue & _element_average_value
 Average value of the domain which can optionally be used to find features in a field. More...
 
std::map< dof_id_type, int > _ghosted_entity_ids
 The map for holding reconstructed ghosted element information. More...
 
std::vector< std::map< dof_id_type, int > > _halo_ids
 The data structure for looking up halos around features. More...
 
std::multimap< dof_id_type, dof_id_type > _periodic_node_map
 The data structure which is a list of nodes that are constrained to other nodes based on the imposed periodic boundary conditions. More...
 
std::set< dof_id_type > _all_boundary_entity_ids
 The set of entities on the boundary of the domain used for determining if features intersect any boundary. More...
 
std::map< dof_id_type, std::vector< unsigned int > > _entity_var_to_features
 
std::vector< unsigned int > _empty_var_to_features
 
const bool _is_elemental
 Determines if the flood counter is elements or not (nodes) More...
 
bool _is_boundary_restricted
 Indicates that this object should only run on one or more boundaries. More...
 
ConstBndElemRange * _bnd_elem_range
 Boundary element range pointer (used when boundary restricting this object. More...
 
const bool _is_master
 Convenience variable for testing master rank. More...
 

Private Attributes

unsigned int _reserve_grain_first_index
 Holds the first unique grain index when using _reserve_op (all the remaining indices are sequential) More...
 
unsigned int _old_max_grain_id
 The previous max grain id (needed to figure out which ids are new in a given step) More...
 
unsigned int & _max_curr_grain_id
 Holds the next "regular" grain ID (a grain found or remapped to the standard op vars) More...
 
const bool _is_transient
 Boolean to indicate whether this is a Steady or Transient solve. More...
 
std::vector< std::pair< dof_id_type, dof_id_type > > _all_ranges
 Data structure to hold element ID ranges when using Distributed Mesh (populated on rank 0 only) More...
 
const PerfID _finalize_timer
 Timers. More...
 
const PerfID _remap_timer
 
const PerfID _track_grains
 
const PerfID _broadcast_update
 
const PerfID _update_field_info
 

Detailed Description

Definition at line 25 of file GrainTracker.h.

Member Enumeration Documentation

◆ FieldType

enum FeatureFloodCount::FieldType
stronginherited
Enumerator
UNIQUE_REGION 
VARIABLE_COLORING 
GHOSTED_ENTITIES 
HALOS 
CENTROID 
ACTIVE_BOUNDS 

Definition at line 98 of file FeatureFloodCount.h.

99  {
100  UNIQUE_REGION,
101  VARIABLE_COLORING,
102  GHOSTED_ENTITIES,
103  HALOS,
104  CENTROID,
105  ACTIVE_BOUNDS,
106  };

◆ RemapCacheMode

Enumerator
FILL 
USE 
BYPASS 

Definition at line 54 of file GrainTracker.h.

55  {
56  FILL,
57  USE,
58  BYPASS
59  };

◆ Status

enum FeatureFloodCount::Status : unsigned char
stronginherited

This enumeration is used to indicate status of the grains in the _unique_grains data structure.

Enumerator
CLEAR 
MARKED 
DIRTY 
INACTIVE 

Definition at line 115 of file FeatureFloodCount.h.

115  : unsigned char
116  {
117  CLEAR = 0x0,
118  MARKED = 0x1,
119  DIRTY = 0x2,
120  INACTIVE = 0x4
121  };

Constructor & Destructor Documentation

◆ GrainTracker()

GrainTracker::GrainTracker ( const InputParameters &  parameters)

Definition at line 68 of file GrainTracker.C.

69  : FeatureFloodCount(parameters),
71  _tracking_step(getParam<int>("tracking_step")),
72  _halo_level(getParam<unsigned short>("halo_level")),
73  _max_remap_recursion_depth(getParam<unsigned short>("max_remap_recursion_depth")),
74  _n_reserve_ops(getParam<unsigned short>("reserve_op")),
76  _reserve_op_threshold(getParam<Real>("reserve_op_threshold")),
77  _remap(getParam<bool>("remap_grains")),
78  _tolerate_failure(getParam<bool>("tolerate_failure")),
79  _nl(_fe_problem.getNonlinearSystemBase()),
80  _poly_ic_uo(parameters.isParamValid("polycrystal_ic_uo")
81  ? &getUserObject<PolycrystalUserObjectBase>("polycrystal_ic_uo")
82  : nullptr),
83  _verbosity_level(getParam<short>("verbosity_level")),
84  _first_time(declareRestartableData<bool>("first_time", true)),
85  _error_on_grain_creation(getParam<bool>("error_on_grain_creation")),
88  _max_curr_grain_id(declareRestartableData<unsigned int>("max_curr_grain_id", invalid_id)),
89  _is_transient(_subproblem.isTransient()),
90  _finalize_timer(registerTimedSection("finalize", 1)),
91  _remap_timer(registerTimedSection("remapGrains", 2)),
92  _track_grains(registerTimedSection("trackGrains", 2)),
93  _broadcast_update(registerTimedSection("broadCastUpdate", 2)),
94  _update_field_info(registerTimedSection("updateFieldInfo", 2))
95 {
97  paramInfo("tolerate_failure",
98  "Tolerate failure has been set to true. Non-physical simulation results "
99  "are possible, you will be notified in the event of a failed remapping operation.");
100 
101  if (_tracking_step > 0 && _poly_ic_uo)
102  mooseError("Can't start tracking after the initial condition when using a polycrystal_ic_uo");
103 }
FeatureFloodCount(const InputParameters &parameters)
This class defines the interface for the GrainTracking objects.
const std::size_t _n_vars
bool & _first_time
Boolean to indicate the first time this object executes.
Definition: GrainTracker.h:225
const bool _error_on_grain_creation
Boolean to terminate with an error if a new grain is created during the simulation.
Definition: GrainTracker.h:232
unsigned int _old_max_grain_id
The previous max grain id (needed to figure out which ids are new in a given step) ...
Definition: GrainTracker.h:239
unsigned int & _max_curr_grain_id
Holds the next "regular" grain ID (a grain found or remapped to the standard op vars) ...
Definition: GrainTracker.h:242
const PerfID _broadcast_update
Definition: GrainTracker.h:254
NonlinearSystemBase & _nl
A reference to the nonlinear system (used for retrieving solution vectors)
Definition: GrainTracker.h:205
const PolycrystalUserObjectBase * _poly_ic_uo
An optional IC UserObject which can provide initial data structures to this object.
Definition: GrainTracker.h:214
const Real _reserve_op_threshold
The threshold above (or below) where a grain may be found on a reserve op field.
Definition: GrainTracker.h:196
const short _verbosity_level
Verbosity level controlling the amount of information printed to the console.
Definition: GrainTracker.h:219
static const unsigned int invalid_id
const PerfID _track_grains
Definition: GrainTracker.h:253
const PerfID _remap_timer
Definition: GrainTracker.h:252
const PerfID _finalize_timer
Timers.
Definition: GrainTracker.h:251
const bool _remap
Inidicates whether remapping should be done or not (remapping is independent of tracking) ...
Definition: GrainTracker.h:199
const PerfID _update_field_info
Definition: GrainTracker.h:255
const bool _is_transient
Boolean to indicate whether this is a Steady or Transient solve.
Definition: GrainTracker.h:245
const int _tracking_step
The timestep to begin tracking grains.
Definition: GrainTracker.h:180
unsigned int _reserve_grain_first_index
Holds the first unique grain index when using _reserve_op (all the remaining indices are sequential) ...
Definition: GrainTracker.h:236
const unsigned short _halo_level
The thickness of the halo surrounding each grain.
Definition: GrainTracker.h:183
const std::size_t _reserve_op_index
The cutoff index where if variable index >= this number, no remapping TO that variable will occur...
Definition: GrainTracker.h:193
const unsigned short _max_remap_recursion_depth
Depth of renumbering recursion (a depth of zero means no recursion)
Definition: GrainTracker.h:186
const bool _tolerate_failure
Indicates whether we should continue after a remap failure (will result in non-physical results) ...
Definition: GrainTracker.h:202
const unsigned short _n_reserve_ops
The number of reserved order parameters.
Definition: GrainTracker.h:189

◆ ~GrainTracker()

GrainTracker::~GrainTracker ( )
virtual

Definition at line 105 of file GrainTracker.C.

105 {}

Member Function Documentation

◆ appendPeriodicNeighborNodes()

void FeatureFloodCount::appendPeriodicNeighborNodes ( FeatureData feature) const
protectedinherited

This routine adds the periodic node information to our data structure prior to packing the data this makes those periodic neighbors appear much like ghosted nodes in a multiprocessor setting.

Definition at line 1625 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::prepareDataForTransfer().

1626 {
1627  if (_is_elemental)
1628  {
1629  for (auto entity : feature._local_ids)
1630  {
1631  Elem * elem = _mesh.elemPtr(entity);
1632 
1633  for (auto node_n = decltype(elem->n_nodes())(0); node_n < elem->n_nodes(); ++node_n)
1634  {
1635  auto iters = _periodic_node_map.equal_range(elem->node(node_n));
1636 
1637  for (auto it = iters.first; it != iters.second; ++it)
1638  {
1639  feature._periodic_nodes.insert(feature._periodic_nodes.end(), it->first);
1640  feature._periodic_nodes.insert(feature._periodic_nodes.end(), it->second);
1641  }
1642  }
1643  }
1644  }
1645  else
1646  {
1647  for (auto entity : feature._local_ids)
1648  {
1649  auto iters = _periodic_node_map.equal_range(entity);
1650 
1651  for (auto it = iters.first; it != iters.second; ++it)
1652  {
1653  feature._periodic_nodes.insert(feature._periodic_nodes.end(), it->first);
1654  feature._periodic_nodes.insert(feature._periodic_nodes.end(), it->second);
1655  }
1656  }
1657  }
1658 
1659  // TODO: Remove duplicates
1660 }
std::multimap< dof_id_type, dof_id_type > _periodic_node_map
The data structure which is a list of nodes that are constrained to other nodes based on the imposed ...
const bool _is_elemental
Determines if the flood counter is elements or not (nodes)
MooseMesh & _mesh
A reference to the mesh.

◆ areFeaturesMergeable()

bool FeatureFloodCount::areFeaturesMergeable ( const FeatureData f1,
const FeatureData f2 
) const
protectedvirtualinherited

Method for determining whether two features are mergeable.

This routine exists because derived classes may need to override this function rather than use the mergeable method in the FeatureData object.

Reimplemented in PolycrystalUserObjectBase.

Definition at line 1143 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::mergeSets().

1144 {
1145  return f1.mergeable(f2);
1146 }

◆ assignGrains()

void GrainTracker::assignGrains ( )
protected

When the tracking phase starts (_t_step == _tracking_step) it assigns a unique id to every FeatureData object found by the FeatureFloodCount object.

We need to assign grainIDs to get the simulation going. We'll use the default sorting that doesn't require valid grainIDs (relies on _min_entity_id and _var_index). These will be the unique grain numbers that we must track for remainder of the simulation.

Definition at line 399 of file GrainTracker.C.

Referenced by finalize().

400 {
401  mooseAssert(_first_time, "assignGrains may only be called on the first tracking step");
402 
408  if (_is_master)
409  {
410  // Find the largest grain ID, this requires sorting if the ID is not already set
411  sortAndLabel();
412 
413  if (_feature_sets.empty())
414  {
417  }
418  else
419  {
420  _max_curr_grain_id = _feature_sets.back()._id;
422  }
423 
424  for (auto & grain : _feature_sets)
425  grain._status = Status::MARKED; // Mark the grain
426 
427  } // is_master
428 
429  /*************************************************************
430  ****************** COLLECTIVE WORK SECTION ******************
431  *************************************************************/
432 
433  // Make IDs on all non-master ranks consistent
435 
436  // Build up an id to index map
437  _communicator.broadcast(_max_curr_grain_id);
439 
440  // Now trigger the newGrainCreated() callback on all ranks
442  for (unsigned int new_id = 0; new_id <= _max_curr_grain_id; ++new_id)
443  newGrainCreated(new_id);
444 }
bool & _first_time
Boolean to indicate the first time this object executes.
Definition: GrainTracker.h:225
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
unsigned int & _max_curr_grain_id
Holds the next "regular" grain ID (a grain found or remapped to the standard op vars) ...
Definition: GrainTracker.h:242
const bool _is_master
Convenience variable for testing master rank.
void sortAndLabel()
Sort and assign ids to features based on their position in the container after sorting.
static const unsigned int invalid_id
unsigned int _reserve_grain_first_index
Holds the first unique grain index when using _reserve_op (all the remaining indices are sequential) ...
Definition: GrainTracker.h:236
void buildFeatureIdToLocalIndices(unsigned int max_id)
This method builds a lookup map for retrieving the right local feature (by index) given a global inde...
void scatterAndUpdateRanks()
Calls buildLocalToGlobalIndices to build the individual local to global indicies for each rank and sc...
virtual void newGrainCreated(unsigned int new_grain_id)
This method is called when a new grain is detected.
Definition: GrainTracker.C:831

◆ attemptGrainRenumber()

bool GrainTracker::attemptGrainRenumber ( FeatureData &  grain,
unsigned int  depth,
unsigned int  max_depth 
)
protected

This is the recursive part of the remapping algorithm.

It attempts to remap a grain to a new index and recurses until max_depth is reached.

We have two grains that are getting close represented by the same order parameter. We need to map to the variable whose closest grain to this one is furthest away by bounding region to bounding region distance.

We have a vector of the distances to the closest grains represented by each of our variables. We just need to pick a suitable grain to replace with. We will start with the maximum of this this list: (max of the mins), but will settle for next to largest and so forth as we make more attempts at remapping grains. This is a graph coloring problem so more work will be required to optimize this process.

Note: We don't have an explicit check here to avoid remapping a variable to itself. This is unnecessary since the min_distance of a variable is explicitly set up above.

If we get to this case and the best distance is less than -1, we are in big trouble. This means that grains represented by all of the remaining order parameters are overlapping this one in at least two places. We'd have to maintain multiple recursive chains, or just start over from scratch... Let's just return false and see if there is another remapping option.

Propose a new variable index for the current grain and recurse. We don't need to mark the status as DIRTY here since the recursion may fail. For now, we'll just add MARKED to the status.

Definition at line 1212 of file GrainTracker.C.

Referenced by remapGrains().

1213 {
1214  // End the recursion of our breadth first search
1215  if (depth > max_depth)
1216  return false;
1217 
1218  std::size_t curr_var_index = grain._var_index;
1219 
1220  std::vector<std::map<Node *, CacheValues>> cache;
1221 
1222  std::vector<std::list<GrainDistance>> min_distances(_vars.size());
1223 
1229  computeMinDistancesFromGrain(grain, min_distances);
1230 
1241  // clang-format off
1242  std::sort(min_distances.begin(), min_distances.end(),
1243  [](const std::list<GrainDistance> & lhs, const std::list<GrainDistance> & rhs)
1244  {
1245  // Sort lists in reverse order (largest distance first)
1246  // These empty cases are here to make this comparison stable
1247  if (lhs.empty())
1248  return false;
1249  else if (rhs.empty())
1250  return true;
1251  else
1252  return lhs.begin()->_distance > rhs.begin()->_distance;
1253  });
1254  // clang-format on
1255 
1256  for (auto & list_ref : min_distances)
1257  {
1258  const auto target_it = list_ref.begin();
1259  if (target_it == list_ref.end())
1260  continue;
1261 
1262  // If the distance is positive we can just remap and be done
1263  if (target_it->_distance > 0)
1264  {
1265  if (_verbosity_level > 0)
1266  {
1267  _console << COLOR_GREEN << "- Depth " << depth << ": Remapping grain #" << grain._id
1268  << " from variable index " << curr_var_index << " to " << target_it->_var_index;
1269  if (target_it->_distance == std::numeric_limits<Real>::max())
1270  _console << " which currently contains zero grains.\n\n" << COLOR_DEFAULT;
1271  else
1272  _console << " whose closest grain (#" << target_it->_grain_id << ") is at a distance of "
1273  << std::sqrt(target_it->_distance) << "\n\n"
1274  << COLOR_DEFAULT;
1275  }
1276 
1277  grain._status |= Status::DIRTY;
1278  grain._var_index = target_it->_var_index;
1279  return true;
1280  }
1281 
1282  // If the distance isn't positive we just need to make sure that none of the grains represented
1283  // by the target variable index would intersect this one if we were to remap
1284  {
1285  auto next_target_it = target_it;
1286  bool intersection_hit = false;
1287  unsigned short num_close_targets = 0;
1288  std::ostringstream oss;
1289  while (!intersection_hit && next_target_it != list_ref.end())
1290  {
1291  if (next_target_it->_distance > 0)
1292  break;
1293 
1294  mooseAssert(next_target_it->_grain_index < _feature_sets.size(),
1295  "Error in indexing target grain in attemptGrainRenumber");
1296  FeatureData & next_target_grain = _feature_sets[next_target_it->_grain_index];
1297 
1298  // If any grains touch we're done here
1299  if (grain.halosIntersect(next_target_grain))
1300  intersection_hit = true;
1301  else
1302  {
1303  if (num_close_targets > 0)
1304  oss << ", "; // delimiter
1305  oss << "#" << next_target_it->_grain_id;
1306  }
1307 
1308  ++next_target_it;
1309  ++num_close_targets;
1310  }
1311 
1312  if (!intersection_hit)
1313  {
1314  if (_verbosity_level > 0)
1315  {
1316  _console << COLOR_GREEN << "- Depth " << depth << ": Remapping grain #" << grain._id
1317  << " from variable index " << curr_var_index << " to " << target_it->_var_index;
1318 
1319  if (num_close_targets == 1)
1320  _console << " whose closest grain (" << oss.str()
1321  << ") is inside our bounding box but whose halo is not touching.\n\n"
1322  << COLOR_DEFAULT;
1323  else
1324  _console << " whose closest grains (" << oss.str()
1325  << ") are inside our bounding box but whose halos are not touching.\n\n"
1326  << COLOR_DEFAULT;
1327  }
1328 
1329  grain._status |= Status::DIRTY;
1330  grain._var_index = target_it->_var_index;
1331  return true;
1332  }
1333  }
1334 
1335  // If we reach this part of the loop, there is no simple renumbering that can be done.
1336  mooseAssert(target_it->_grain_index < _feature_sets.size(),
1337  "Error in indexing target grain in attemptGrainRenumber");
1338  FeatureData & target_grain = _feature_sets[target_it->_grain_index];
1339 
1347  if (target_it->_distance < -1)
1348  return false;
1349 
1350  // Make sure this grain isn't marked. If it is, we can't recurse here
1351  if ((target_grain._status & Status::MARKED) == Status::MARKED)
1352  return false;
1353 
1359  grain._var_index = target_it->_var_index;
1360  grain._status |= Status::MARKED;
1361  if (attemptGrainRenumber(target_grain, depth + 1, max_depth))
1362  {
1363  // SUCCESS!
1364  if (_verbosity_level > 0)
1365  _console << COLOR_GREEN << "- Depth " << depth << ": Remapping grain #" << grain._id
1366  << " from variable index " << curr_var_index << " to " << target_it->_var_index
1367  << "\n\n"
1368  << COLOR_DEFAULT;
1369 
1370  // Now we need to mark the grain as DIRTY since the recursion succeeded.
1371  grain._status |= Status::DIRTY;
1372  return true;
1373  }
1374  else
1375  // FAILURE, We need to set our var index back after failed recursive step
1376  grain._var_index = curr_var_index;
1377 
1378  // ALWAYS "unmark" (or clear the MARKED status) after recursion so it can be used by other remap
1379  // operations
1380  grain._status &= ~Status::MARKED;
1381  }
1382 
1383  return false;
1384 }
Status
This enumeration is used to indicate status of the grains in the _unique_grains data structure...
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
std::vector< MooseVariable * > _vars
The vector of coupled in variables cast to MooseVariable.
void computeMinDistancesFromGrain(FeatureData &grain, std::vector< std::list< GrainDistance >> &min_distances)
Populates and sorts a min_distances vector with the minimum distances to all grains in the simulation...
const short _verbosity_level
Verbosity level controlling the amount of information printed to the console.
Definition: GrainTracker.h:219
bool attemptGrainRenumber(FeatureData &grain, unsigned int depth, unsigned int max_depth)
This is the recursive part of the remapping algorithm.

◆ boundingRegionDistance()

Real GrainTracker::boundingRegionDistance ( std::vector< MeshTools::BoundingBox > &  bboxes1,
std::vector< MeshTools::BoundingBox > &  bboxes2 
) const
protected

This method returns the minimum periodic distance between two vectors of bounding boxes.

If the bounding boxes overlap the result is always -1.0.

The region that each grain covers is represented by a bounding box large enough to encompassing all the points within that grain. When using periodic boundaries, we may have several discrete "pieces" of a grain each represented by a bounding box. The distance between any two grains is defined as the minimum distance between any pair of boxes, one selected from each grain.

Definition at line 1698 of file GrainTracker.C.

Referenced by computeMinDistancesFromGrain().

1700 {
1707  auto min_distance = std::numeric_limits<Real>::max();
1708  for (const auto & bbox1 : bboxes1)
1709  {
1710  for (const auto & bbox2 : bboxes2)
1711  {
1712  // AABB squared distance
1713  Real curr_distance = 0.0;
1714  bool boxes_overlap = true;
1715  for (unsigned int dim = 0; dim < LIBMESH_DIM; ++dim)
1716  {
1717  const auto & min1 = bbox1.min()(dim);
1718  const auto & max1 = bbox1.max()(dim);
1719  const auto & min2 = bbox2.min()(dim);
1720  const auto & max2 = bbox2.max()(dim);
1721 
1722  if (min1 > max2)
1723  {
1724  const auto delta = max2 - min1;
1725  curr_distance += delta * delta;
1726  boxes_overlap = false;
1727  }
1728  else if (min2 > max1)
1729  {
1730  const auto delta = max1 - min2;
1731  curr_distance += delta * delta;
1732  boxes_overlap = false;
1733  }
1734  }
1735 
1736  if (boxes_overlap)
1737  return -1.0; /* all overlaps are treated the same */
1738 
1739  if (curr_distance < min_distance)
1740  min_distance = curr_distance;
1741  }
1742  }
1743 
1744  return min_distance;
1745 }

◆ broadcastAndUpdateGrainData()

void GrainTracker::broadcastAndUpdateGrainData ( )
protected

Broadcast essential Grain information to all processors.

This method is used to get certain attributes like centroids distributed and whether or not a grain intersects a boundary updated.

Definition at line 337 of file GrainTracker.C.

Referenced by finalize().

338 {
339  TIME_SECTION(_broadcast_update);
340 
341  std::vector<PartialFeatureData> root_feature_data;
342  std::vector<std::string> send_buffer(1), recv_buffer;
343 
344  if (_is_master)
345  {
346  root_feature_data.reserve(_feature_sets.size());
347 
348  // Populate a subset of the information in a small data structure
349  std::transform(_feature_sets.begin(),
350  _feature_sets.end(),
351  std::back_inserter(root_feature_data),
352  [](FeatureData & feature) {
353  PartialFeatureData partial_feature;
354  partial_feature.intersects_boundary = feature._intersects_boundary;
355  partial_feature.id = feature._id;
356  partial_feature.centroid = feature._centroid;
357  partial_feature.status = feature._status;
358  return partial_feature;
359  });
360 
361  std::ostringstream oss;
362  dataStore(oss, root_feature_data, this);
363  send_buffer[0].assign(oss.str());
364  }
365 
366  // Broadcast the data to all ranks
367  _communicator.broadcast_packed_range((void *)(nullptr),
368  send_buffer.begin(),
369  send_buffer.end(),
370  (void *)(nullptr),
371  std::back_inserter(recv_buffer));
372 
373  // Unpack and update
374  if (!_is_master)
375  {
376  std::istringstream iss;
377  iss.str(recv_buffer[0]);
378  iss.clear();
379 
380  dataLoad(iss, root_feature_data, this);
381 
382  for (const auto & partial_data : root_feature_data)
383  {
384  // See if this processor has a record of this grain
385  if (partial_data.id < _feature_id_to_local_index.size() &&
386  _feature_id_to_local_index[partial_data.id] != invalid_size_t)
387  {
388  auto & grain = _feature_sets[_feature_id_to_local_index[partial_data.id]];
389  grain._intersects_boundary = partial_data.intersects_boundary;
390  grain._centroid = partial_data.centroid;
391  if (partial_data.status == Status::INACTIVE)
392  grain._status = Status::INACTIVE;
393  }
394  }
395  }
396 }
static const std::size_t invalid_size_t
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
const bool _is_master
Convenience variable for testing master rank.
const PerfID _broadcast_update
Definition: GrainTracker.h:254
void dataLoad(std::istream &stream, GrainTracker::PartialFeatureData &feature, void *context)
Definition: GrainTracker.C:38
std::vector< std::size_t > _feature_id_to_local_index
The vector recording the grain_id to local index (several indices will contain invalid_size_t) ...
void dataStore(std::ostream &stream, GrainTracker::PartialFeatureData &feature, void *context)
Definition: GrainTracker.C:28

◆ buildFeatureIdToLocalIndices()

void FeatureFloodCount::buildFeatureIdToLocalIndices ( unsigned int  max_id)
protectedinherited

This method builds a lookup map for retrieving the right local feature (by index) given a global index or id.

max_id is passed to size the vector properly and may or may not be a globally consistent number. The assumption is that any id that is later queried from this object that is higher simply doesn't exist on the local processor.

Definition at line 618 of file FeatureFloodCount.C.

Referenced by assignGrains(), FeatureFloodCount::scatterAndUpdateRanks(), and trackGrains().

619 {
620  _feature_id_to_local_index.assign(max_id + 1, invalid_size_t);
621  for (auto feature_index = beginIndex(_feature_sets); feature_index < _feature_sets.size();
622  ++feature_index)
623  {
624  if (_feature_sets[feature_index]._status != Status::INACTIVE)
625  {
626  mooseAssert(_feature_sets[feature_index]._id <= max_id,
627  "Feature ID out of range(" << _feature_sets[feature_index]._id << ')');
628  _feature_id_to_local_index[_feature_sets[feature_index]._id] = feature_index;
629  }
630  }
631 }
static const std::size_t invalid_size_t
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
std::vector< std::size_t > _feature_id_to_local_index
The vector recording the grain_id to local index (several indices will contain invalid_size_t) ...

◆ buildLocalToGlobalIndices()

void FeatureFloodCount::buildLocalToGlobalIndices ( std::vector< std::size_t > &  local_to_global_all,
std::vector< int > &  counts 
) const
protectedvirtualinherited

This routine populates a stacked vector of local to global indices per rank and the associated count vector for scattering the vector to the ranks.

The individual vectors can be different sizes. The ith vector will be distributed to the ith processor including the master rank. e.g. [ ... n_0 ] [ ... n_1 ] ... [ ... n_m ]

It is intended to be overridden in derived classes.

Definition at line 572 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::scatterAndUpdateRanks().

574 {
575  mooseAssert(_is_master, "This method must only be called on the root processor");
576 
577  counts.assign(_n_procs, 0);
578  // Now size the individual counts vectors based on the largest index seen per processor
579  for (const auto & feature : _feature_sets)
580  for (const auto & local_index_pair : feature._orig_ids)
581  {
582  // local_index_pair.first = ranks, local_index_pair.second = local_index
583  mooseAssert(local_index_pair.first < _n_procs, "Processor ID is out of range");
584  if (local_index_pair.second >= static_cast<std::size_t>(counts[local_index_pair.first]))
585  counts[local_index_pair.first] = local_index_pair.second + 1;
586  }
587 
588  // Build the offsets vector
589  unsigned int globalsize = 0;
590  std::vector<int> offsets(_n_procs); // Type is signed for use with the MPI API
591  for (auto i = beginIndex(offsets); i < offsets.size(); ++i)
592  {
593  offsets[i] = globalsize;
594  globalsize += counts[i];
595  }
596 
597  // Finally populate the master vector
598  local_to_global_all.resize(globalsize, FeatureFloodCount::invalid_size_t);
599  for (const auto & feature : _feature_sets)
600  {
601  // Get the local indices from the feature and build a map
602  for (const auto & local_index_pair : feature._orig_ids)
603  {
604  auto rank = local_index_pair.first;
605  mooseAssert(rank < _n_procs, rank << ", " << _n_procs);
606 
607  auto local_index = local_index_pair.second;
608  auto stacked_local_index = offsets[rank] + local_index;
609 
610  mooseAssert(stacked_local_index < globalsize,
611  "Global index: " << stacked_local_index << " is out of range");
612  local_to_global_all[stacked_local_index] = feature._id;
613  }
614  }
615 }
static const std::size_t invalid_size_t
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
const bool _is_master
Convenience variable for testing master rank.
const processor_id_type _n_procs
Convenience variable holding the number of processors in this simulation.

◆ centroidRegionDistance()

Real GrainTracker::centroidRegionDistance ( std::vector< MeshTools::BoundingBox > &  bboxes1,
std::vector< MeshTools::BoundingBox > &  bboxes2 
) const
protected

This method returns the minimum periodic distance between the centroids of two vectors of bounding boxes.

Find the minimum centroid distance between any to pieces of the grains.

Definition at line 1671 of file GrainTracker.C.

Referenced by trackGrains().

1673 {
1677  auto min_distance = std::numeric_limits<Real>::max();
1678  for (const auto & bbox1 : bboxes1)
1679  {
1680  const auto centroid_point1 = (bbox1.max() + bbox1.min()) / 2.0;
1681 
1682  for (const auto & bbox2 : bboxes2)
1683  {
1684  const auto centroid_point2 = (bbox2.max() + bbox2.min()) / 2.0;
1685 
1686  // Here we'll calculate a distance between the centroids
1687  auto curr_distance = _mesh.minPeriodicDistance(_var_number, centroid_point1, centroid_point2);
1688 
1689  if (curr_distance < min_distance)
1690  min_distance = curr_distance;
1691  }
1692  }
1693 
1694  return min_distance;
1695 }
unsigned long _var_number
This variable is used to build the periodic node map.
MooseMesh & _mesh
A reference to the mesh.

◆ clearDataStructures()

void FeatureFloodCount::clearDataStructures ( )
protectedvirtualinherited

Helper routine for clearing up data structures during initialize and prior to parallel communication.

Definition at line 284 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::communicateAndMerge().

285 {
286 }

◆ communicateAndMerge()

void FeatureFloodCount::communicateAndMerge ( )
protectedinherited

This routine handles all of the serialization, communication and deserialization of the data structures containing FeatureData objects.

The libMesh packed range routines handle the communication of the individual string buffers. Here we need to create a container to hold our type to serialize. It'll always be size one because we are sending a single byte stream of all the data to other processors. The stream need not be the same size on all processors.

Additionally we need to create a different container to hold the received byte buffers. The container type need not match the send container type. However, We do know the number of incoming buffers (num processors) so we'll go ahead and use a vector.

When we distribute merge work, we are reducing computational work by adding more communication. Each of the first _n_vars processors will receive one variable worth of information to merge. After each of those processors has merged that information, it'll be sent to the master processor where final consolidation will occur.

Send the data from all processors to the first _n_vars processors to create a complete global feature maps for each variable.

A call to gather_packed_range seems to populate the receiving buffer on all processors, not just the receiving buffer on the actual receiving processor. If we plan to call this function repeatedly, we must clear the buffers each time on all non-receiving processors. On the actual receiving processor, we'll save off the buffer for use later.

The FeatureFloodCount and derived algorithms rely on having the data structures intact on all non-zero ranks. This is because local-only information (local entities) is never communicated and thus must remain intact. However, the distributed merging will destroy that information. The easiest thing to do is to swap out the data structure while we perform the distributed merge work.

Send the data from the merging processors to the root to create a complete global feature map.

Send the data from all processors to the root to create a complete global feature map.

Definition at line 365 of file FeatureFloodCount.C.

Referenced by finalize(), and FeatureFloodCount::finalize().

366 {
367  TIME_SECTION(_comm_and_merge);
368 
369  // First we need to transform the raw data into a usable data structure
371 
379  std::vector<std::string> send_buffers(1);
380 
387  std::vector<std::string> recv_buffers, deserialize_buffers;
388 
396  {
397  auto rank = processor_id();
398  bool is_merging_processor = rank < _n_vars;
399 
400  if (is_merging_processor)
401  recv_buffers.reserve(_app.n_processors());
402 
403  for (auto i = decltype(_n_vars)(0); i < _n_vars; ++i)
404  {
405  serialize(send_buffers[0], i);
406 
411  _communicator.gather_packed_range(i,
412  (void *)(nullptr),
413  send_buffers.begin(),
414  send_buffers.end(),
415  std::back_inserter(recv_buffers));
416 
423  if (rank == i)
424  recv_buffers.swap(deserialize_buffers);
425  else
426  recv_buffers.clear();
427  }
428 
429  // Setup a new communicator for doing merging communication operations
430  Parallel::Communicator merge_comm;
431 
432  // TODO: Update to MPI_UNDEFINED when libMesh bug is fixed.
433  _communicator.split(is_merging_processor ? 0 : 1, rank, merge_comm);
434 
435  if (is_merging_processor)
436  {
444  std::vector<std::list<FeatureData>> tmp_data(_partial_feature_sets.size());
445  tmp_data.swap(_partial_feature_sets);
446 
447  deserialize(deserialize_buffers, processor_id());
448 
449  send_buffers[0].clear();
450  recv_buffers.clear();
451  deserialize_buffers.clear();
452 
453  // Merge one variable's worth of data
454  mergeSets();
455 
456  // Now we need to serialize again to send to the master (only the processors who did work)
457  serialize(send_buffers[0]);
458 
459  // Free up as much memory as possible here before we do global communication
461 
466  merge_comm.gather_packed_range(0,
467  (void *)(nullptr),
468  send_buffers.begin(),
469  send_buffers.end(),
470  std::back_inserter(recv_buffers));
471 
472  if (_is_master)
473  {
474  // The root process now needs to deserialize all of the data
475  deserialize(recv_buffers);
476 
477  send_buffers[0].clear();
478  recv_buffers.clear();
479 
480  consolidateMergedFeatures(&tmp_data);
481  }
482  else
483  // Restore our original data on non-zero ranks
484  tmp_data.swap(_partial_feature_sets);
485  }
486  }
487 
488  // Serialized merging (master does all the work)
489  else
490  {
491  if (_is_master)
492  recv_buffers.reserve(_app.n_processors());
493 
494  serialize(send_buffers[0]);
495 
496  // Free up as much memory as possible here before we do global communication
498 
503  _communicator.gather_packed_range(0,
504  (void *)(nullptr),
505  send_buffers.begin(),
506  send_buffers.end(),
507  std::back_inserter(recv_buffers));
508 
509  if (_is_master)
510  {
511  // The root process now needs to deserialize all of the data
512  deserialize(recv_buffers);
513  recv_buffers.clear();
514 
515  mergeSets();
516 
518  }
519  }
520 
521  // Make sure that feature count is communicated to all ranks
522  _communicator.broadcast(_feature_count);
523 }
const std::size_t _n_vars
void serialize(std::string &serialized_buffer, unsigned int var_num=invalid_id)
This routines packs the _partial_feature_sets data into a structure suitable for parallel communicati...
const PerfID _comm_and_merge
const bool _is_master
Convenience variable for testing master rank.
void consolidateMergedFeatures(std::vector< std::list< FeatureData >> *saved_data=nullptr)
This method consolidates all of the merged information from _partial_feature_sets into the _feature_s...
virtual void clearDataStructures()
Helper routine for clearing up data structures during initialize and prior to parallel communication...
unsigned int _feature_count
The number of features seen by this object (same as summing _feature_counts_per_map) ...
virtual void mergeSets()
This routine is called on the master rank only and stitches together the partial feature pieces seen ...
std::vector< std::list< FeatureData > > _partial_feature_sets
The data structure used to hold partial and communicated feature data, during the discovery and mergi...
const bool _distribute_merge_work
Keeps track of whether we are distributing the merge work.
void deserialize(std::vector< std::string > &serialized_buffers, unsigned int var_num=invalid_id)
This routine takes the vector of byte buffers (one for each processor), deserializes them into a seri...
void prepareDataForTransfer()
This routine uses the local flooded data to build up the local feature data structures (_feature_sets...

◆ communicateHaloMap()

void GrainTracker::communicateHaloMap ( )
protected

Finally remove halo markings from interior regions. This step is necessary because we expand halos before we do communication but that expansion can and will likely go into the interior of the grain (from a single processor's perspective). We could expand halos after merging, but that would likely be less scalable.

Definition at line 1585 of file GrainTracker.C.

Referenced by updateFieldInfo().

1586 {
1587  if (_compute_halo_maps)
1588  {
1589  // rank var_index entity_id
1590  std::vector<std::pair<std::size_t, dof_id_type>> halo_ids_all;
1591 
1592  std::vector<int> counts;
1593  std::vector<std::pair<std::size_t, dof_id_type>> local_halo_ids;
1594  std::size_t counter = 0;
1595 
1596  const bool isDistributedMesh = _mesh.isDistributedMesh();
1597 
1598  if (_is_master)
1599  {
1600  std::vector<std::vector<std::pair<std::size_t, dof_id_type>>> root_halo_ids(_n_procs);
1601  counts.resize(_n_procs);
1602 
1603  // Loop over the _halo_ids "field" and build minimal lists for all of the other ranks
1604  for (auto var_index = beginIndex(_halo_ids); var_index < _halo_ids.size(); ++var_index)
1605  {
1606  for (const auto & entity_pair : _halo_ids[var_index])
1607  {
1608  auto entity_id = entity_pair.first;
1609  if (isDistributedMesh)
1610  {
1611  // Check to see which contiguous range this entity ID falls into
1612  auto range_it =
1613  std::lower_bound(_all_ranges.begin(),
1614  _all_ranges.end(),
1615  entity_id,
1616  [](const std::pair<dof_id_type, dof_id_type> range,
1617  dof_id_type entity_id) { return range.second < entity_id; });
1618 
1619  mooseAssert(range_it != _all_ranges.end(), "No range round?");
1620 
1621  // Recover the index from the iterator
1622  auto proc_id = std::distance(_all_ranges.begin(), range_it);
1623 
1624  // Now add this halo entity to the map for the corresponding proc to scatter latter
1625  root_halo_ids[proc_id].push_back(std::make_pair(var_index, entity_id));
1626  }
1627  else
1628  {
1629  DofObject * halo_entity;
1630  if (_is_elemental)
1631  halo_entity = _mesh.queryElemPtr(entity_id);
1632  else
1633  halo_entity = _mesh.queryNodePtr(entity_id);
1634 
1635  if (halo_entity)
1636  root_halo_ids[halo_entity->processor_id()].push_back(
1637  std::make_pair(var_index, entity_id));
1638  }
1639  }
1640  }
1641 
1642  // Build up the counts vector for MPI scatter
1643  std::size_t global_count = 0;
1644  for (const auto & vector_ref : root_halo_ids)
1645  {
1646  std::copy(vector_ref.begin(), vector_ref.end(), std::back_inserter(halo_ids_all));
1647  counts[counter] = vector_ref.size();
1648  global_count += counts[counter++];
1649  }
1650  }
1651 
1652  _communicator.scatter(halo_ids_all, counts, local_halo_ids);
1653 
1654  // Now add the contributions from the root process to the processor local maps
1655  for (const auto & halo_pair : local_halo_ids)
1656  _halo_ids[halo_pair.first].emplace(std::make_pair(halo_pair.second, halo_pair.first));
1657 
1664  for (const auto & grain : _feature_sets)
1665  for (auto local_id : grain._local_ids)
1666  _halo_ids[grain._var_index].erase(local_id);
1667  }
1668 }
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
const bool _is_master
Convenience variable for testing master rank.
std::vector< std::map< dof_id_type, int > > _halo_ids
The data structure for looking up halos around features.
const bool _compute_halo_maps
Indicates whether or not to communicate halo map information with all ranks.
std::vector< std::pair< dof_id_type, dof_id_type > > _all_ranges
Data structure to hold element ID ranges when using Distributed Mesh (populated on rank 0 only) ...
Definition: GrainTracker.h:248
const bool _is_elemental
Determines if the flood counter is elements or not (nodes)
const processor_id_type _n_procs
Convenience variable holding the number of processors in this simulation.
MooseMesh & _mesh
A reference to the mesh.
static unsigned int counter

◆ compareValueWithThreshold()

bool FeatureFloodCount::compareValueWithThreshold ( Real  entity_value,
Real  threshold 
) const
protectedinherited

This method is used to determine whether the current entity value is part of a feature or not.

Comparisons can either be greater than or less than the threshold which is controlled via input parameter.

Definition at line 1319 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::isNewFeatureOrConnectedRegion().

1320 {
1321  return ((_use_less_than_threshold_comparison && (entity_value >= threshold)) ||
1322  (!_use_less_than_threshold_comparison && (entity_value <= threshold)));
1323 }
const bool _use_less_than_threshold_comparison
Use less-than when comparing values against the threshold value.

◆ computeMinDistancesFromGrain()

void GrainTracker::computeMinDistancesFromGrain ( FeatureData &  grain,
std::vector< std::list< GrainDistance >> &  min_distances 
)
protected

Populates and sorts a min_distances vector with the minimum distances to all grains in the simulation for a given grain.

There are _vars.size() entries in the outer vector, one for each order parameter. A list of grains with the same OP are ordered in lists per OP.

In the diagram below assume we have 4 order parameters. The grain with the asterisk needs to be remapped. All order parameters are used in neighboring grains. For all "touching" grains, the value of the corresponding entry in min_distances will be a negative integer representing the number of immediate neighbors with that order parameter.

Note: Only the first member of the pair (the distance) is shown in the array below. e.g. [-2.0, -max, -1.0, -2.0]

After sorting, variable index 2 (value: -1.0) be at the end of the array and will be the first variable we attempt to renumber the current grain to.

   __       ___
     \  0  /   \
   2  \___/  1  \___
      /   \     /   \
   __/  1  \___/  2  \
     \  *  /   \     /
   3  \___/  3  \___/
      /   \     /
   __/  0  \___/

See if we have any completely open OPs (excluding reserve order parameters) or the order parameter corresponding to this grain, we need to put them in the list or the grain tracker won't realize that those vars are available for remapping.

Definition at line 1138 of file GrainTracker.C.

Referenced by attemptGrainRenumber().

1140 {
1164  for (auto i = beginIndex(_feature_sets); i < _feature_sets.size(); ++i)
1165  {
1166  auto & other_grain = _feature_sets[i];
1167 
1168  if (other_grain._var_index == grain._var_index || other_grain._var_index >= _reserve_op_index)
1169  continue;
1170 
1171  auto target_var_index = other_grain._var_index;
1172  auto target_grain_index = i;
1173  auto target_grain_id = other_grain._id;
1174 
1175  Real curr_bbox_diff = boundingRegionDistance(grain._bboxes, other_grain._bboxes);
1176 
1177  GrainDistance grain_distance_obj(
1178  curr_bbox_diff, target_var_index, target_grain_index, target_grain_id);
1179 
1180  // To handle touching halos we penalize the top pick each time we see another
1181  if (curr_bbox_diff == -1.0 && !min_distances[target_var_index].empty())
1182  {
1183  Real last_distance = min_distances[target_var_index].begin()->_distance;
1184  if (last_distance < 0)
1185  grain_distance_obj._distance += last_distance;
1186  }
1187 
1188  // Insertion sort into a list
1189  auto insert_it = min_distances[target_var_index].begin();
1190  while (insert_it != min_distances[target_var_index].end() && !(grain_distance_obj < *insert_it))
1191  ++insert_it;
1192  min_distances[target_var_index].insert(insert_it, grain_distance_obj);
1193  }
1194 
1200  for (auto var_index = beginIndex(_vars); var_index < _reserve_op_index; ++var_index)
1201  {
1202  // Don't put an entry in for matching variable indices (i.e. we can't remap to ourselves)
1203  if (grain._var_index == var_index)
1204  continue;
1205 
1206  if (min_distances[var_index].empty())
1207  min_distances[var_index].emplace_front(std::numeric_limits<Real>::max(), var_index);
1208  }
1209 }
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
This struct is used to hold distance information to other grains in the simulation.
Definition: GrainTracker.h:262
Real boundingRegionDistance(std::vector< MeshTools::BoundingBox > &bboxes1, std::vector< MeshTools::BoundingBox > &bboxes2) const
This method returns the minimum periodic distance between two vectors of bounding boxes...
std::vector< MooseVariable * > _vars
The vector of coupled in variables cast to MooseVariable.
const std::size_t _reserve_op_index
The cutoff index where if variable index >= this number, no remapping TO that variable will occur...
Definition: GrainTracker.h:193

◆ deserialize()

void FeatureFloodCount::deserialize ( std::vector< std::string > &  serialized_buffers,
unsigned int  var_num = invalid_id 
)
protectedinherited

This routine takes the vector of byte buffers (one for each processor), deserializes them into a series of FeatureSet objects, and appends them to the _feature_sets data structure.

Note: It is assumed that local processor information may already be stored in the _feature_sets data structure so it is not cleared before insertion.

Usually we have the local processor data already in the _partial_feature_sets data structure. However, if we are doing distributed merge work, we also need to preserve all of the original data for use in later stages of the algorithm so it'll have been swapped out with clean buffers. This leaves us a choice, either we just duplicate the Features from the original data structure after we've swapped out the buffer, or we go ahead and unpack data that we would normally already have. So during distributed merging, that's exactly what we'll do. Later however when the master is doing the final consolidating, we'll opt to just skip the local unpacking. To tell the difference, between these two modes, we just need to see if a var_num was passed in.

Definition at line 985 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::communicateAndMerge().

986 {
987  // The input string stream used for deserialization
988  std::istringstream iss;
989 
990  auto rank = processor_id();
991 
992  for (auto proc_id = beginIndex(serialized_buffers); proc_id < serialized_buffers.size();
993  ++proc_id)
994  {
1006  if (var_num == invalid_id && proc_id == rank)
1007  continue;
1008 
1009  iss.str(serialized_buffers[proc_id]); // populate the stream with a new buffer
1010  iss.clear(); // reset the string stream state
1011 
1012  // Load the gathered data into the data structure.
1013  if (var_num == invalid_id)
1014  dataLoad(iss, _partial_feature_sets, this);
1015  else
1016  dataLoad(iss, _partial_feature_sets[var_num], this);
1017  }
1018 }
void dataLoad(std::istream &stream, FeatureFloodCount::FeatureData &feature, void *context)
static const unsigned int invalid_id
std::vector< std::list< FeatureData > > _partial_feature_sets
The data structure used to hold partial and communicated feature data, during the discovery and mergi...

◆ doesFeatureIntersectBoundary()

bool GrainTracker::doesFeatureIntersectBoundary ( unsigned int  feature_id) const
overridevirtual

Returns a Boolean indicating whether this feature intersects any boundary.

Reimplemented from FeatureFloodCount.

Definition at line 163 of file GrainTracker.C.

164 {
165  // TODO: This data structure may need to be turned into a Multimap
166  mooseAssert(feature_id < _feature_id_to_local_index.size(), "Grain ID out of bounds");
167 
168  auto feature_index = _feature_id_to_local_index[feature_id];
169  if (feature_index != invalid_size_t)
170  {
171  mooseAssert(feature_index < _feature_sets.size(), "Grain index out of bounds");
172  return _feature_sets[feature_index]._intersects_boundary;
173  }
174 
175  return false;
176 }
static const std::size_t invalid_size_t
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
std::vector< std::size_t > _feature_id_to_local_index
The vector recording the grain_id to local index (several indices will contain invalid_size_t) ...

◆ execute()

void GrainTracker::execute ( )
overridevirtual

Reimplemented from FeatureFloodCount.

Definition at line 222 of file GrainTracker.C.

223 {
224  // Don't track grains if the current simulation step is before the specified tracking step
225  if (_t_step < _tracking_step)
226  return;
227 
228  if (_poly_ic_uo && _first_time)
229  return;
230 
232 }
bool & _first_time
Boolean to indicate the first time this object executes.
Definition: GrainTracker.h:225
virtual void execute() override
const PolycrystalUserObjectBase * _poly_ic_uo
An optional IC UserObject which can provide initial data structures to this object.
Definition: GrainTracker.h:214
const int _tracking_step
The timestep to begin tracking grains.
Definition: GrainTracker.h:180

◆ expandEdgeHalos()

void FeatureFloodCount::expandEdgeHalos ( unsigned int  num_layers_to_expand)
protectedinherited

This method expands the existing halo set by some width determined by the passed in value.

This method does NOT mask off any local IDs.

Create a copy of the halo set so that as we insert new ids into the set we don't continue to iterate on those new ids.

We have to handle disjoint halo IDs slightly differently. Once you are disjoint, you can't go back so make sure that we keep placing these IDs in the disjoint set.

Definition at line 1428 of file FeatureFloodCount.C.

Referenced by finalize(), and PolycrystalUserObjectBase::finalize().

1429 {
1430  if (num_layers_to_expand == 0)
1431  return;
1432 
1433  TIME_SECTION(_expand_halos);
1434 
1435  for (auto & list_ref : _partial_feature_sets)
1436  {
1437  for (auto & feature : list_ref)
1438  {
1439  for (auto halo_level = decltype(num_layers_to_expand)(0); halo_level < num_layers_to_expand;
1440  ++halo_level)
1441  {
1446  FeatureData::container_type orig_halo_ids(feature._halo_ids);
1447  for (auto entity : orig_halo_ids)
1448  {
1449  if (_is_elemental)
1450  visitElementalNeighbors(_mesh.elemPtr(entity),
1451  &feature,
1452  /*expand_halos_only =*/true,
1453  /*disjoint_only =*/false);
1454  else
1455  visitNodalNeighbors(_mesh.nodePtr(entity),
1456  &feature,
1457  /*expand_halos_only =*/true);
1458  }
1459 
1464  FeatureData::container_type disjoint_orig_halo_ids(feature._disjoint_halo_ids);
1465  for (auto entity : disjoint_orig_halo_ids)
1466  {
1467  if (_is_elemental)
1468  visitElementalNeighbors(_mesh.elemPtr(entity),
1469 
1470  &feature,
1471  /*expand_halos_only =*/true,
1472  /*disjoint_only =*/true);
1473  else
1474  visitNodalNeighbors(_mesh.nodePtr(entity),
1475 
1476  &feature,
1477  /*expand_halos_only =*/true);
1478  }
1479  }
1480  }
1481  }
1482 }
void visitNodalNeighbors(const Node *node, FeatureData *feature, bool expand_halos_only)
These two routines are utility routines used by the flood routine and by derived classes for visiting...
std::set< dof_id_type > container_type
The primary underlying container type used to hold the data in each FeatureData.
void visitElementalNeighbors(const Elem *elem, FeatureData *feature, bool expand_halos_only, bool disjoint_only)
std::vector< std::list< FeatureData > > _partial_feature_sets
The data structure used to hold partial and communicated feature data, during the discovery and mergi...
const bool _is_elemental
Determines if the flood counter is elements or not (nodes)
const PerfID _expand_halos
MooseMesh & _mesh
A reference to the mesh.

◆ expandPointHalos()

void FeatureFloodCount::expandPointHalos ( )
protectedinherited

This method takes all of the partial features and expands the local, ghosted, and halo sets around those regions to account for the diffuse interface.

Rather than using any kind of recursion here, we simply expand the region by all "point" neighbors from the actual grain cells since all point neighbors will contain contributions to the region.

To expand the feature element region to the actual flooded region (nodal basis) we need to add in all point neighbors of the current local region for each feature. This is because the elemental variable influence spreads from the elemental data out exactly one element from every mesh point.

Definition at line 1366 of file FeatureFloodCount.C.

1367 {
1368  const auto & node_to_elem_map = _mesh.nodeToActiveSemilocalElemMap();
1369  FeatureData::container_type expanded_local_ids;
1370  auto my_processor_id = processor_id();
1371 
1378  for (auto & list_ref : _partial_feature_sets)
1379  {
1380  for (auto & feature : list_ref)
1381  {
1382  expanded_local_ids.clear();
1383 
1384  for (auto entity : feature._local_ids)
1385  {
1386  const Elem * elem = _mesh.elemPtr(entity);
1387  mooseAssert(elem, "elem pointer is NULL");
1388 
1389  // Get the nodes on a current element so that we can add in point neighbors
1390  auto n_nodes = elem->n_vertices();
1391  for (auto i = decltype(n_nodes)(0); i < n_nodes; ++i)
1392  {
1393  const Node * current_node = elem->get_node(i);
1394 
1395  auto elem_vector_it = node_to_elem_map.find(current_node->id());
1396  if (elem_vector_it == node_to_elem_map.end())
1397  mooseError("Error in node to elem map");
1398 
1399  const auto & elem_vector = elem_vector_it->second;
1400 
1401  std::copy(elem_vector.begin(),
1402  elem_vector.end(),
1403  std::insert_iterator<FeatureData::container_type>(expanded_local_ids,
1404  expanded_local_ids.end()));
1405 
1406  // Now see which elements need to go into the ghosted set
1407  for (auto entity : elem_vector)
1408  {
1409  const Elem * neighbor = _mesh.elemPtr(entity);
1410  mooseAssert(neighbor, "neighbor pointer is NULL");
1411 
1412  if (neighbor->processor_id() != my_processor_id)
1413  feature._ghosted_ids.insert(feature._ghosted_ids.end(), elem->id());
1414  }
1415  }
1416  }
1417 
1418  // Replace the existing local ids with the expanded local ids
1419  feature._local_ids.swap(expanded_local_ids);
1420 
1421  // Copy the expanded local_ids into the halo_ids container
1422  feature._halo_ids = feature._local_ids;
1423  }
1424  }
1425 }
std::set< dof_id_type > container_type
The primary underlying container type used to hold the data in each FeatureData.
std::vector< std::list< FeatureData > > _partial_feature_sets
The data structure used to hold partial and communicated feature data, during the discovery and mergi...
MooseMesh & _mesh
A reference to the mesh.

◆ featureCentroid()

Point FeatureFloodCount::featureCentroid ( unsigned int  feature_id) const
virtualinherited

Returns the centroid of the designated feature (only suppored without periodic boundaries)

Definition at line 802 of file FeatureFloodCount.C.

Referenced by FeatureVolumeVectorPostprocessor::execute().

803 {
804  if (feature_id >= _feature_id_to_local_index.size())
805  return invalid_id;
806 
807  auto local_index = _feature_id_to_local_index[feature_id];
808 
809  Real invalid_coord = std::numeric_limits<Real>::max();
810  Point p(invalid_coord, invalid_coord, invalid_coord);
811  if (local_index != invalid_size_t)
812  {
813  mooseAssert(local_index < _feature_sets.size(), "local_index out of bounds");
814  p = _feature_sets[local_index]._centroid;
815  }
816  return p;
817 }
static const std::size_t invalid_size_t
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
static const unsigned int invalid_id
std::vector< std::size_t > _feature_id_to_local_index
The vector recording the grain_id to local index (several indices will contain invalid_size_t) ...

◆ finalize()

void GrainTracker::finalize ( )
overridevirtual

Assign or Track Grains

Broadcast essential data

Remap Grains

Reimplemented from FeatureFloodCount.

Definition at line 279 of file GrainTracker.C.

280 {
281  // Don't track grains if the current simulation step is before the specified tracking step
282  if (_t_step < _tracking_step)
283  return;
284 
285  TIME_SECTION(_finalize_timer);
286 
287  // Expand the depth of the halos around all grains
288  auto num_halo_layers = _halo_level >= 1
289  ? _halo_level - 1
290  : 0; // The first level of halos already exists so subtract one
291 
292  if (_poly_ic_uo && _first_time)
294  else
295  {
296  expandEdgeHalos(num_halo_layers);
297 
298  // Build up the grain map on the root processor
300  }
301 
305  if (_first_time)
306  assignGrains();
307  else
308  trackGrains();
309 
310  if (_verbosity_level > 1)
311  _console << "Finished inside of trackGrains" << std::endl;
312 
317 
321  if (_remap)
322  remapGrains();
323 
324  updateFieldInfo();
325  if (_verbosity_level > 1)
326  _console << "Finished inside of updateFieldInfo\n";
327 
328  // Set the first time flag false here (after all methods of finalize() have completed)
329  _first_time = false;
330 
331  // TODO: Release non essential memory
332  if (_verbosity_level > 0)
333  _console << "Finished inside of GrainTracker\n" << std::endl;
334 }
void remapGrains()
This method is called after trackGrains to remap grains that are too close to each other...
Definition: GrainTracker.C:864
void expandEdgeHalos(unsigned int num_layers_to_expand)
This method expands the existing halo set by some width determined by the passed in value...
bool & _first_time
Boolean to indicate the first time this object executes.
Definition: GrainTracker.h:225
void trackGrains()
On subsequent time_steps, incoming FeatureData objects are compared to previous time_step information...
Definition: GrainTracker.C:447
void communicateAndMerge()
This routine handles all of the serialization, communication and deserialization of the data structur...
virtual void updateFieldInfo() override
This method is used to populate any of the data structures used for storing field data (nodal or elem...
const PolycrystalUserObjectBase * _poly_ic_uo
An optional IC UserObject which can provide initial data structures to this object.
Definition: GrainTracker.h:214
void prepopulateState(const FeatureFloodCount &ffc_object)
This method extracts the necessary state from the passed in object necessary to continue tracking gra...
Definition: GrainTracker.C:247
void broadcastAndUpdateGrainData()
Broadcast essential Grain information to all processors.
Definition: GrainTracker.C:337
const short _verbosity_level
Verbosity level controlling the amount of information printed to the console.
Definition: GrainTracker.h:219
const PerfID _finalize_timer
Timers.
Definition: GrainTracker.h:251
const bool _remap
Inidicates whether remapping should be done or not (remapping is independent of tracking) ...
Definition: GrainTracker.h:199
void assignGrains()
When the tracking phase starts (_t_step == _tracking_step) it assigns a unique id to every FeatureDat...
Definition: GrainTracker.C:399
const int _tracking_step
The timestep to begin tracking grains.
Definition: GrainTracker.h:180
const unsigned short _halo_level
The thickness of the halo surrounding each grain.
Definition: GrainTracker.h:183

◆ flood()

bool FeatureFloodCount::flood ( const DofObject *  dof_object,
std::size_t  current_index 
)
protectedinherited

This method will check if the current entity is above the supplied threshold and "mark" it.

It will then inspect neighboring entities that are above the connecting threshold and add them to the current feature.

Returns
Boolean indicating whether a new feature was found while exploring the current entity.

If we reach this point (i.e. we haven't continued to the next queue entry), we've found a new mesh entity that's part of a feature. We need to mark the entity as visited at this point (and not before!) to avoid infinite recursion. If you mark the node too early you risk not coloring in a whole feature any time a "connecting threshold" is used since we may have already visited this entity earlier but it was in-between two thresholds.

See if this particular entity cell contributes to the centroid calculation. We only deal with elemental floods and only count it if it's owned by the current processor to avoid skewing the result.

Definition at line 1194 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::execute(), and PolycrystalUserObjectBase::execute().

1196 {
1197  // if (dof_object == nullptr || dof_object == libMesh::remote_elem)
1198  // return false;
1199  mooseAssert(dof_object, "DOF object is nullptr");
1200  mooseAssert(_entity_queue.empty(), "Entity queue is not empty when starting a feature");
1201 
1202  // Kick off the exploration of a new feature
1203  _entity_queue.push_front(dof_object);
1204 
1205  bool return_value = false;
1206  FeatureData * feature = nullptr;
1207  while (!_entity_queue.empty())
1208  {
1209  const DofObject * curr_dof_object = _entity_queue.back();
1210  _entity_queue.pop_back();
1211 
1212  // Retrieve the id of the current entity
1213  auto entity_id = curr_dof_object->id();
1214 
1215  // Has this entity already been marked? - if so move along
1216  if (current_index != invalid_size_t &&
1217  _entities_visited[current_index].find(entity_id) != _entities_visited[current_index].end())
1218  continue;
1219 
1220  // Are we outside of the range we should be working in?
1221  if (_is_elemental)
1222  {
1223  const Elem & elem = static_cast<const Elem &>(*curr_dof_object);
1224 
1225  if (!_dof_map.is_evaluable(elem))
1226  continue;
1227  }
1228 
1229  // See if the current entity either starts a new feature or continues an existing feature
1230  auto new_id = invalid_id; // Writable reference to hold an optional id;
1231  Status status =
1232  Status::INACTIVE; // Status is inactive until we find an entity above the starting threshold
1233 
1234  if (!isNewFeatureOrConnectedRegion(curr_dof_object, current_index, feature, status, new_id))
1235  {
1236  // If we have an active feature, we just found a halo entity
1237  if (feature)
1238  feature->_halo_ids.insert(feature->_halo_ids.end(), entity_id);
1239  continue;
1240  }
1241 
1242  mooseAssert(current_index != invalid_size_t, "current_index is invalid");
1243 
1252  return_value = true;
1253  _entities_visited[current_index].insert(entity_id);
1254 
1255  auto map_num = _single_map_mode ? decltype(current_index)(0) : current_index;
1256 
1257  // New Feature (we need to create it and add it to our data structure)
1258  if (!feature)
1259  {
1260  _partial_feature_sets[map_num].emplace_back(
1261  current_index, _feature_count++, processor_id(), status);
1262 
1263  // Get a handle to the feature we will update (always the last feature in the data structure)
1264  feature = &_partial_feature_sets[map_num].back();
1265 
1266  // If new_id is valid, we'll set it in the feature here.
1267  if (new_id != invalid_id)
1268  feature->_id = new_id;
1269  }
1270 
1271  // Insert the current entity into the local ids data structure
1272  feature->_local_ids.insert(feature->_local_ids.end(), entity_id);
1273 
1279  if (_is_elemental && processor_id() == curr_dof_object->processor_id())
1280  {
1281  const Elem * elem = static_cast<const Elem *>(curr_dof_object);
1282 
1283  // Keep track of how many elements participate in the centroid averaging
1284  feature->_vol_count++;
1285 
1286  // Sum the centroid values for now, we'll average them later
1287  feature->_centroid += elem->centroid();
1288 
1289  // Does the volume intersect the boundary?
1290  if (_all_boundary_entity_ids.find(elem->id()) != _all_boundary_entity_ids.end())
1291  feature->_intersects_boundary = true;
1292  }
1293 
1294  if (_is_elemental)
1295  visitElementalNeighbors(static_cast<const Elem *>(curr_dof_object),
1296  feature,
1297  /*expand_halos_only =*/false,
1298  /*disjoint_only =*/false);
1299  else
1300  visitNodalNeighbors(static_cast<const Node *>(curr_dof_object),
1301  feature,
1302  /*expand_halos_only =*/false);
1303  }
1304 
1305  return return_value;
1306 }
void visitNodalNeighbors(const Node *node, FeatureData *feature, bool expand_halos_only)
These two routines are utility routines used by the flood routine and by derived classes for visiting...
static const std::size_t invalid_size_t
Status
This enumeration is used to indicate status of the grains in the _unique_grains data structure...
std::vector< std::set< dof_id_type > > _entities_visited
This variable keeps track of which nodes have been visited during execution.
std::set< dof_id_type > _all_boundary_entity_ids
The set of entities on the boundary of the domain used for determining if features intersect any boun...
void visitElementalNeighbors(const Elem *elem, FeatureData *feature, bool expand_halos_only, bool disjoint_only)
const DofMap & _dof_map
Reference to the dof_map containing the coupled variables.
static const unsigned int invalid_id
const bool _single_map_mode
This variable is used to indicate whether or not multiple maps are used during flooding.
unsigned int _feature_count
The number of features seen by this object (same as summing _feature_counts_per_map) ...
virtual bool isNewFeatureOrConnectedRegion(const DofObject *dof_object, std::size_t &current_index, FeatureData *&feature, Status &status, unsigned int &new_id)
Method called during the recursive flood routine that should return whether or not the current entity...
std::vector< std::list< FeatureData > > _partial_feature_sets
The data structure used to hold partial and communicated feature data, during the discovery and mergi...
const bool _is_elemental
Determines if the flood counter is elements or not (nodes)
std::deque< const DofObject * > _entity_queue
The data structure for maintaining entities to flood during discovery.

◆ getConnectingThreshold()

Real FeatureFloodCount::getConnectingThreshold ( std::size_t  current_index) const
protectedvirtualinherited

Return the "connecting" comparison threshold to use when inspecting an entity during the flood stage.

Definition at line 1313 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::isNewFeatureOrConnectedRegion().

1314 {
1316 }

◆ getCoupledVars()

const std::vector<MooseVariable *>& FeatureFloodCount::getCoupledVars ( ) const
inlineinherited

Returns a const vector to the coupled variable pointers.

Definition at line 93 of file FeatureFloodCount.h.

Referenced by AverageGrainVolume::AverageGrainVolume(), and FeatureVolumeVectorPostprocessor::FeatureVolumeVectorPostprocessor().

93 { return _vars; }
std::vector< MooseVariable * > _vars
The vector of coupled in variables cast to MooseVariable.

◆ getEntityValue()

Real GrainTracker::getEntityValue ( dof_id_type  node_id,
FieldType  field_type,
std::size_t  var_index = 0 
) const
overridevirtual

Reimplemented from FeatureFloodCount.

Definition at line 108 of file GrainTracker.C.

Referenced by EulerAngleProvider2RGBAux::precalculateValue(), and OutputEulerAngles::precalculateValue().

111 {
112  if (_t_step < _tracking_step)
113  return 0;
114 
115  return FeatureFloodCount::getEntityValue(entity_id, field_type, var_index);
116 }
const int _tracking_step
The timestep to begin tracking grains.
Definition: GrainTracker.h:180
virtual Real getEntityValue(dof_id_type entity_id, FieldType field_type, std::size_t var_index=0) const

◆ getFeatures()

const std::vector<FeatureData>& FeatureFloodCount::getFeatures ( ) const
inlineinherited

Return a constant reference to the vector of all discovered features.

Definition at line 325 of file FeatureFloodCount.h.

Referenced by prepopulateState().

325 { return _feature_sets; }
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.

◆ getFeatureVar()

unsigned int GrainTracker::getFeatureVar ( unsigned int  feature_id) const
overridevirtual

Returns the variable representing the passed in feature.

Reimplemented from FeatureFloodCount.

Definition at line 125 of file GrainTracker.C.

126 {
127  return FeatureFloodCount::getFeatureVar(feature_id);
128 }
virtual unsigned int getFeatureVar(unsigned int feature_id) const
Returns the variable representing the passed in feature.

◆ getFECoupledVars()

const std::vector<MooseVariableFEBase *>& FeatureFloodCount::getFECoupledVars ( ) const
inlineinherited

Returns a const vector to the coupled MooseVariableFEBase pointers.

Definition at line 96 of file FeatureFloodCount.h.

Referenced by AverageGrainVolume::AverageGrainVolume().

96 { return _fe_vars; }
std::vector< MooseVariableFEBase * > _fe_vars
The vector of coupled in variables.

◆ getGrainCentroid()

Point GrainTracker::getGrainCentroid ( unsigned int  grain_id) const
overridevirtual

Returns the centroid for the given grain number.

Implements GrainTrackerInterface.

Definition at line 145 of file GrainTracker.C.

146 {
147  mooseAssert(grain_id < _feature_id_to_local_index.size(), "Grain ID out of bounds");
148  auto grain_index = _feature_id_to_local_index[grain_id];
149 
150  if (grain_index != invalid_size_t)
151  {
152  mooseAssert(_feature_id_to_local_index[grain_id] < _feature_sets.size(),
153  "Grain index out of bounds");
154  // Note: This value is parallel consistent, see GrainTracker::broadcastAndUpdateGrainData()
155  return _feature_sets[_feature_id_to_local_index[grain_id]]._centroid;
156  }
157 
158  // Inactive grain
159  return Point();
160 }
static const std::size_t invalid_size_t
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
std::vector< std::size_t > _feature_id_to_local_index
The vector recording the grain_id to local index (several indices will contain invalid_size_t) ...

◆ getNewGrainIDs()

std::vector< unsigned int > GrainTracker::getNewGrainIDs ( ) const
overridevirtual

This method returns all of the new ids generated in an invocation of the GrainTracker.

Reimplemented from GrainTrackerInterface.

Definition at line 852 of file GrainTracker.C.

853 {
854  std::vector<unsigned int> new_ids(_max_curr_grain_id - _old_max_grain_id);
855  auto new_id = _old_max_grain_id + 1;
856 
857  // Generate the new ids
858  std::iota(new_ids.begin(), new_ids.end(), new_id);
859 
860  return new_ids;
861 }
unsigned int _old_max_grain_id
The previous max grain id (needed to figure out which ids are new in a given step) ...
Definition: GrainTracker.h:239
unsigned int & _max_curr_grain_id
Holds the next "regular" grain ID (a grain found or remapped to the standard op vars) ...
Definition: GrainTracker.h:242

◆ getNextUniqueID()

unsigned int GrainTracker::getNextUniqueID ( )
protected

Retrieve the next unique grain number if a new grain is detected during trackGrains.

This method handles reserve order parameter indices properly. Direct access to the next index should be avoided.

Get the next unique grain ID but make sure to respect reserve ids. Note, that the first valid ID for a new grain is _reserve_grain_first_index + _n_reserve_ops because _reserve_grain_first_index IS a valid index. It does not point to the last valid index of the non-reserved grains.

Definition at line 1748 of file GrainTracker.C.

Referenced by trackGrains().

1749 {
1758  _reserve_grain_first_index + _n_reserve_ops /* no +1 here!*/);
1759 
1760  return _max_curr_grain_id;
1761 }
unsigned int & _max_curr_grain_id
Holds the next "regular" grain ID (a grain found or remapped to the standard op vars) ...
Definition: GrainTracker.h:242
static const unsigned int invalid_id
unsigned int _reserve_grain_first_index
Holds the first unique grain index when using _reserve_op (all the remaining indices are sequential) ...
Definition: GrainTracker.h:236
const unsigned short _n_reserve_ops
The number of reserved order parameters.
Definition: GrainTracker.h:189

◆ getNumberActiveFeatures()

std::size_t FeatureFloodCount::getNumberActiveFeatures ( ) const
inherited

Return the number of active features.

Definition at line 743 of file FeatureFloodCount.C.

Referenced by AverageGrainVolume::getValue().

744 {
745  // Note: This value is parallel consistent, see FeatureFloodCount::communicateAndMerge()
746  return _feature_count;
747 }
unsigned int _feature_count
The number of features seen by this object (same as summing _feature_counts_per_map) ...

◆ getNumberActiveGrains()

std::size_t GrainTracker::getNumberActiveGrains ( ) const
overridevirtual

Returns the number of active grains current stored in the GrainTracker.

This value is the same value reported when the GrainTracker (FeatureFloodObject) is used as a Postprocessor.

Note: This value will count each piece of a split grain (often encountered in EBSD data sets).

Implements GrainTrackerInterface.

Definition at line 131 of file GrainTracker.C.

132 {
133  // Note: This value is parallel consistent, see FeatureFloodCount::communicateAndMerge()
134  return _feature_count;
135 }
unsigned int _feature_count
The number of features seen by this object (same as summing _feature_counts_per_map) ...

◆ getThreshold()

Real GrainTracker::getThreshold ( std::size_t  current_index) const
overrideprotectedvirtual

Return the starting comparison threshold to use when inspecting an entity during the flood stage.

Reimplemented from FeatureFloodCount.

Definition at line 235 of file GrainTracker.C.

236 {
237  // If we are inspecting a reserve op parameter, we need to make sure
238  // that there is an entity above the reserve_op threshold before
239  // starting the flood of the feature.
240  if (var_index >= _reserve_op_index)
241  return _reserve_op_threshold;
242  else
243  return _step_threshold;
244 }
const Real _reserve_op_threshold
The threshold above (or below) where a grain may be found on a reserve op field.
Definition: GrainTracker.h:196
const std::size_t _reserve_op_index
The cutoff index where if variable index >= this number, no remapping TO that variable will occur...
Definition: GrainTracker.h:193

◆ getTotalFeatureCount()

std::size_t GrainTracker::getTotalFeatureCount ( ) const
overridevirtual

Returns the total feature count (active and inactive ids, useful for sizing vectors)

Since the FeatureFloodCount object doesn't maintain any information about features between invocations. The maximum id in use is simply the number of features.

Reimplemented from FeatureFloodCount.

Definition at line 138 of file GrainTracker.C.

139 {
140  // Note: This value is parallel consistent, see assignGrains()/trackGrains()
142 }
unsigned int & _max_curr_grain_id
Holds the next "regular" grain ID (a grain found or remapped to the standard op vars) ...
Definition: GrainTracker.h:242
static const unsigned int invalid_id

◆ getValue()

Real FeatureFloodCount::getValue ( )
overridevirtualinherited

Reimplemented in FauxGrainTracker.

Definition at line 737 of file FeatureFloodCount.C.

738 {
739  return static_cast<Real>(_feature_count);
740 }
unsigned int _feature_count
The number of features seen by this object (same as summing _feature_counts_per_map) ...

◆ getVarToFeatureVector()

const std::vector< unsigned int > & GrainTracker::getVarToFeatureVector ( dof_id_type  elem_id) const
overridevirtual

Returns a list of active unique feature ids for a particular element.

The vector is indexed by variable number with each entry containing either an invalid size_t type (no feature active at that location) or a feature id if the variable is non-zero at that location.

Reimplemented from FeatureFloodCount.

Definition at line 119 of file GrainTracker.C.

Referenced by ComputePolycrystalElasticityTensor::computeQpElasticityTensor().

120 {
122 }
virtual const std::vector< unsigned int > & getVarToFeatureVector(dof_id_type elem_id) const
Returns a list of active unique feature ids for a particular element.

◆ initialize()

void GrainTracker::initialize ( )
overridevirtual

If we are passed the first time, we need to save the existing grains before beginning the tracking on the current step. We'll do that with a swap since the _feature_sets contents will be cleared anyway.

Reimplemented from FeatureFloodCount.

Definition at line 179 of file GrainTracker.C.

180 {
181  // Don't track grains if the current simulation step is before the specified tracking step
182  if (_t_step < _tracking_step)
183  return;
184 
190  if (!_first_time)
192 
194 }
bool & _first_time
Boolean to indicate the first time this object executes.
Definition: GrainTracker.h:225
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
std::vector< FeatureData > _feature_sets_old
This data structure holds the map of unique grains from the previous time step.
Definition: GrainTracker.h:211
virtual void initialize() override
const int _tracking_step
The timestep to begin tracking grains.
Definition: GrainTracker.h:180

◆ initialSetup()

void FeatureFloodCount::initialSetup ( )
overridevirtualinherited

Size the empty var to features vector to the number of coupled variables. This empty vector (but properly sized) vector is returned for elements that are queried but are not in the structure (which also shouldn't happen). The user is warned in this case but this helps avoid extra bounds checking in user code and avoids segfaults.

Reimplemented in PolycrystalUserObjectBase.

Definition at line 231 of file FeatureFloodCount.C.

Referenced by PolycrystalUserObjectBase::initialSetup().

232 {
233  // We need one map per coupled variable for normal runs to support overlapping features
234  _entities_visited.resize(_vars.size());
235 
236  // Get a pointer to the PeriodicBoundaries buried in libMesh
237  _pbs = _fe_problem.getNonlinearSystemBase().dofMap().get_periodic_boundaries();
238 
239  meshChanged();
240 
249 }
const std::size_t _n_vars
std::vector< std::set< dof_id_type > > _entities_visited
This variable keeps track of which nodes have been visited during execution.
std::vector< MooseVariable * > _vars
The vector of coupled in variables cast to MooseVariable.
static const unsigned int invalid_id
PeriodicBoundaries * _pbs
A pointer to the periodic boundary constraints object.
std::vector< unsigned int > _empty_var_to_features
virtual void meshChanged() override

◆ isBoundaryEntity()

template<typename T >
bool FeatureFloodCount::isBoundaryEntity ( const T *  entity) const
protectedinherited

Returns a Boolean indicating whether the entity is on one of the desired boundaries.

Definition at line 1664 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::visitNeighborsHelper().

1665 {
1666  mooseAssert(_bnd_elem_range, "Boundary Element Range is nullptr");
1667 
1668  if (entity)
1669  for (const auto & belem : *_bnd_elem_range)
1670  // Only works for Elements
1671  if (belem->_elem->id() == entity->id() && hasBoundary(belem->_bnd_id))
1672  return true;
1673 
1674  return false;
1675 }
ConstBndElemRange * _bnd_elem_range
Boundary element range pointer (used when boundary restricting this object.

◆ isElemental()

bool FeatureFloodCount::isElemental ( ) const
inlineinherited

Definition at line 112 of file FeatureFloodCount.h.

Referenced by FeatureFloodCountAux::FeatureFloodCountAux().

112 { return _is_elemental; }
const bool _is_elemental
Determines if the flood counter is elements or not (nodes)

◆ isNewFeatureOrConnectedRegion()

bool FeatureFloodCount::isNewFeatureOrConnectedRegion ( const DofObject *  dof_object,
std::size_t &  current_index,
FeatureData *&  feature,
Status status,
unsigned int &  new_id 
)
protectedvirtualinherited

Method called during the recursive flood routine that should return whether or not the current entity is part of the current feature (if one is being explored), or if it's the start of a new feature.

If the value is only above the connecting threshold, it's still part of a feature but possibly part of one that we'll discard if there is never any starting threshold encountered.

Reimplemented in PolycrystalUserObjectBase.

Definition at line 1326 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::flood().

1331 {
1332  // Get the value of the current variable for the current entity
1333  Real entity_value;
1334  if (_is_elemental)
1335  {
1336  const Elem * elem = static_cast<const Elem *>(dof_object);
1337  std::vector<Point> centroid(1, elem->centroid());
1338  _subproblem.reinitElemPhys(elem, centroid, 0, /* suppress_displaced_init = */ true);
1339  entity_value = _vars[current_index]->sln()[0];
1340  }
1341  else
1342  entity_value = _vars[current_index]->getNodalValue(*static_cast<const Node *>(dof_object));
1343 
1344  // If the value compares against our starting threshold, this is definitely part of a feature
1345  // we'll keep
1346  if (compareValueWithThreshold(entity_value, getThreshold(current_index)))
1347  {
1348  Status * status_ptr = &status;
1349 
1350  if (feature)
1351  status_ptr = &feature->_status;
1352 
1353  // Update an existing feature's status or clear the flag on the passed in status
1354  *status_ptr &= ~Status::INACTIVE;
1355  return true;
1356  }
1357 
1362  return compareValueWithThreshold(entity_value, getConnectingThreshold(current_index));
1363 }
Status
This enumeration is used to indicate status of the grains in the _unique_grains data structure...
std::vector< MooseVariable * > _vars
The vector of coupled in variables cast to MooseVariable.
virtual Real getConnectingThreshold(std::size_t current_index) const
Return the "connecting" comparison threshold to use when inspecting an entity during the flood stage...
const bool _is_elemental
Determines if the flood counter is elements or not (nodes)
bool compareValueWithThreshold(Real entity_value, Real threshold) const
This method is used to determine whether the current entity value is part of a feature or not...
virtual Real getThreshold(std::size_t current_index) const
Return the starting comparison threshold to use when inspecting an entity during the flood stage...

◆ mergeSets()

void FeatureFloodCount::mergeSets ( )
protectedvirtualinherited

This routine is called on the master rank only and stitches together the partial feature pieces seen on any processor.

Insert the new entity at the end of the list so that it may be checked against all other partial features again.

Now remove both halves the merged features: it2 contains the "moved" feature cell just inserted at the back of the list, it1 contains the mostly empty other half. We have to be careful about the order in which these two elements are deleted. We delete it2 first since we don't care where its iterator points after the deletion. We are going to break out of this loop anyway. If we delete it1 first, it may end up pointing at the same location as it2 which after the second deletion would cause both of the iterators to be invalidated.

Reimplemented in PolycrystalUserObjectBase.

Definition at line 1021 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::communicateAndMerge().

1022 {
1023  TIME_SECTION(_merge_timer);
1024 
1025  // When working with _distribute_merge_work all of the maps will be empty except for one
1026  for (auto map_num = decltype(_maps_size)(0); map_num < _maps_size; ++map_num)
1027  {
1028  for (auto it1 = _partial_feature_sets[map_num].begin();
1029  it1 != _partial_feature_sets[map_num].end();
1030  /* No increment on it1 */)
1031  {
1032  bool merge_occured = false;
1033  for (auto it2 = _partial_feature_sets[map_num].begin();
1034  it2 != _partial_feature_sets[map_num].end();
1035  ++it2)
1036  {
1037  if (it1 != it2 && areFeaturesMergeable(*it1, *it2))
1038  {
1039  it2->merge(std::move(*it1));
1040 
1045  _partial_feature_sets[map_num].emplace_back(std::move(*it2));
1046 
1056  _partial_feature_sets[map_num].erase(it2);
1057  it1 = _partial_feature_sets[map_num].erase(it1); // it1 is incremented here!
1058 
1059  // A merge occurred, this is used to determine whether or not we increment the outer
1060  // iterator
1061  merge_occured = true;
1062 
1063  // We need to start the list comparison over for the new it1 so break here
1064  break;
1065  }
1066  } // it2 loop
1067 
1068  if (!merge_occured) // No merges so we need to manually increment the outer iterator
1069  ++it1;
1070 
1071  } // it1 loop
1072  } // map loop
1073 }
const PerfID _merge_timer
virtual bool areFeaturesMergeable(const FeatureData &f1, const FeatureData &f2) const
Method for determining whether two features are mergeable.
const std::size_t _maps_size
Convenience variable holding the size of all the datastructures size by the number of maps...
std::vector< std::list< FeatureData > > _partial_feature_sets
The data structure used to hold partial and communicated feature data, during the discovery and mergi...

◆ meshChanged()

void GrainTracker::meshChanged ( )
overridevirtual

Reimplemented from FeatureFloodCount.

Definition at line 197 of file GrainTracker.C.

198 {
199  // Update the element ID ranges for use when computing halo maps
200  if (_compute_halo_maps && _mesh.isDistributedMesh())
201  {
202  _all_ranges.clear();
203 
204  auto range = std::make_pair(std::numeric_limits<dof_id_type>::max(),
205  std::numeric_limits<dof_id_type>::min());
206  for (const auto & current_elem : _mesh.getMesh().active_local_element_ptr_range())
207  {
208  auto id = current_elem->id();
209  if (id < range.first)
210  range.first = id;
211  else if (id > range.second)
212  range.second = id;
213  }
214 
215  _communicator.gather(0, range, _all_ranges);
216  }
217 
219 }
const bool _compute_halo_maps
Indicates whether or not to communicate halo map information with all ranks.
std::vector< std::pair< dof_id_type, dof_id_type > > _all_ranges
Data structure to hold element ID ranges when using Distributed Mesh (populated on rank 0 only) ...
Definition: GrainTracker.h:248
virtual void meshChanged() override
MooseMesh & _mesh
A reference to the mesh.

◆ newGrainCreated()

void GrainTracker::newGrainCreated ( unsigned int  new_grain_id)
protectedvirtual

This method is called when a new grain is detected.

It can be overridden by a derived class to handle setting new properties on the newly created grain.

Reimplemented in GrainDataTracker< T >, and GrainDataTracker< RankFourTensor >.

Definition at line 831 of file GrainTracker.C.

Referenced by assignGrains(), and trackGrains().

832 {
833  if (!_first_time && _is_master)
834  {
835  mooseAssert(new_grain_id < _feature_id_to_local_index.size(), "new_grain_id is out of bounds");
836  auto grain_index = _feature_id_to_local_index[new_grain_id];
837  mooseAssert(grain_index != invalid_size_t && grain_index < _feature_sets.size(),
838  "new_grain_id appears to be invalid");
839 
840  const auto & grain = _feature_sets[grain_index];
841  _console << COLOR_YELLOW
842  << "\n*****************************************************************************"
843  << "\nCouldn't find a matching grain while working on variable index: "
844  << grain._var_index << "\nCreating new unique grain: " << new_grain_id << '\n'
845  << grain
846  << "\n*****************************************************************************\n"
847  << COLOR_DEFAULT;
848  }
849 }
static const std::size_t invalid_size_t
bool & _first_time
Boolean to indicate the first time this object executes.
Definition: GrainTracker.h:225
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
const bool _is_master
Convenience variable for testing master rank.
std::vector< std::size_t > _feature_id_to_local_index
The vector recording the grain_id to local index (several indices will contain invalid_size_t) ...

◆ numCoupledVars()

std::size_t FeatureFloodCount::numCoupledVars ( ) const
inlineinherited

Returns the number of coupled varaibles.

Definition at line 84 of file FeatureFloodCount.h.

84 { return _n_vars; }
const std::size_t _n_vars

◆ prepareDataForTransfer()

void FeatureFloodCount::prepareDataForTransfer ( )
protectedinherited

This routine uses the local flooded data to build up the local feature data structures (_feature_sets).

This routine does not perform any communication so the _feature_sets data structure will only contain information from the local processor after calling this routine. Any existing data in the _feature_sets structure is destroyed by calling this routine.

_feature_sets layout: The outer vector is sized to one when _single_map_mode == true, otherwise it is sized for the number of coupled variables. The inner list represents the flooded regions (local only after this call but fully populated after parallel communication and stitching).

If using a vector container, we need to sort all of the data structures for later operations such as checking for intersection and merging. The following "sort" function does nothing when invoked on a std::set.

Save off the min entity id present in the feature to uniquely identify the feature regardless of n_procs

Definition at line 919 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::communicateAndMerge().

920 {
921  TIME_SECTION(_prepare_for_transfer);
922 
923  MeshBase & mesh = _mesh.getMesh();
924 
925  FeatureData::container_type local_ids_no_ghost, set_difference;
926 
927  for (auto & list_ref : _partial_feature_sets)
928  {
929  for (auto & feature : list_ref)
930  {
931  // Periodic node ids
933 
939  FeatureFloodCount::sort(feature._ghosted_ids);
940  FeatureFloodCount::sort(feature._local_ids);
941  FeatureFloodCount::sort(feature._halo_ids);
942  FeatureFloodCount::sort(feature._disjoint_halo_ids);
943  FeatureFloodCount::sort(feature._periodic_nodes);
944 
945  // Now extend the bounding box by the halo region
946  if (_is_elemental)
947  feature.updateBBoxExtremes(mesh);
948  else
949  {
950  for (auto & halo_id : feature._halo_ids)
951  updateBBoxExtremesHelper(feature._bboxes[0], mesh.node(halo_id));
952  }
953 
954  mooseAssert(!feature._local_ids.empty(), "local entity ids cannot be empty");
955 
960  feature._min_entity_id = *feature._local_ids.begin();
961  }
962  }
963 }
void appendPeriodicNeighborNodes(FeatureData &feature) const
This routine adds the periodic node information to our data structure prior to packing the data this ...
static void sort(std::set< T > &)
std::set< dof_id_type > container_type
The primary underlying container type used to hold the data in each FeatureData.
void updateBBoxExtremesHelper(MeshTools::BoundingBox &bbox, const Point &node)
std::vector< std::list< FeatureData > > _partial_feature_sets
The data structure used to hold partial and communicated feature data, during the discovery and mergi...
const bool _is_elemental
Determines if the flood counter is elements or not (nodes)
const PerfID _prepare_for_transfer
MooseMesh & _mesh
A reference to the mesh.

◆ prepopulateState()

void GrainTracker::prepopulateState ( const FeatureFloodCount ffc_object)
protected

This method extracts the necessary state from the passed in object necessary to continue tracking grains.

This method is meant to be used with the PolycrystalUserobjectBase class that sets up initial conditions for Polycrystal simulations. We can use the state of that object rather than rediscovering everything ourselves.

The minimum information needed to bootstrap the GrainTracker is as follows: _feature_sets _feature_count

Definition at line 247 of file GrainTracker.C.

Referenced by finalize().

248 {
249  mooseAssert(_first_time, "This method should only be called on the first invocation");
250 
251  _feature_sets.clear();
252 
258  if (_is_master)
259  {
260  const auto & features = ffc_object.getFeatures();
261  for (auto & feature : features)
262  _feature_sets.emplace_back(feature.duplicate());
263 
264  _feature_count = _feature_sets.size();
265  }
266  else
267  {
268  const auto & features = ffc_object.getFeatures();
269  _partial_feature_sets[0].clear();
270  for (auto & feature : features)
271  _partial_feature_sets[0].emplace_back(feature.duplicate());
272  }
273 
274  // Make sure that feature count is communicated to all ranks
275  _communicator.broadcast(_feature_count);
276 }
bool & _first_time
Boolean to indicate the first time this object executes.
Definition: GrainTracker.h:225
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
const std::vector< FeatureData > & getFeatures() const
Return a constant reference to the vector of all discovered features.
const bool _is_master
Convenience variable for testing master rank.
unsigned int _feature_count
The number of features seen by this object (same as summing _feature_counts_per_map) ...
std::vector< std::list< FeatureData > > _partial_feature_sets
The data structure used to hold partial and communicated feature data, during the discovery and mergi...

◆ remapGrains()

void GrainTracker::remapGrains ( )
protected

This method is called after trackGrains to remap grains that are too close to each other.

Map used for communicating remap indices to all ranks This map isn't populated until after the remap loop. It's declared here before we enter the root scope since it's needed by all ranks during the broadcast.

The remapping algorithm is recursive. We will use the status variable in each FeatureData to track which grains are currently being remapped so we don't have runaway recursion. To begin we need to clear all of the active (MARKED) flags (CLEAR).

Additionally we need to record each grain's variable index so that we can communicate changes to the non-root ranks later in a single batch.

We're not going to try very hard to look for a suitable remapping. Just set it to what we want and hope it all works out. Make the GrainTracker great again!

Loop over each grain and see if any grains represented by the same variable are "touching"

The remapping loop is complete but only on the master process. Now we need to build the remap map and communicate it to the remaining processors.

Since the remapping algorithm only runs on the root process, the variable index on the master's grains is inconsistent from the rest of the ranks. These are the grains with a status of DIRTY. As we build this map we will temporarily switch these variable indices back to the correct value so that all processors use the same algorithm to remap.

Definition at line 864 of file GrainTracker.C.

Referenced by finalize().

865 {
866  // Don't remap grains if the current simulation step is before the specified tracking step
867  if (_t_step < _tracking_step)
868  return;
869 
870  TIME_SECTION(_remap_timer);
871 
872  if (_verbosity_level > 1)
873  _console << "Running remap Grains\n" << std::endl;
874 
881  std::map<unsigned int, std::size_t> grain_id_to_new_var;
882 
883  // Items are added to this list when split grains are found
884  std::list<std::pair<std::size_t, std::size_t>> split_pairs;
885 
894  if (_is_master)
895  {
896  // Build the map to detect difference in _var_index mappings after the remap operation
897  std::map<unsigned int, std::size_t> grain_id_to_existing_var_index;
898  for (auto & grain : _feature_sets)
899  {
900  // Unmark the grain so it can be used in the remap loop
901  grain._status = Status::CLEAR;
902 
903  grain_id_to_existing_var_index[grain._id] = grain._var_index;
904  }
905 
906  // Make sure that all split pieces of any grain are on the same OP
907  for (auto i = beginIndex(_feature_sets); i < _feature_sets.size(); ++i)
908  {
909  auto & grain1 = _feature_sets[i];
910 
911  for (auto j = beginIndex(_feature_sets); j < _feature_sets.size(); ++j)
912  {
913  auto & grain2 = _feature_sets[j];
914  if (i == j)
915  continue;
916 
917  // The first condition below is there to prevent symmetric checks (duplicate values)
918  if (i < j && grain1._id == grain2._id)
919  {
920  split_pairs.push_front(std::make_pair(i, j));
921  if (grain1._var_index != grain2._var_index)
922  {
923  if (_verbosity_level > 0)
924  _console << COLOR_YELLOW << "Split Grain (#" << grain1._id
925  << ") detected on unmatched OPs (" << grain1._var_index << ", "
926  << grain2._var_index << ") attempting to remap to " << grain1._var_index
927  << ".\n"
928  << COLOR_DEFAULT;
929 
934  grain1._var_index = grain2._var_index;
935  grain1._status |= Status::DIRTY;
936  }
937  }
938  }
939  }
940 
944  bool any_grains_remapped = false;
945  bool grains_remapped;
946 
947  std::set<unsigned int> notify_ids;
948  do
949  {
950  grains_remapped = false;
951  notify_ids.clear();
952 
953  for (auto & grain1 : _feature_sets)
954  {
955  // We need to remap any grains represented on any variable index above the cuttoff
956  if (grain1._var_index >= _reserve_op_index)
957  {
958  if (_verbosity_level > 0)
959  _console << COLOR_YELLOW << "\nGrain #" << grain1._id
960  << " detected on a reserved order parameter #" << grain1._var_index
961  << ", remapping to another variable\n"
962  << COLOR_DEFAULT;
963 
964  for (auto max = decltype(_max_remap_recursion_depth)(0);
966  ++max)
967  if (max < _max_remap_recursion_depth)
968  {
969  if (attemptGrainRenumber(grain1, 0, max))
970  break;
971  }
972  else if (!attemptGrainRenumber(grain1, 0, max))
973  {
974  _console << std::flush;
975  std::stringstream oss;
976  oss << "Unable to find any suitable order parameters for remapping while working "
977  << "with Grain #" << grain1._id << ", which is on a reserve order parameter.\n"
978  << "\n\nPossible Resolutions:\n"
979  << "\t- Add more order parameters to your simulation (8 for 2D, 28 for 3D)\n"
980  << "\t- Increase adaptivity or reduce your grain boundary widths\n"
981  << "\t- Make sure you are not starting with too many grains for the mesh size\n";
982  mooseError(oss.str());
983  }
984 
985  grains_remapped = true;
986  }
987 
988  for (auto & grain2 : _feature_sets)
989  {
990  // Don't compare a grain with itself and don't try to remap inactive grains
991  if (&grain1 == &grain2)
992  continue;
993 
994  if (grain1._var_index == grain2._var_index && // grains represented by same variable?
995  grain1._id != grain2._id && // are they part of different grains?
996  grain1.boundingBoxesIntersect(grain2) && // do bboxes intersect (coarse level)?
997  grain1.halosIntersect(grain2)) // do they actually overlap (fine level)?
998  {
999  if (_verbosity_level > 0)
1000  _console << COLOR_YELLOW << "Grain #" << grain1._id << " intersects Grain #"
1001  << grain2._id << " (variable index: " << grain1._var_index << ")\n"
1002  << COLOR_DEFAULT;
1003 
1004  for (auto max = decltype(_max_remap_recursion_depth)(0);
1006  ++max)
1007  {
1008  if (max < _max_remap_recursion_depth)
1009  {
1010  if (attemptGrainRenumber(grain1, 0, max))
1011  {
1012  grains_remapped = true;
1013  break;
1014  }
1015  }
1016  else if (!attemptGrainRenumber(grain1, 0, max) &&
1017  !attemptGrainRenumber(grain2, 0, max))
1018  {
1019  notify_ids.insert(grain1._id);
1020  notify_ids.insert(grain2._id);
1021  }
1022  }
1023  }
1024  }
1025  }
1026  any_grains_remapped |= grains_remapped;
1027  } while (grains_remapped);
1028 
1029  if (!notify_ids.empty())
1030  {
1031  _console << std::flush;
1032  std::stringstream oss;
1033  oss << "Unable to find any suitable order parameters for remapping while working "
1034  << "with the following grain IDs:\n"
1035  << Moose::stringify(notify_ids, ", ", "", true) << "\n\nPossible Resolutions:\n"
1036  << "\t- Add more order parameters to your simulation (8 for 2D, 28 for 3D)\n"
1037  << "\t- Increase adaptivity or reduce your grain boundary widths\n"
1038  << "\t- Make sure you are not starting with too many grains for the mesh size\n";
1039 
1040  if (_tolerate_failure)
1041  mooseWarning(oss.str());
1042  else
1043  mooseError(oss.str());
1044  }
1045 
1046  // Verify that split grains are still intact
1047  for (auto & split_pair : split_pairs)
1048  if (_feature_sets[split_pair.first]._var_index != _feature_sets[split_pair.first]._var_index)
1049  mooseError("Split grain remapped - This case is currently not handled");
1050 
1056  for (auto & grain : _feature_sets)
1057  {
1058  mooseAssert(grain_id_to_existing_var_index.find(grain._id) !=
1059  grain_id_to_existing_var_index.end(),
1060  "Missing unique ID");
1061 
1062  auto old_var_index = grain_id_to_existing_var_index[grain._id];
1063 
1064  if (old_var_index != grain._var_index)
1065  {
1066  mooseAssert(static_cast<bool>(grain._status & Status::DIRTY), "grain status is incorrect");
1067 
1068  grain_id_to_new_var.emplace_hint(
1069  grain_id_to_new_var.end(),
1070  std::pair<unsigned int, std::size_t>(grain._id, grain._var_index));
1071 
1080  grain._var_index = old_var_index;
1081  // Clear the DIRTY status as well for consistency
1082  grain._status &= ~Status::DIRTY;
1083  }
1084  }
1085 
1086  if (!grain_id_to_new_var.empty())
1087  {
1088  if (_verbosity_level > 1)
1089  {
1090  _console << "Final remapping tally:\n";
1091  for (const auto & remap_pair : grain_id_to_new_var)
1092  _console << "Grain #" << remap_pair.first << " var_index "
1093  << grain_id_to_existing_var_index[remap_pair.first] << " -> "
1094  << remap_pair.second << '\n';
1095  _console << "Communicating swaps with remaining processors..." << std::endl;
1096  }
1097  }
1098  } // root processor
1099 
1100  // Communicate the std::map to all ranks
1101  _communicator.broadcast(grain_id_to_new_var);
1102 
1103  // Perform swaps if any occurred
1104  if (!grain_id_to_new_var.empty())
1105  {
1106  // Cache for holding values during swaps
1107  std::vector<std::map<Node *, CacheValues>> cache(_n_vars);
1108 
1109  // Perform the actual swaps on all processors
1110  for (auto & grain : _feature_sets)
1111  {
1112  // See if this grain was remapped
1113  auto new_var_it = grain_id_to_new_var.find(grain._id);
1114  if (new_var_it != grain_id_to_new_var.end())
1115  swapSolutionValues(grain, new_var_it->second, cache, RemapCacheMode::FILL);
1116  }
1117 
1118  for (auto & grain : _feature_sets)
1119  {
1120  // See if this grain was remapped
1121  auto new_var_it = grain_id_to_new_var.find(grain._id);
1122  if (new_var_it != grain_id_to_new_var.end())
1123  swapSolutionValues(grain, new_var_it->second, cache, RemapCacheMode::USE);
1124  }
1125 
1126  _nl.solution().close();
1127  _nl.solutionOld().close();
1128  _nl.solutionOlder().close();
1129 
1130  _fe_problem.getNonlinearSystemBase().system().update();
1131 
1132  if (_verbosity_level > 1)
1133  _console << "Swaps complete" << std::endl;
1134  }
1135 }
const std::size_t _n_vars
Status
This enumeration is used to indicate status of the grains in the _unique_grains data structure...
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
const bool _is_master
Convenience variable for testing master rank.
NonlinearSystemBase & _nl
A reference to the nonlinear system (used for retrieving solution vectors)
Definition: GrainTracker.h:205
void swapSolutionValues(FeatureData &grain, std::size_t new_var_index, std::vector< std::map< Node *, CacheValues >> &cache, RemapCacheMode cache_mode)
A routine for moving all of the solution values from a given grain to a new variable number...
const short _verbosity_level
Verbosity level controlling the amount of information printed to the console.
Definition: GrainTracker.h:219
const PerfID _remap_timer
Definition: GrainTracker.h:252
bool attemptGrainRenumber(FeatureData &grain, unsigned int depth, unsigned int max_depth)
This is the recursive part of the remapping algorithm.
const int _tracking_step
The timestep to begin tracking grains.
Definition: GrainTracker.h:180
const std::size_t _reserve_op_index
The cutoff index where if variable index >= this number, no remapping TO that variable will occur...
Definition: GrainTracker.h:193
const unsigned short _max_remap_recursion_depth
Depth of renumbering recursion (a depth of zero means no recursion)
Definition: GrainTracker.h:186
const bool _tolerate_failure
Indicates whether we should continue after a remap failure (will result in non-physical results) ...
Definition: GrainTracker.h:202

◆ scatterAndUpdateRanks()

void FeatureFloodCount::scatterAndUpdateRanks ( )
protectedinherited

Calls buildLocalToGlobalIndices to build the individual local to global indicies for each rank and scatters that information to all ranks.

Finally, the non-master ranks update their own data structures to reflect the global mappings.

On non-root processors we can't maintain the full _feature_sets data structure since we don't have all of the global information. We'll move the items from the partial feature sets into a flat structure maintaining order and update the internal IDs with the proper global ID.

Important: Make sure we clear the local status if we received a valid global index for this feature. It's possible that we have a status of INVALID on the local processor because there was never any starting threshold found. However, the root processor wouldn't have sent an index if it didn't find a starting threshold connected to our local piece.

Definition at line 669 of file FeatureFloodCount.C.

Referenced by assignGrains(), FeatureFloodCount::finalize(), and trackGrains().

670 {
671  // local to global map (one per processor)
672  std::vector<int> counts;
673  std::vector<std::size_t> local_to_global_all;
674  if (_is_master)
675  buildLocalToGlobalIndices(local_to_global_all, counts);
676 
677  // Scatter local_to_global indices to all processors and store in class member variable
678  _communicator.scatter(local_to_global_all, counts, _local_to_global_feature_map);
679 
680  std::size_t largest_global_index = std::numeric_limits<std::size_t>::lowest();
681  if (!_is_master)
682  {
684 
691  for (auto & list_ref : _partial_feature_sets)
692  {
693  for (auto & feature : list_ref)
694  {
695  mooseAssert(feature._orig_ids.size() == 1, "feature._orig_ids length doesn't make sense");
696 
697  auto global_index = FeatureFloodCount::invalid_size_t;
698  auto local_index = feature._orig_ids.begin()->second;
699 
700  if (local_index < _local_to_global_feature_map.size())
701  global_index = _local_to_global_feature_map[local_index];
702 
703  if (global_index != FeatureFloodCount::invalid_size_t)
704  {
705  if (global_index > largest_global_index)
706  largest_global_index = global_index;
707 
708  // Set the correct global index
709  feature._id = global_index;
710 
718  feature._status &= ~Status::INACTIVE;
719 
720  // Move the feature into the correct place
721  _feature_sets[local_index] = std::move(feature);
722  }
723  }
724  }
725  }
726  else
727  {
728  for (auto global_index : local_to_global_all)
729  if (global_index != FeatureFloodCount::invalid_size_t && global_index > largest_global_index)
730  largest_global_index = global_index;
731  }
732 
733  buildFeatureIdToLocalIndices(largest_global_index);
734 }
static const std::size_t invalid_size_t
Status
This enumeration is used to indicate status of the grains in the _unique_grains data structure...
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
const bool _is_master
Convenience variable for testing master rank.
virtual void buildLocalToGlobalIndices(std::vector< std::size_t > &local_to_global_all, std::vector< int > &counts) const
This routine populates a stacked vector of local to global indices per rank and the associated count ...
std::vector< std::list< FeatureData > > _partial_feature_sets
The data structure used to hold partial and communicated feature data, during the discovery and mergi...
void buildFeatureIdToLocalIndices(unsigned int max_id)
This method builds a lookup map for retrieving the right local feature (by index) given a global inde...
std::vector< std::size_t > _local_to_global_feature_map
The vector recording the local to global feature indices.

◆ serialize()

void FeatureFloodCount::serialize ( std::string &  serialized_buffer,
unsigned int  var_num = invalid_id 
)
protectedinherited

This routines packs the _partial_feature_sets data into a structure suitable for parallel communication operations.

Definition at line 966 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::communicateAndMerge().

967 {
968  // stream for serializing the _partial_feature_sets data structure to a byte stream
969  std::ostringstream oss;
970 
971  mooseAssert(var_num == invalid_id || var_num < _partial_feature_sets.size(),
972  "var_num out of range");
973 
974  // Serialize everything
975  if (var_num == invalid_id)
976  dataStore(oss, _partial_feature_sets, this);
977  else
978  dataStore(oss, _partial_feature_sets[var_num], this);
979 
980  // Populate the passed in string pointer with the string stream's buffer contents
981  serialized_buffer.assign(oss.str());
982 }
void dataStore(std::ostream &stream, FeatureFloodCount::FeatureData &feature, void *context)
static const unsigned int invalid_id
std::vector< std::list< FeatureData > > _partial_feature_sets
The data structure used to hold partial and communicated feature data, during the discovery and mergi...

◆ setsIntersect()

template<class InputIterator >
static bool FeatureFloodCount::setsIntersect ( InputIterator  first1,
InputIterator  last1,
InputIterator  first2,
InputIterator  last2 
)
inlinestaticprotectedinherited

This method detects whether two sets intersect without building a result set.

It exits as soon as any intersection is detected.

Definition at line 523 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::FeatureData::ghostedIntersect(), FeatureFloodCount::FeatureData::halosIntersect(), and FeatureFloodCount::FeatureData::periodicBoundariesIntersect().

527  {
528  while (first1 != last1 && first2 != last2)
529  {
530  if (*first1 == *first2)
531  return true;
532 
533  if (*first1 < *first2)
534  ++first1;
535  else if (*first1 > *first2)
536  ++first2;
537  }
538  return false;
539  }

◆ sortAndLabel()

void FeatureFloodCount::sortAndLabel ( )
protectedinherited

Sort and assign ids to features based on their position in the container after sorting.

Perform a sort to give a parallel unique sorting to the identified features. We use the "min_entity_id" inside each feature to assign it's position in the sorted vector.

Sanity check. Now that we've sorted the flattened vector of features we need to make sure that the counts vector still lines up appropriately with each feature's _var_index.

Definition at line 526 of file FeatureFloodCount.C.

Referenced by assignGrains(), and FeatureFloodCount::finalize().

527 {
528  mooseAssert(_is_master, "sortAndLabel can only be called on the master");
529 
535  std::sort(_feature_sets.begin(), _feature_sets.end());
536 
537 #ifndef NDEBUG
538 
543  unsigned int feature_offset = 0;
544  for (auto map_num = beginIndex(_feature_counts_per_map); map_num < _maps_size; ++map_num)
545  {
546  // Skip empty map checks
547  if (_feature_counts_per_map[map_num] == 0)
548  continue;
549 
550  // Check the begin and end of the current range
551  auto range_front = feature_offset;
552  auto range_back = feature_offset + _feature_counts_per_map[map_num] - 1;
553 
554  mooseAssert(range_front <= range_back && range_back < _feature_count,
555  "Indexing error in feature sets");
556 
557  if (!_single_map_mode && (_feature_sets[range_front]._var_index != map_num ||
558  _feature_sets[range_back]._var_index != map_num))
559  mooseError("Error in _feature_sets sorting, map index: ", map_num);
560 
561  feature_offset += _feature_counts_per_map[map_num];
562  }
563 #endif
564 
565  // Label the features with an ID based on the sorting (processor number independent value)
566  for (auto i = beginIndex(_feature_sets); i < _feature_sets.size(); ++i)
567  if (_feature_sets[i]._id == invalid_id)
568  _feature_sets[i]._id = i;
569 }
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
const bool _is_master
Convenience variable for testing master rank.
const std::size_t _maps_size
Convenience variable holding the size of all the datastructures size by the number of maps...
static const unsigned int invalid_id
const bool _single_map_mode
This variable is used to indicate whether or not multiple maps are used during flooding.
unsigned int _feature_count
The number of features seen by this object (same as summing _feature_counts_per_map) ...
std::vector< unsigned int > _feature_counts_per_map
The number of features seen by this object per map.

◆ swapSolutionValues()

void GrainTracker::swapSolutionValues ( FeatureData &  grain,
std::size_t  new_var_index,
std::vector< std::map< Node *, CacheValues >> &  cache,
RemapCacheMode  cache_mode 
)
protected

A routine for moving all of the solution values from a given grain to a new variable number.

It is called with different modes to only cache, or actually do the work, or bypass the cache altogether.

Definition at line 1387 of file GrainTracker.C.

Referenced by remapGrains().

1391 {
1392  MeshBase & mesh = _mesh.getMesh();
1393 
1394  // Remap the grain
1395  std::set<Node *> updated_nodes_tmp; // Used only in the elemental case
1396  for (auto entity : grain._local_ids)
1397  {
1398  if (_is_elemental)
1399  {
1400  Elem * elem = mesh.query_elem(entity);
1401  if (!elem)
1402  continue;
1403 
1404  for (unsigned int i = 0; i < elem->n_nodes(); ++i)
1405  {
1406  Node * curr_node = elem->get_node(i);
1407  if (updated_nodes_tmp.find(curr_node) == updated_nodes_tmp.end())
1408  {
1409  // cache this node so we don't attempt to remap it again within this loop
1410  updated_nodes_tmp.insert(curr_node);
1411  swapSolutionValuesHelper(curr_node, grain._var_index, new_var_index, cache, cache_mode);
1412  }
1413  }
1414  }
1415  else
1417  mesh.query_node_ptr(entity), grain._var_index, new_var_index, cache, cache_mode);
1418  }
1419 
1420  // Update the variable index in the unique grain datastructure after swaps are complete
1421  if (cache_mode == RemapCacheMode::USE || cache_mode == RemapCacheMode::BYPASS)
1422  grain._var_index = new_var_index;
1423 }
void swapSolutionValuesHelper(Node *curr_node, std::size_t curr_var_index, std::size_t new_var_index, std::vector< std::map< Node *, CacheValues >> &cache, RemapCacheMode cache_mode)
Helper method for actually performing the swaps.
const bool _is_elemental
Determines if the flood counter is elements or not (nodes)
MooseMesh & _mesh
A reference to the mesh.

◆ swapSolutionValuesHelper()

void GrainTracker::swapSolutionValuesHelper ( Node *  curr_node,
std::size_t  curr_var_index,
std::size_t  new_var_index,
std::vector< std::map< Node *, CacheValues >> &  cache,
RemapCacheMode  cache_mode 
)
protected

Helper method for actually performing the swaps.

Finally zero out the old variable. When using the FILL/USE combination to read/write variables, it's important to zero the variable on the FILL stage and not the USE stage. The reason for this is handling swaps as illustrated in the following diagram


/ \/ \ If adjacent grains (overlapping flood region) end up / 1 /\ 2 \ swapping variable indices and variables are zeroed on \ 2*\/ 1* / "USE", the overlap region will be incorrectly zeroed ___/___/ by whichever variable is written to second.

Definition at line 1426 of file GrainTracker.C.

Referenced by swapSolutionValues().

1431 {
1432  if (curr_node && curr_node->processor_id() == processor_id())
1433  {
1434  // Reinit the node so we can get and set values of the solution here
1435  _subproblem.reinitNode(curr_node, 0);
1436 
1437  // Local variables to hold values being transferred
1438  Real current, old = 0, older = 0;
1439  // Retrieve the value either from the old variable or cache
1440  if (cache_mode == RemapCacheMode::FILL || cache_mode == RemapCacheMode::BYPASS)
1441  {
1442  current = _vars[curr_var_index]->dofValues()[0];
1443  if (_is_transient)
1444  {
1445  old = _vars[curr_var_index]->dofValuesOld()[0];
1446  older = _vars[curr_var_index]->dofValuesOlder()[0];
1447  }
1448  }
1449  else // USE
1450  {
1451  const auto cache_it = cache[curr_var_index].find(curr_node);
1452  mooseAssert(cache_it != cache[curr_var_index].end(), "Error in cache");
1453  current = cache_it->second.current;
1454  old = cache_it->second.old;
1455  older = cache_it->second.older;
1456  }
1457 
1458  // Cache the value or use it!
1459  if (cache_mode == RemapCacheMode::FILL)
1460  {
1461  cache[curr_var_index][curr_node].current = current;
1462  cache[curr_var_index][curr_node].old = old;
1463  cache[curr_var_index][curr_node].older = older;
1464  }
1465  else // USE or BYPASS
1466  {
1467  const auto & dof_index = _vars[new_var_index]->nodalDofIndex();
1468 
1469  // Transfer this solution from the old to the current
1470  _nl.solution().set(dof_index, current);
1471  if (_is_transient)
1472  {
1473  _nl.solutionOld().set(dof_index, old);
1474  _nl.solutionOlder().set(dof_index, older);
1475  }
1476  }
1477 
1490  if (cache_mode == RemapCacheMode::FILL || cache_mode == RemapCacheMode::BYPASS)
1491  {
1492  const auto & dof_index = _vars[curr_var_index]->nodalDofIndex();
1493 
1494  // Set the DOF for the current variable to zero
1495  _nl.solution().set(dof_index, 0.0);
1496  if (_is_transient)
1497  {
1498  _nl.solutionOld().set(dof_index, 0.0);
1499  _nl.solutionOlder().set(dof_index, 0.0);
1500  }
1501  }
1502  }
1503 }
NonlinearSystemBase & _nl
A reference to the nonlinear system (used for retrieving solution vectors)
Definition: GrainTracker.h:205
std::vector< MooseVariable * > _vars
The vector of coupled in variables cast to MooseVariable.
const bool _is_transient
Boolean to indicate whether this is a Steady or Transient solve.
Definition: GrainTracker.h:245

◆ trackGrains()

void GrainTracker::trackGrains ( )
protected

On subsequent time_steps, incoming FeatureData objects are compared to previous time_step information to track grains between time steps.

This method updates the _feature_sets data structure. This method should only be called on the root processor

Only the master rank does tracking, the remaining ranks wait to receive local to global indices from the master.

To track grains across time steps, we will loop over our unique grains and link each one up with one of our new unique grains. The criteria for doing this will be to find the unique grain in the new list with a matching variable index whose centroid is closest to this unique grain.

The _feature_sets vector is constructed by _var_index so we can avoid looping over all indices. We can quickly jump to the first matching index to reduce the number of comparisons and terminate our loop when our variable index stops matching.

Don't try to do any matching unless the bounding boxes at least overlap. This is to avoid the corner case of having a grain split and a grain disappear during the same time step!

It's possible that multiple existing grains will map to a single new grain (indicated by finding multiple matches when we are building this map). This will happen any time a grain disappears during this time step. We need to figure out the rightful owner in this case and inactivate the old grain.

If the grain we just marked inactive was the one whose index was in the new grain to existing grain map (other_old_grain). Then we need to update the map to point to the new match winner.

At this point we have should have only two cases left to handle: Case 1: A grain in the new set who has an unset status (These are new grains, previously untracked) This case is easy to understand. Since we are matching up grains by looking at the old set and finding closest matches in the new set, any grain in the new set that isn't matched up is simply new since some other grain satisfied each and every request from the old set.

Case 2: A grain in the old set who has an unset status (These are inactive grains that haven't been marked) We can only fall into this case when the very last grain on a given variable disappears during the current time step. In that case we never have a matching _var_index in the comparison loop above so that old grain never competes for any new grain which means it can't be marked inactive in the loop above.

Now we need to figure out what kind of "new" grain this is. Is it a nucleating grain that we're just barely seeing for the first time or is it a "splitting" grain. A grain that gets pinched into two or more pieces usually as it is being absorbed by other grains or possibly due to external forces. We have to handle splitting grains this way so as to no confuse them with regular grains that just happen to be in contact in this step.

Splitting Grain: An grain that is unmatched by any old grain on the same order parameter with touching halos.

Nucleating Grain: A completely new grain appearing somewhere in the domain not overlapping any other grain's halo.

To figure out which case we are dealing with, we have to make another pass over all of the existing grains with matching variable indices to see if any of them have overlapping halos.

The "try-harder loop": OK so we still have an extra grain in the new set that isn't matched up against the old set and since the order parameter isn't reserved. We aren't really expecting a new grain. Let's try to make a few more attempts to see if this is a split grain even though it failed to match the criteria above. This might happen if the halo front is advancing too fast!

In this loop we'll make an attempt to match up this new grain to the old halos. If adaptivity is happening this could fail as elements in the new set may be at a different level than in the old set. If we get multiple matches, we'll compare the grain volumes (based on elements, not integrated to choose the closest).

Future ideas: Look at the volume fraction of the new grain and overlay it over the volume fraction of the old grain (would require more saved information, or an aux field hanging around (subject to projection problems).

Note that the old grains we are looking at will already be marked from the earlier tracking phase. We are trying to see if this unmatched grain is part of a larger whole. To do that we'll look at the halos across the time step.

Trigger callback for new grains

Definition at line 447 of file GrainTracker.C.

Referenced by finalize().

448 {
449  TIME_SECTION(_track_grains);
450 
451  mooseAssert(!_first_time, "Track grains may only be called when _tracking_step > _t_step");
452 
453  // Used to track indices for which to trigger the new grain callback on (used on all ranks)
455 
460  if (_is_master)
461  {
462  // Reset Status on active unique grains
463  std::vector<unsigned int> map_sizes(_maps_size);
464  for (auto & grain : _feature_sets_old)
465  {
466  if (grain._status != Status::INACTIVE)
467  {
468  grain._status = Status::CLEAR;
469  map_sizes[grain._var_index]++;
470  }
471  }
472 
473  // Print out stats on overall tracking changes per var_index
474  if (_verbosity_level > 0)
475  {
476  _console << "\nGrain Tracker Status:";
477  for (auto map_num = decltype(_maps_size)(0); map_num < _maps_size; ++map_num)
478  {
479  _console << "\nGrains active index " << map_num << ": " << map_sizes[map_num] << " -> "
480  << _feature_counts_per_map[map_num];
481  if (map_sizes[map_num] > _feature_counts_per_map[map_num])
482  _console << "--";
483  else if (map_sizes[map_num] < _feature_counts_per_map[map_num])
484  _console << "++";
485  }
486  _console << '\n' << std::endl;
487  }
488 
489  // Before we track grains, lets sort them so that we get parallel consistent answers
490  std::sort(_feature_sets.begin(), _feature_sets.end());
491 
498  std::vector<std::size_t> new_grain_index_to_existing_grain_index(_feature_sets.size(),
500 
501  for (auto old_grain_index = beginIndex(_feature_sets_old);
502  old_grain_index < _feature_sets_old.size();
503  ++old_grain_index)
504  {
505  auto & old_grain = _feature_sets_old[old_grain_index];
506 
507  if (old_grain._status == Status::INACTIVE) // Don't try to find matches for inactive grains
508  continue;
509 
510  std::size_t closest_match_index = invalid_size_t;
511  Real min_centroid_diff = std::numeric_limits<Real>::max();
512 
518  // clang-format off
519  auto start_it =
520  std::lower_bound(_feature_sets.begin(), _feature_sets.end(), old_grain._var_index,
521  [](const FeatureData & item, std::size_t var_index)
522  {
523  return item._var_index < var_index;
524  });
525  // clang-format on
526 
527  // We only need to examine grains that have matching variable indices
528  bool any_boxes_intersect = false;
529  for (decltype(_feature_sets.size()) new_grain_index =
530  std::distance(_feature_sets.begin(), start_it);
531  new_grain_index < _feature_sets.size() &&
532  _feature_sets[new_grain_index]._var_index == old_grain._var_index;
533  ++new_grain_index)
534  {
535  auto & new_grain = _feature_sets[new_grain_index];
536 
541  if (new_grain.boundingBoxesIntersect(old_grain))
542  {
543  any_boxes_intersect = true;
544  Real curr_centroid_diff = centroidRegionDistance(old_grain._bboxes, new_grain._bboxes);
545  if (curr_centroid_diff <= min_centroid_diff)
546  {
547  closest_match_index = new_grain_index;
548  min_centroid_diff = curr_centroid_diff;
549  }
550  }
551  }
552 
553  if (_verbosity_level > 2 && !any_boxes_intersect)
554  _console << "\nNo intersecting bounding boxes found while trying to match grain "
555  << old_grain;
556 
557  // found a match
558  if (closest_match_index != invalid_size_t)
559  {
566  auto curr_index = new_grain_index_to_existing_grain_index[closest_match_index];
567  if (curr_index != invalid_size_t)
568  {
569  // The new feature being competed for
570  auto & new_grain = _feature_sets[closest_match_index];
571 
572  // The other old grain competing to match up to the same new grain
573  auto & other_old_grain = _feature_sets_old[curr_index];
574 
575  auto centroid_diff1 = centroidRegionDistance(new_grain._bboxes, old_grain._bboxes);
576  auto centroid_diff2 = centroidRegionDistance(new_grain._bboxes, other_old_grain._bboxes);
577 
578  auto & inactive_grain = (centroid_diff1 < centroid_diff2) ? other_old_grain : old_grain;
579 
580  inactive_grain._status = Status::INACTIVE;
581  if (_verbosity_level > 0)
582  {
583  _console << COLOR_GREEN << "Marking Grain " << inactive_grain._id
584  << " as INACTIVE (variable index: " << inactive_grain._var_index << ")\n"
585  << COLOR_DEFAULT;
586  if (_verbosity_level > 1)
587  _console << inactive_grain;
588  }
589 
595  if (&inactive_grain == &other_old_grain)
596  new_grain_index_to_existing_grain_index[closest_match_index] = old_grain_index;
597  }
598  else
599  new_grain_index_to_existing_grain_index[closest_match_index] = old_grain_index;
600  }
601  }
602 
603  // Mark all resolved grain matches
604  for (auto new_index = beginIndex(new_grain_index_to_existing_grain_index);
605  new_index < new_grain_index_to_existing_grain_index.size();
606  ++new_index)
607  {
608  auto curr_index = new_grain_index_to_existing_grain_index[new_index];
609 
610  // This may be a new grain, we'll handle that case below
611  if (curr_index == invalid_size_t)
612  continue;
613 
614  mooseAssert(_feature_sets_old[curr_index]._id != invalid_id,
615  "Invalid ID in old grain structure");
616 
617  _feature_sets[new_index]._id = _feature_sets_old[curr_index]._id; // Transfer ID
618  _feature_sets[new_index]._status = Status::MARKED; // Mark the status in the new set
619  _feature_sets_old[curr_index]._status = Status::MARKED; // Mark the status in the old set
620  }
621 
636  // Case 1 (new grains in _feature_sets):
637  for (auto grain_num = beginIndex(_feature_sets); grain_num < _feature_sets.size(); ++grain_num)
638  {
639  auto & grain = _feature_sets[grain_num];
640 
641  // New Grain
642  if (grain._status == Status::CLEAR)
643  {
662  // clang-format off
663  auto start_it =
664  std::lower_bound(_feature_sets.begin(), _feature_sets.end(), grain._var_index,
665  [](const FeatureData & item, std::size_t var_index)
666  {
667  return item._var_index < var_index;
668  });
669  // clang-format on
670 
671  // Loop over matching variable indices
672  for (decltype(_feature_sets.size()) new_grain_index =
673  std::distance(_feature_sets.begin(), start_it);
674  new_grain_index < _feature_sets.size() &&
675  _feature_sets[new_grain_index]._var_index == grain._var_index;
676  ++new_grain_index)
677  {
678  auto & other_grain = _feature_sets[new_grain_index];
679 
680  // Splitting grain?
681  if (grain_num != new_grain_index && // Make sure indices aren't pointing at the same grain
682  other_grain._status == Status::MARKED && // and that the other grain is indeed marked
683  other_grain.boundingBoxesIntersect(grain) && // and the bboxes intersect
684  other_grain.halosIntersect(grain)) // and the halos also intersect
685  // TODO: Inspect combined volume and see if it's "close" to the expected value
686  {
687  grain._id = other_grain._id; // Set the duplicate ID
688  grain._status = Status::MARKED; // Mark it
689 
690  if (_verbosity_level > 0)
691  _console << COLOR_YELLOW << "Split Grain Detected #" << grain._id
692  << " (variable index: " << grain._var_index << ")\n"
693  << COLOR_DEFAULT;
694  if (_verbosity_level > 1)
695  _console << grain << other_grain;
696  }
697  }
698 
699  if (grain._var_index < _reserve_op_index)
700  {
719  if (_verbosity_level > 1)
720  _console << COLOR_YELLOW
721  << "Trying harder to detect a split grain while examining grain on variable "
722  "index "
723  << grain._var_index << '\n'
724  << COLOR_DEFAULT;
725 
726  std::vector<std::size_t> old_grain_indices;
727  for (auto old_grain_index = beginIndex(_feature_sets_old);
728  old_grain_index < _feature_sets_old.size();
729  ++old_grain_index)
730  {
731  auto & old_grain = _feature_sets_old[old_grain_index];
732 
733  if (old_grain._status == Status::INACTIVE)
734  continue;
735 
741  if (grain._var_index == old_grain._var_index &&
742  grain.boundingBoxesIntersect(old_grain) && grain.halosIntersect(old_grain))
743  old_grain_indices.push_back(old_grain_index);
744  }
745 
746  if (old_grain_indices.size() == 1)
747  {
748  grain._id = _feature_sets_old[old_grain_indices[0]]._id;
749  grain._status = Status::MARKED;
750 
751  if (_verbosity_level > 0)
752  _console << COLOR_YELLOW << "Split Grain Detected #" << grain._id
753  << " (variable index: " << grain._var_index << ")\n"
754  << COLOR_DEFAULT;
755  }
756  else if (old_grain_indices.size() > 1)
757  _console
758  << COLOR_RED << "Split Grain Likely Detected #" << grain._id
759  << " Need more information to find correct candidate - contact a developer!\n\n"
760  << COLOR_DEFAULT;
761  }
762 
763  // Must be a nucleating grain (status is still not set)
764  if (grain._status == Status::CLEAR)
765  {
766  auto new_index = getNextUniqueID();
767  grain._id = new_index; // Set the ID
768  grain._status = Status::MARKED; // Mark it
769 
770  if (_verbosity_level > 0)
771  _console << COLOR_YELLOW << "Nucleating Grain Detected "
772  << " (variable index: " << grain._var_index << ")\n"
773  << COLOR_DEFAULT;
774  if (_verbosity_level > 1)
775  _console << grain;
776  }
777  }
778  }
779 
780  // Case 2 (inactive grains in _feature_sets_old)
781  for (auto & grain : _feature_sets_old)
782  {
783  if (grain._status == Status::CLEAR)
784  {
785  grain._status = Status::INACTIVE;
786  if (_verbosity_level > 0)
787  {
788  _console << COLOR_GREEN << "Marking Grain " << grain._id
789  << " as INACTIVE (variable index: " << grain._var_index << ")\n"
790  << COLOR_DEFAULT;
791  if (_verbosity_level > 1)
792  _console << grain;
793  }
794  }
795  }
796  } // is_master
797 
798  /*************************************************************
799  ****************** COLLECTIVE WORK SECTION ******************
800  *************************************************************/
801 
802  // Make IDs on all non-master ranks consistent
804 
805  // Build up an id to index map
806  _communicator.broadcast(_max_curr_grain_id);
808 
813  {
814  for (auto new_id = _old_max_grain_id + 1; new_id <= _max_curr_grain_id; ++new_id)
815  {
816  // Don't trigger the callback on the reserve IDs
818  {
819  // See if we've been instructed to terminate with an error
821  mooseError(
822  "Error: New grain detected and \"error_on_new_grain_creation\" is set to true");
823  else
824  newGrainCreated(new_id);
825  }
826  }
827  }
828 }
static const std::size_t invalid_size_t
bool & _first_time
Boolean to indicate the first time this object executes.
Definition: GrainTracker.h:225
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
std::vector< FeatureData > _feature_sets_old
This data structure holds the map of unique grains from the previous time step.
Definition: GrainTracker.h:211
const bool _error_on_grain_creation
Boolean to terminate with an error if a new grain is created during the simulation.
Definition: GrainTracker.h:232
unsigned int _old_max_grain_id
The previous max grain id (needed to figure out which ids are new in a given step) ...
Definition: GrainTracker.h:239
unsigned int & _max_curr_grain_id
Holds the next "regular" grain ID (a grain found or remapped to the standard op vars) ...
Definition: GrainTracker.h:242
const bool _is_master
Convenience variable for testing master rank.
Real centroidRegionDistance(std::vector< MeshTools::BoundingBox > &bboxes1, std::vector< MeshTools::BoundingBox > &bboxes2) const
This method returns the minimum periodic distance between the centroids of two vectors of bounding bo...
const std::size_t _maps_size
Convenience variable holding the size of all the datastructures size by the number of maps...
const short _verbosity_level
Verbosity level controlling the amount of information printed to the console.
Definition: GrainTracker.h:219
static const unsigned int invalid_id
const PerfID _track_grains
Definition: GrainTracker.h:253
std::vector< unsigned int > _feature_counts_per_map
The number of features seen by this object per map.
unsigned int _reserve_grain_first_index
Holds the first unique grain index when using _reserve_op (all the remaining indices are sequential) ...
Definition: GrainTracker.h:236
const std::size_t _reserve_op_index
The cutoff index where if variable index >= this number, no remapping TO that variable will occur...
Definition: GrainTracker.h:193
void buildFeatureIdToLocalIndices(unsigned int max_id)
This method builds a lookup map for retrieving the right local feature (by index) given a global inde...
void scatterAndUpdateRanks()
Calls buildLocalToGlobalIndices to build the individual local to global indicies for each rank and sc...
virtual void newGrainCreated(unsigned int new_grain_id)
This method is called when a new grain is detected.
Definition: GrainTracker.C:831
unsigned int getNextUniqueID()
Retrieve the next unique grain number if a new grain is detected during trackGrains.
const unsigned short _n_reserve_ops
The number of reserved order parameters.
Definition: GrainTracker.h:189

◆ updateFieldInfo()

void GrainTracker::updateFieldInfo ( )
overrideprotectedvirtual

This method is used to populate any of the data structures used for storing field data (nodal or elemental).

It is called at the end of finalize and can make use of any of the data structures created during the execution of this postprocessor.

Reimplemented from FeatureFloodCount.

Definition at line 1506 of file GrainTracker.C.

Referenced by finalize().

1507 {
1508  TIME_SECTION(_update_field_info);
1509 
1510  for (auto map_num = decltype(_maps_size)(0); map_num < _maps_size; ++map_num)
1511  _feature_maps[map_num].clear();
1512 
1513  std::map<dof_id_type, Real> tmp_map;
1514 
1515  for (const auto & grain : _feature_sets)
1516  {
1517  std::size_t curr_var = grain._var_index;
1518  std::size_t map_index = (_single_map_mode || _condense_map_info) ? 0 : curr_var;
1519 
1520  for (auto entity : grain._local_ids)
1521  {
1522  // Highest variable value at this entity wins
1523  Real entity_value = std::numeric_limits<Real>::lowest();
1524  if (_is_elemental)
1525  {
1526  const Elem * elem = _mesh.elemPtr(entity);
1527  std::vector<Point> centroid(1, elem->centroid());
1528  if (_poly_ic_uo && _first_time)
1529  {
1530  entity_value = _poly_ic_uo->getVariableValue(grain._var_index, centroid[0]);
1531  }
1532  else
1533  {
1534  _fe_problem.reinitElemPhys(elem, centroid, 0, /* suppress_displaced_init = */ true);
1535  entity_value = _vars[curr_var]->sln()[0];
1536  }
1537  }
1538  else
1539  {
1540  auto node_ptr = _mesh.nodePtr(entity);
1541  entity_value = _vars[curr_var]->getNodalValue(*node_ptr);
1542  }
1543 
1544  if (entity_value != std::numeric_limits<Real>::lowest() &&
1545  (tmp_map.find(entity) == tmp_map.end() || entity_value > tmp_map[entity]))
1546  {
1547  mooseAssert(grain._id != invalid_id, "Missing Grain ID");
1548  _feature_maps[map_index][entity] = grain._id;
1549 
1550  if (_var_index_mode)
1551  _var_index_maps[map_index][entity] = grain._var_index;
1552 
1553  tmp_map[entity] = entity_value;
1554  }
1555 
1557  {
1558  auto insert_pair = moose_try_emplace(
1559  _entity_var_to_features, entity, std::vector<unsigned int>(_n_vars, invalid_id));
1560  auto & vec_ref = insert_pair.first->second;
1561 
1562  if (insert_pair.second)
1563  {
1564  // insert the reserve op numbers (if appropriate)
1565  for (auto reserve_index = decltype(_n_reserve_ops)(0); reserve_index < _n_reserve_ops;
1566  ++reserve_index)
1567  vec_ref[reserve_index] = _reserve_grain_first_index + reserve_index;
1568  }
1569  vec_ref[grain._var_index] = grain._id;
1570  }
1571  }
1572 
1573  if (_compute_halo_maps)
1574  for (auto entity : grain._halo_ids)
1575  _halo_ids[grain._var_index][entity] = grain._var_index;
1576 
1577  for (auto entity : grain._ghosted_ids)
1578  _ghosted_entity_ids[entity] = 1;
1579  }
1580 
1582 }
const std::size_t _n_vars
const bool _condense_map_info
virtual Real getVariableValue(unsigned int op_index, const Point &p) const =0
Returns the variable value for a given op_index and mesh point.
bool & _first_time
Boolean to indicate the first time this object executes.
Definition: GrainTracker.h:225
std::vector< FeatureData > & _feature_sets
The data structure used to hold the globally unique features.
std::map< dof_id_type, std::vector< unsigned int > > _entity_var_to_features
std::map< dof_id_type, int > _ghosted_entity_ids
The map for holding reconstructed ghosted element information.
void communicateHaloMap()
std::vector< std::map< dof_id_type, int > > _halo_ids
The data structure for looking up halos around features.
std::vector< MooseVariable * > _vars
The vector of coupled in variables cast to MooseVariable.
const PolycrystalUserObjectBase * _poly_ic_uo
An optional IC UserObject which can provide initial data structures to this object.
Definition: GrainTracker.h:214
const std::size_t _maps_size
Convenience variable holding the size of all the datastructures size by the number of maps...
static const unsigned int invalid_id
std::vector< std::map< dof_id_type, int > > _feature_maps
The feature maps contain the raw flooded node information and eventually the unique grain numbers...
const bool _single_map_mode
This variable is used to indicate whether or not multiple maps are used during flooding.
const bool _compute_halo_maps
Indicates whether or not to communicate halo map information with all ranks.
const bool _is_elemental
Determines if the flood counter is elements or not (nodes)
const PerfID _update_field_info
Definition: GrainTracker.h:255
unsigned int _reserve_grain_first_index
Holds the first unique grain index when using _reserve_op (all the remaining indices are sequential) ...
Definition: GrainTracker.h:236
MooseMesh & _mesh
A reference to the mesh.
const bool _compute_var_to_feature_map
Indicates whether or not the var to feature map is populated.
const bool _var_index_mode
This variable is used to indicate whether the maps will contain unique region information or just the...
std::vector< std::map< dof_id_type, int > > _var_index_maps
This map keeps track of which variables own which nodes.
const unsigned short _n_reserve_ops
The number of reserved order parameters.
Definition: GrainTracker.h:189

◆ updateRegionOffsets()

void FeatureFloodCount::updateRegionOffsets ( )
protectedinherited

This routine updates the _region_offsets variable which is useful for quickly determining the proper global number for a feature when using multimap mode.

◆ visitElementalNeighbors()

void FeatureFloodCount::visitElementalNeighbors ( const Elem *  elem,
FeatureData feature,
bool  expand_halos_only,
bool  disjoint_only 
)
protectedinherited

Retrieve only the active neighbors for each side of this element, append them to the list of active neighbors

If the current element (passed into this method) doesn't have a connected neighbor but does have a topological neighbor, this might be a new disjoint region that we'll need to represent with a separate bounding box. To find out for sure, we'll need see if the new neighbors are present in any of the halo or disjoint halo sets. If they are not present, this is a new region.

This neighbor is NULL which means we need to expand the bounding box here in case this grain is up against multiple domain edges so we don't end up with a degenerate bounding box.

Definition at line 1485 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::expandEdgeHalos(), and FeatureFloodCount::flood().

1489 {
1490  mooseAssert(elem, "Elem is NULL");
1491 
1492  std::vector<const Elem *> all_active_neighbors;
1493  MeshBase & mesh = _mesh.getMesh();
1494 
1495  // Loop over all neighbors (at the the same level as the current element)
1496  for (auto i = decltype(elem->n_neighbors())(0); i < elem->n_neighbors(); ++i)
1497  {
1498  const Elem * neighbor_ancestor = nullptr;
1499  bool topological_neighbor = false;
1500 
1505  neighbor_ancestor = elem->neighbor(i);
1506  if (neighbor_ancestor)
1507  {
1508  if (neighbor_ancestor == libMesh::remote_elem)
1509  continue;
1510 
1511  neighbor_ancestor->active_family_tree_by_neighbor(all_active_neighbors, elem, false);
1512  }
1513  else
1514  {
1515  neighbor_ancestor = elem->topological_neighbor(i, mesh, *_point_locator, _pbs);
1516 
1524  if (neighbor_ancestor)
1525  {
1526  neighbor_ancestor->active_family_tree_by_topological_neighbor(
1527  all_active_neighbors, elem, mesh, *_point_locator, _pbs, false);
1528 
1529  topological_neighbor = true;
1530  }
1531  else
1532  {
1538  updateBBoxExtremesHelper(feature->_bboxes[0], *elem);
1539  }
1540  }
1541 
1542  visitNeighborsHelper(elem,
1543  all_active_neighbors,
1544  feature,
1545  expand_halos_only,
1546  topological_neighbor,
1547  disjoint_only);
1548 
1549  all_active_neighbors.clear();
1550  }
1551 }
void updateBBoxExtremesHelper(MeshTools::BoundingBox &bbox, const Point &node)
std::unique_ptr< PointLocatorBase > _point_locator
PeriodicBoundaries * _pbs
A pointer to the periodic boundary constraints object.
void visitNeighborsHelper(const T *curr_entity, std::vector< const T *> neighbor_entities, FeatureData *feature, bool expand_halos_only, bool topological_neighbor, bool disjoint_only)
The actual logic for visiting neighbors is abstracted out here.
MooseMesh & _mesh
A reference to the mesh.

◆ visitNeighborsHelper()

template<typename T >
void FeatureFloodCount::visitNeighborsHelper ( const T *  curr_entity,
std::vector< const T *>  neighbor_entities,
FeatureData feature,
bool  expand_halos_only,
bool  topological_neighbor,
bool  disjoint_only 
)
protectedinherited

The actual logic for visiting neighbors is abstracted out here.

This method is templated to handle the Nodal and Elemental cases together.

Only recurse where we own this entity and it's a topologically connected entity. We shouldn't even attempt to flood to the periodic boundary because we won't have solution information and if we are using DistributedMesh we probably won't have geometric information either.

When we only recurse on entities we own, we can never get more than one away from a local entity which should be in the ghosted zone.

Premark neighboring entities with a halo mark. These entities may or may not end up being part of the feature. We will not update the _entities_visited data structure here.

Definition at line 1568 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::visitElementalNeighbors(), and FeatureFloodCount::visitNodalNeighbors().

1574 {
1575  // Loop over all active element neighbors
1576  for (const auto neighbor : neighbor_entities)
1577  {
1578  if (neighbor && (!_is_boundary_restricted || isBoundaryEntity(neighbor)))
1579  {
1580  if (expand_halos_only)
1581  {
1582  auto entity_id = neighbor->id();
1583 
1584  if (topological_neighbor || disjoint_only)
1585  feature->_disjoint_halo_ids.insert(feature->_disjoint_halo_ids.end(), entity_id);
1586  else if (feature->_local_ids.find(entity_id) == feature->_local_ids.end())
1587  feature->_halo_ids.insert(feature->_halo_ids.end(), entity_id);
1588  }
1589  else
1590  {
1591  auto my_processor_id = processor_id();
1592 
1593  if (!topological_neighbor && neighbor->processor_id() != my_processor_id)
1594  feature->_ghosted_ids.insert(feature->_ghosted_ids.end(), curr_entity->id());
1595 
1605  if (curr_entity->processor_id() == my_processor_id ||
1606  neighbor->processor_id() == my_processor_id)
1607  {
1614  if (topological_neighbor || disjoint_only)
1615  feature->_disjoint_halo_ids.insert(feature->_disjoint_halo_ids.end(), neighbor->id());
1616  else
1617  _entity_queue.push_front(neighbor);
1618  }
1619  }
1620  }
1621  }
1622 }
bool isBoundaryEntity(const T *entity) const
Returns a Boolean indicating whether the entity is on one of the desired boundaries.
bool _is_boundary_restricted
Indicates that this object should only run on one or more boundaries.
std::deque< const DofObject * > _entity_queue
The data structure for maintaining entities to flood during discovery.

◆ visitNodalNeighbors()

void FeatureFloodCount::visitNodalNeighbors ( const Node *  node,
FeatureData feature,
bool  expand_halos_only 
)
protectedinherited

These two routines are utility routines used by the flood routine and by derived classes for visiting neighbors.

Since the logic is different for the elemental versus nodal case it's easier to split them up.

Definition at line 1554 of file FeatureFloodCount.C.

Referenced by FeatureFloodCount::expandEdgeHalos(), and FeatureFloodCount::flood().

1557 {
1558  mooseAssert(node, "Node is NULL");
1559 
1560  std::vector<const Node *> all_active_neighbors;
1561  MeshTools::find_nodal_neighbors(_mesh.getMesh(), *node, _nodes_to_elem_map, all_active_neighbors);
1562 
1563  visitNeighborsHelper(node, all_active_neighbors, feature, expand_halos_only, false, false);
1564 }
std::vector< std::vector< const Elem * > > _nodes_to_elem_map
The data structure used to find neighboring elements give a node ID.
void visitNeighborsHelper(const T *curr_entity, std::vector< const T *> neighbor_entities, FeatureData *feature, bool expand_halos_only, bool topological_neighbor, bool disjoint_only)
The actual logic for visiting neighbors is abstracted out here.
MooseMesh & _mesh
A reference to the mesh.

Member Data Documentation

◆ _all_boundary_entity_ids

std::set<dof_id_type> FeatureFloodCount::_all_boundary_entity_ids
protectedinherited

The set of entities on the boundary of the domain used for determining if features intersect any boundary.

Definition at line 692 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::flood(), and FeatureFloodCount::meshChanged().

◆ _all_ranges

std::vector<std::pair<dof_id_type, dof_id_type> > GrainTracker::_all_ranges
private

Data structure to hold element ID ranges when using Distributed Mesh (populated on rank 0 only)

Definition at line 248 of file GrainTracker.h.

Referenced by communicateHaloMap(), and meshChanged().

◆ _bnd_elem_range

ConstBndElemRange* FeatureFloodCount::_bnd_elem_range
protectedinherited

Boundary element range pointer (used when boundary restricting this object.

Definition at line 705 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::execute(), and FeatureFloodCount::isBoundaryEntity().

◆ _broadcast_update

const PerfID GrainTracker::_broadcast_update
private

Definition at line 254 of file GrainTracker.h.

Referenced by broadcastAndUpdateGrainData().

◆ _compute_halo_maps

const bool FeatureFloodCount::_compute_halo_maps
protectedinherited

Indicates whether or not to communicate halo map information with all ranks.

Definition at line 585 of file FeatureFloodCount.h.

Referenced by communicateHaloMap(), meshChanged(), updateFieldInfo(), and FeatureFloodCount::updateFieldInfo().

◆ _compute_var_to_feature_map

const bool FeatureFloodCount::_compute_var_to_feature_map
protectedinherited

Indicates whether or not the var to feature map is populated.

Definition at line 588 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::getVarToFeatureVector(), updateFieldInfo(), and FeatureFloodCount::updateFieldInfo().

◆ _condense_map_info

const bool FeatureFloodCount::_condense_map_info
protectedinherited

Definition at line 574 of file FeatureFloodCount.h.

Referenced by updateFieldInfo(), and FeatureFloodCount::updateFieldInfo().

◆ _connecting_threshold

const Real FeatureFloodCount::_connecting_threshold
protectedinherited

The threshold above (or below) which neighboring entities are flooded (where regions can be extended but not started)

Definition at line 558 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::initialize().

◆ _dof_map

const DofMap& FeatureFloodCount::_dof_map
protectedinherited

Reference to the dof_map containing the coupled variables.

Definition at line 550 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::flood().

◆ _element_average_value

const PostprocessorValue& FeatureFloodCount::_element_average_value
protectedinherited

Average value of the domain which can optionally be used to find features in a field.

Definition at line 673 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::initialize().

◆ _empty_var_to_features

std::vector<unsigned int> FeatureFloodCount::_empty_var_to_features
protectedinherited

◆ _entities_visited

std::vector<std::set<dof_id_type> > FeatureFloodCount::_entities_visited
protectedinherited

This variable keeps track of which nodes have been visited during execution.

We don't use the _feature_map for this since we don't want to explicitly store data for all the unmarked nodes in a serialized datastructures. This keeps our overhead down since this variable never needs to be communicated.

Definition at line 612 of file FeatureFloodCount.h.

Referenced by PolycrystalUserObjectBase::execute(), FeatureFloodCount::flood(), FeatureFloodCount::initialize(), FeatureFloodCount::initialSetup(), and PolycrystalUserObjectBase::isNewFeatureOrConnectedRegion().

◆ _entity_var_to_features

std::map<dof_id_type, std::vector<unsigned int> > FeatureFloodCount::_entity_var_to_features
protectedinherited

◆ _error_on_grain_creation

const bool GrainTracker::_error_on_grain_creation
protected

Boolean to terminate with an error if a new grain is created during the simulation.

This is for simulations where new grains are not expected. Note, this does not impact the initial callback to newGrainCreated() nor does it get triggered for splitting grains.

Definition at line 232 of file GrainTracker.h.

Referenced by trackGrains().

◆ _fe_vars

std::vector<MooseVariableFEBase *> FeatureFloodCount::_fe_vars
protectedinherited

The vector of coupled in variables.

Definition at line 545 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::FeatureFloodCount(), and FeatureFloodCount::getFECoupledVars().

◆ _feature_count

unsigned int FeatureFloodCount::_feature_count
protectedinherited

◆ _feature_counts_per_map

std::vector<unsigned int> FeatureFloodCount::_feature_counts_per_map
protectedinherited

The number of features seen by this object per map.

Definition at line 626 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::consolidateMergedFeatures(), FeatureFloodCount::sortAndLabel(), and trackGrains().

◆ _feature_id_to_local_index

std::vector<std::size_t> FeatureFloodCount::_feature_id_to_local_index
protectedinherited

◆ _feature_maps

std::vector<std::map<dof_id_type, int> > FeatureFloodCount::_feature_maps
protectedinherited

The feature maps contain the raw flooded node information and eventually the unique grain numbers.

We have a vector of them so we can create one per variable if that level of detail is desired.

Definition at line 659 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::getEntityValue(), FeatureFloodCount::initialize(), updateFieldInfo(), and FeatureFloodCount::updateFieldInfo().

◆ _feature_sets

std::vector<FeatureData>& FeatureFloodCount::_feature_sets
protectedinherited

◆ _feature_sets_old

std::vector<FeatureData> GrainTracker::_feature_sets_old
protected

This data structure holds the map of unique grains from the previous time step.

The information is updated each timestep to track grains over time.

Definition at line 211 of file GrainTracker.h.

Referenced by initialize(), and trackGrains().

◆ _finalize_timer

const PerfID GrainTracker::_finalize_timer
private

Timers.

Definition at line 251 of file GrainTracker.h.

Referenced by finalize().

◆ _first_time

bool& GrainTracker::_first_time
protected

Boolean to indicate the first time this object executes.

Note: _tracking_step isn't enough if people skip initial or execute more than once per step.

Definition at line 225 of file GrainTracker.h.

Referenced by assignGrains(), execute(), finalize(), initialize(), newGrainCreated(), prepopulateState(), trackGrains(), and updateFieldInfo().

◆ _ghosted_entity_ids

std::map<dof_id_type, int> FeatureFloodCount::_ghosted_entity_ids
protectedinherited

The map for holding reconstructed ghosted element information.

Definition at line 676 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::getEntityValue(), FeatureFloodCount::initialize(), updateFieldInfo(), and FeatureFloodCount::updateFieldInfo().

◆ _global_numbering

const bool FeatureFloodCount::_global_numbering
protectedinherited

This variable is used to indicate whether or not we identify features with unique numbers on multiple maps.

Definition at line 578 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::updateFieldInfo().

◆ _halo_ids

std::vector<std::map<dof_id_type, int> > FeatureFloodCount::_halo_ids
protectedinherited

The data structure for looking up halos around features.

The outer vector is for splitting out the information per variable. The inner map holds the actual halo information

Definition at line 682 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::FeatureData::clear(), communicateHaloMap(), FeatureFloodCount::getEntityValue(), FeatureFloodCount::FeatureData::halosIntersect(), FeatureFloodCount::initialize(), FeatureFloodCount::FeatureData::merge(), updateFieldInfo(), and FeatureFloodCount::updateFieldInfo().

◆ _halo_level

const unsigned short GrainTracker::_halo_level
protected

The thickness of the halo surrounding each grain.

Definition at line 183 of file GrainTracker.h.

Referenced by finalize().

◆ _is_boundary_restricted

bool FeatureFloodCount::_is_boundary_restricted
protectedinherited

Indicates that this object should only run on one or more boundaries.

Definition at line 702 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::execute(), FeatureFloodCount::FeatureFloodCount(), and FeatureFloodCount::visitNeighborsHelper().

◆ _is_elemental

const bool FeatureFloodCount::_is_elemental
protectedinherited

◆ _is_master

const bool FeatureFloodCount::_is_master
protectedinherited

◆ _is_transient

const bool GrainTracker::_is_transient
private

Boolean to indicate whether this is a Steady or Transient solve.

Definition at line 245 of file GrainTracker.h.

Referenced by swapSolutionValuesHelper().

◆ _local_to_global_feature_map

std::vector<std::size_t> FeatureFloodCount::_local_to_global_feature_map
protectedinherited

The vector recording the local to global feature indices.

Definition at line 662 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::scatterAndUpdateRanks().

◆ _maps_size

const std::size_t FeatureFloodCount::_maps_size
protectedinherited

◆ _max_curr_grain_id

unsigned int& GrainTracker::_max_curr_grain_id
private

Holds the next "regular" grain ID (a grain found or remapped to the standard op vars)

Definition at line 242 of file GrainTracker.h.

Referenced by assignGrains(), getNewGrainIDs(), getNextUniqueID(), getTotalFeatureCount(), and trackGrains().

◆ _max_remap_recursion_depth

const unsigned short GrainTracker::_max_remap_recursion_depth
protected

Depth of renumbering recursion (a depth of zero means no recursion)

Definition at line 186 of file GrainTracker.h.

Referenced by remapGrains().

◆ _mesh

MooseMesh& FeatureFloodCount::_mesh
protectedinherited

◆ _n_procs

const processor_id_type FeatureFloodCount::_n_procs
protectedinherited

Convenience variable holding the number of processors in this simulation.

Definition at line 604 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::buildLocalToGlobalIndices(), and communicateHaloMap().

◆ _n_reserve_ops

const unsigned short GrainTracker::_n_reserve_ops
protected

The number of reserved order parameters.

Definition at line 189 of file GrainTracker.h.

Referenced by getNextUniqueID(), trackGrains(), and updateFieldInfo().

◆ _n_vars

const std::size_t FeatureFloodCount::_n_vars
protectedinherited

◆ _nl

NonlinearSystemBase& GrainTracker::_nl
protected

A reference to the nonlinear system (used for retrieving solution vectors)

Definition at line 205 of file GrainTracker.h.

Referenced by remapGrains(), and swapSolutionValuesHelper().

◆ _nodes_to_elem_map

std::vector<std::vector<const Elem *> > FeatureFloodCount::_nodes_to_elem_map
protectedinherited

The data structure used to find neighboring elements give a node ID.

Definition at line 623 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::meshChanged(), and FeatureFloodCount::visitNodalNeighbors().

◆ _old_max_grain_id

unsigned int GrainTracker::_old_max_grain_id
private

The previous max grain id (needed to figure out which ids are new in a given step)

Definition at line 239 of file GrainTracker.h.

Referenced by getNewGrainIDs(), and trackGrains().

◆ _partial_feature_sets

std::vector<std::list<FeatureData> > FeatureFloodCount::_partial_feature_sets
protectedinherited

The data structure used to hold partial and communicated feature data, during the discovery and merging phases.

The outer vector is indexed by map number (often variable number). The inner list is an unordered list of partially discovered features.

Definition at line 636 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::communicateAndMerge(), FeatureFloodCount::consolidateMergedFeatures(), FeatureFloodCount::deserialize(), FeatureFloodCount::expandEdgeHalos(), FeatureFloodCount::expandPointHalos(), FeatureFloodCount::flood(), FeatureFloodCount::initialize(), PolycrystalUserObjectBase::mergeSets(), FeatureFloodCount::mergeSets(), FeatureFloodCount::prepareDataForTransfer(), prepopulateState(), FeatureFloodCount::scatterAndUpdateRanks(), and FeatureFloodCount::serialize().

◆ _pbs

PeriodicBoundaries* FeatureFloodCount::_pbs
protectedinherited

◆ _periodic_node_map

std::multimap<dof_id_type, dof_id_type> FeatureFloodCount::_periodic_node_map
protectedinherited

The data structure which is a list of nodes that are constrained to other nodes based on the imposed periodic boundary conditions.

Definition at line 688 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::appendPeriodicNeighborNodes(), FauxGrainTracker::getEntityValue(), FeatureFloodCount::getEntityValue(), and FeatureFloodCount::meshChanged().

◆ _point_locator

std::unique_ptr<PointLocatorBase> FeatureFloodCount::_point_locator
protectedinherited

◆ _poly_ic_uo

const PolycrystalUserObjectBase* GrainTracker::_poly_ic_uo
protected

An optional IC UserObject which can provide initial data structures to this object.

Definition at line 214 of file GrainTracker.h.

Referenced by execute(), finalize(), GrainTracker(), and updateFieldInfo().

◆ _remap

const bool GrainTracker::_remap
protected

Inidicates whether remapping should be done or not (remapping is independent of tracking)

Definition at line 199 of file GrainTracker.h.

Referenced by finalize().

◆ _remap_timer

const PerfID GrainTracker::_remap_timer
private

Definition at line 252 of file GrainTracker.h.

Referenced by remapGrains().

◆ _reserve_grain_first_index

unsigned int GrainTracker::_reserve_grain_first_index
private

Holds the first unique grain index when using _reserve_op (all the remaining indices are sequential)

Definition at line 236 of file GrainTracker.h.

Referenced by assignGrains(), getNextUniqueID(), trackGrains(), and updateFieldInfo().

◆ _reserve_op_index

const std::size_t GrainTracker::_reserve_op_index
protected

The cutoff index where if variable index >= this number, no remapping TO that variable will occur.

Definition at line 193 of file GrainTracker.h.

Referenced by computeMinDistancesFromGrain(), getThreshold(), remapGrains(), and trackGrains().

◆ _reserve_op_threshold

const Real GrainTracker::_reserve_op_threshold
protected

The threshold above (or below) where a grain may be found on a reserve op field.

Definition at line 196 of file GrainTracker.h.

Referenced by getThreshold().

◆ _single_map_mode

const bool FeatureFloodCount::_single_map_mode
protectedinherited

This variable is used to indicate whether or not multiple maps are used during flooding.

Definition at line 572 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::flood(), PolycrystalUserObjectBase::PolycrystalUserObjectBase(), FeatureFloodCount::sortAndLabel(), updateFieldInfo(), and FeatureFloodCount::updateFieldInfo().

◆ _step_connecting_threshold

Real FeatureFloodCount::_step_connecting_threshold
protectedinherited

◆ _step_threshold

Real FeatureFloodCount::_step_threshold
protectedinherited

◆ _threshold

const Real FeatureFloodCount::_threshold
protectedinherited

The threshold above (or below) where an entity may begin a new region (feature)

Definition at line 553 of file FeatureFloodCount.h.

Referenced by FauxGrainTracker::execute(), and FeatureFloodCount::initialize().

◆ _tolerate_failure

const bool GrainTracker::_tolerate_failure
protected

Indicates whether we should continue after a remap failure (will result in non-physical results)

Definition at line 202 of file GrainTracker.h.

Referenced by GrainTracker(), and remapGrains().

◆ _track_grains

const PerfID GrainTracker::_track_grains
private

Definition at line 253 of file GrainTracker.h.

Referenced by trackGrains().

◆ _tracking_step

const int GrainTracker::_tracking_step
protected

The timestep to begin tracking grains.

Definition at line 180 of file GrainTracker.h.

Referenced by execute(), finalize(), getEntityValue(), GrainTracker(), initialize(), and remapGrains().

◆ _update_field_info

const PerfID GrainTracker::_update_field_info
private

Definition at line 255 of file GrainTracker.h.

Referenced by updateFieldInfo().

◆ _use_less_than_threshold_comparison

const bool FeatureFloodCount::_use_less_than_threshold_comparison
protectedinherited

Use less-than when comparing values against the threshold value.

True by default. If false, then greater-than comparison is used instead.

Definition at line 595 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::compareValueWithThreshold(), and FauxGrainTracker::execute().

◆ _var_index_maps

std::vector<std::map<dof_id_type, int> > FeatureFloodCount::_var_index_maps
protectedinherited

This map keeps track of which variables own which nodes.

We need a vector of them for multimap mode where multiple variables can own a single mode.

Note: This map is only populated when "show_var_coloring" is set to true.

Definition at line 620 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::FeatureFloodCount(), FeatureFloodCount::getEntityValue(), FeatureFloodCount::initialize(), updateFieldInfo(), and FeatureFloodCount::updateFieldInfo().

◆ _var_index_mode

const bool FeatureFloodCount::_var_index_mode
protectedinherited

This variable is used to indicate whether the maps will contain unique region information or just the variable numbers owning those regions.

Definition at line 582 of file FeatureFloodCount.h.

Referenced by FeatureFloodCount::FeatureFloodCount(), FeatureFloodCount::getEntityValue(), FeatureFloodCount::initialize(), updateFieldInfo(), and FeatureFloodCount::updateFieldInfo().

◆ _var_number

unsigned long FeatureFloodCount::_var_number
protectedinherited

This variable is used to build the periodic node map.

Assumption: We are going to assume that either all variables are periodic or none are. This assumption can be relaxed at a later time if necessary.

Definition at line 569 of file FeatureFloodCount.h.

Referenced by centroidRegionDistance(), and FeatureFloodCount::meshChanged().

◆ _vars

std::vector<MooseVariable *> FeatureFloodCount::_vars
protectedinherited

◆ _verbosity_level

const short GrainTracker::_verbosity_level
protected

Verbosity level controlling the amount of information printed to the console.

Definition at line 219 of file GrainTracker.h.

Referenced by attemptGrainRenumber(), finalize(), remapGrains(), and trackGrains().

◆ _volatile_feature_sets

std::vector<FeatureData> FeatureFloodCount::_volatile_feature_sets
protectedinherited

Derived objects (e.g.

the GrainTracker) may require restartable data to track information across time steps. The FeatureFloodCounter however does not. This container is here so that we have the flexabilty to switch between volatile and non-volatile storage. The _feature_sets data structure can conditionally refer to this structure or a MOOSE-provided structure, which is backed up.

Definition at line 652 of file FeatureFloodCount.h.

◆ invalid_id

const unsigned int FeatureFloodCount::invalid_id = std::numeric_limits<unsigned int>::max()
staticinherited

◆ invalid_size_t

const std::size_t FeatureFloodCount::invalid_size_t = std::numeric_limits<std::size_t>::max()
staticinherited

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