MoFEM::BitRefManager Struct Reference

Managing BitRefLevels. More...

#include <src/interfaces/BitRefManager.hpp>

Inheritance diagram for MoFEM::BitRefManager:

Collaboration diagram for MoFEM::BitRefManager:

Public Member Functions
MoFEMErrorCode	query_interface (const MOFEMuuid &uuid, UnknownInterface **iface) const
	BitRefManager (const MoFEM::Core &core)
	~BitRefManager ()
	Destructor. More...
Public Member Functions inherited from MoFEM::UnknownInterface
template<class IFACE >
MoFEMErrorCode	registerInterface (const MOFEMuuid &uuid, bool error_if_registration_failed=true)
	Register interface. More...
template<class IFACE , bool VERIFY = false>
MoFEMErrorCode	getInterface (const MOFEMuuid &uuid, IFACE *&iface) const
	Get interface by uuid and return reference to pointer of interface. More...
template<class IFACE >
MoFEMErrorCode	getInterface (IFACE *&iface) const
	Get interface refernce to pointer of interface. More...
template<class IFACE >
MoFEMErrorCode	getInterface (IFACE **const iface) const
	Get interface pointer to pointer of interface. More...
template<class IFACE , typename boost::enable_if< boost::is_pointer< IFACE >, int >::type = 0>
IFACE	getInterface () const
	Get interface pointer to pointer of interface. More...
template<class IFACE , typename boost::enable_if< boost::is_reference< IFACE >, int >::type = 0>
IFACE	getInterface () const
	Get reference to interface. More...
template<class IFACE >
IFACE *	getInterface () const
	Function returning pointer to interface. More...
virtual	~UnknownInterface ()=default
virtual MoFEMErrorCode	getLibVersion (Version &version) const
	Get library version. More...
virtual const MoFEMErrorCode	getFileVersion (moab::Interface &moab, Version &version) const
	Get database major version. More...
virtual MoFEMErrorCode	getInterfaceVersion (Version &version) const
	Get database major version. More...
template<>
MoFEMErrorCode	getInterface (const MOFEMuuid &uuid, UnknownInterface *&iface) const

Public Attributes
MoFEM::Core &	cOre
bool	dEbug

Setting and shifting bits
MoFEMErrorCode	setBitRefLevel (const Range &ents, const BitRefLevel bit, const bool only_tets=true, int verb=0) const
	add entities to database and set bit ref levelThis function set bit ref level, add entries to core database and create ref finite elements. Finite elements are create of entities in function argument, whereas all lower dimension entities are added as a field entities More...
MoFEMErrorCode	setElementsBitRefLevel (const Range &ents, const BitRefLevel bit=BitRefLevel(), int verb=QUIET) const
	add entities to database and set bit ref level More...
MoFEMErrorCode	setEntitiesBitRefLevel (const Range &ents, const BitRefLevel bit=BitRefLevel(), int verb=QUIET) const
	add entities to database and set bit ref level More...
MoFEMErrorCode	setFieldEntitiesBitRefLevel (const std::string field_name, const BitRefLevel bit=BitRefLevel(), int verb=QUIET) const
	Set the bit ref level to entities in the field meshset. More...
MoFEMErrorCode	setBitRefLevelByDim (const EntityHandle meshset, const int dim, const BitRefLevel bit, int verb=QUIET) const
	Set the Bit Ref Level By Dim object. More...
MoFEMErrorCode	setBitRefLevelByType (const EntityHandle meshset, const EntityType type, const BitRefLevel bit, int verb=QUIET) const
	Set the Bit Ref Level By Type object. More...
MoFEMErrorCode	setBitLevelToMeshset (const EntityHandle meshset, const BitRefLevel bit, int verb=0) const
MoFEMErrorCode	addToDatabaseBitRefLevelByType (const EntityType type, const BitRefLevel bit, const BitRefLevel mask=BitRefLevel().set(), int verb=QUIET) const
	Add entities which exist in MoAB database, and have set appropiate BitRef level tag, to multi-indices in MoFEM. More...
MoFEMErrorCode	addToDatabaseBitRefLevelByDim (const int dim, const BitRefLevel bit, const BitRefLevel mask=BitRefLevel().set(), int verb=QUIET) const
	Add entities which exist in MoAB database, and have set appropiate BitRef level tag, to multi-indices in MoFEM. More...
MoFEMErrorCode	addBitRefLevel (const Range &ents, const BitRefLevel bit, int verb=QUIET) const
	add bit ref level to ref entity More...
MoFEMErrorCode	addBitRefLevelByDim (const EntityHandle meshset, const int dim, const BitRefLevel bit, int verb=QUIET) const
	add bit ref level by dimension More...
MoFEMErrorCode	setNthBitRefLevel (const Range &ents, const int n, const bool b, int verb=0) const
	Set nth bit ref level. More...
MoFEMErrorCode	setNthBitRefLevel (const int n, const bool b, int verb=0) const
	Set nth bit ref level. More...
MoFEMErrorCode	shiftLeftBitRef (const int shift, const BitRefLevel mask=BitRefLevel().set(), int verb=-1) const
	left shift bit ref levelthis results of deletion of entities on far left side More...
MoFEMErrorCode	shiftRightBitRef (const int shift, const BitRefLevel mask=BitRefLevel().set(), int verb=-1) const
	right shift bit ref level More...

Entity handlers by bit ref level
MoFEMErrorCode	filterEntitiesByRefLevel (const BitRefLevel bit, const BitRefLevel mask, Range &ents, int verb=QUIET) const
	filter entities by bit ref level More...
MoFEMErrorCode	getEntitiesByTypeAndRefLevel (const BitRefLevel bit, const BitRefLevel mask, const EntityType type, const EntityHandle meshset, int verb=0) const
	add all ents from ref level given by bit to meshset More...
MoFEMErrorCode	getEntitiesByTypeAndRefLevel (const BitRefLevel bit, const BitRefLevel mask, const EntityType type, Range &ents, int verb=0) const
	add all ents from ref level given by bit to meshset More...
MoFEMErrorCode	getEntitiesByDimAndRefLevel (const BitRefLevel bit, const BitRefLevel mask, const int dim, const EntityHandle meshset, int verb=0) const
	add all ents from ref level given by bit to meshset More...
MoFEMErrorCode	getEntitiesByDimAndRefLevel (const BitRefLevel bit, const BitRefLevel mask, const int dim, Range &ents, int verb=0) const
	add all ents from ref level given by bit to meshset More...
MoFEMErrorCode	getEntitiesByRefLevel (const BitRefLevel bit, const BitRefLevel mask, const EntityHandle meshset, const int verb=QUIET) const
	add all ents from ref level given by bit to meshset More...
MoFEMErrorCode	getEntitiesByRefLevel (const BitRefLevel bit, const BitRefLevel mask, Range &ents, const int verb=QUIET) const
	add all ents from ref level given by bit to meshset More...
MoFEMErrorCode	getEntitiesByParentType (const BitRefLevel bit, const BitRefLevel mask, const EntityType type, Range &ents, const int verb=QUIET) const
	get entities by bit ref level and type of parent More...
MoFEMErrorCode	getAllEntitiesNotInDatabase (Range &ents) const
	Get all entities not in database. More...
MoFEMErrorCode	filterEntitiesNotInDatabase (Range &ents) const
	Get entities not in database. More...

Get adjacencies bit ref level
virtual MoFEMErrorCode	getAdjacenciesEquality (const EntityHandle from_entity, const int to_dimension, Range &adj_entities) const
	Get the adjacencies associated with a entity to entities of a specified dimension.bit ref level of adjacent entities is equal to bit ref level of adjacent entities. More...
virtual MoFEMErrorCode	getAdjacenciesAny (const EntityHandle from_entity, const int to_dimension, Range &adj_entities) const
	Get the adjacencies associated with a entity to entities of a specified dimension.bit ref level of adjacent entities is any of bit ref level of adjacent entities. More...
virtual MoFEMErrorCode	getAdjacencies (const Problem *problem_ptr, const EntityHandle *from_entities, const int num_entities, const int to_dimension, Range &adj_entities, const int operation_type=moab::Interface::INTERSECT, const int verb=0) const
	Get the adjacencies associated with a entity to entities of a specified dimension.bit ref level of adjacent entities is equal to bit ref level of adjacent entities. More...
virtual MoFEMErrorCode	getAdjacencies (const BitRefLevel bit, const EntityHandle *from_entities, const int num_entities, const int to_dimension, Range &adj_entities, const int operation_type=moab::Interface::INTERSECT, const int verb=0) const
	Get the adjacencies associated with a entity to entities of a specified dimension.bit ref level of adjacent entities is equal to bit ref level of adjacent entities. More...

Update meshsets and ranges by children
MoFEMErrorCode	updateMeshsetByEntitiesChildren (const EntityHandle parent, const BitRefLevel &parent_bit, const BitRefLevel &parent_mask, const BitRefLevel &child_bit, const BitRefLevel &child_mask, const EntityHandle child, EntityType child_type, const bool recursive=false, int verb=0)
	Get child entities form meshset containing parent entitiesSearch for refined entities of given type whose parent are entities in the parent meshset. It can be used for example to transfer information about boundary conditions to refined mesh or split mesh by interface elements. It is used by function refine_MESHSET, to update MESHSET finite elements. More...
MoFEMErrorCode	updateMeshsetByEntitiesChildren (const EntityHandle parent, const BitRefLevel &child_bit, const EntityHandle child, EntityType child_type, const bool recursive=false, int verb=0)
	Get child entities form meshset containing parent entities. More...
MoFEMErrorCode	updateFieldMeshsetByEntitiesChildren (const BitRefLevel &child_bit, int verb=0)
	update fields meshesets by child entities More...
MoFEMErrorCode	updateFieldMeshsetByEntitiesChildren (const std::string name, const BitRefLevel &child_bit, int verb=0)
	update field meshset by child entities More...
MoFEMErrorCode	updateFiniteElementMeshsetByEntitiesChildren (const std::string name, const BitRefLevel &child_bit, const EntityType fe_ent_type, int verb=0)
	update finite element meshset by child entities More...
MoFEMErrorCode	updateRange (const Range &parent, Range &child)
	Update range by prents. More...

Writting files
MoFEMErrorCode	writeBitLevelByType (const BitRefLevel bit, const BitRefLevel mask, const EntityType type, const char *file_name, const char *file_type, const char *options, const bool check_for_empty=true) const
	Write bit ref level to file. More...
MoFEMErrorCode	writeEntitiesNotInDatabase (const char *file_name, const char *file_type, const char *options, const bool check_for_empty=true) const
	Write ents not in database. More...
MoFEMErrorCode	writeEntitiesAllBitLevelsByType (const BitRefLevel mask, const EntityType type, const char *file_name, const char *file_type, const char *options)
	Write all entities by bit levels and type. More...

Additional Inherited Members
Protected Member Functions inherited from MoFEM::UnknownInterface
boost::typeindex::type_index	getClassIdx (const MOFEMuuid &uid) const
	Get type name for interface Id. More...
MOFEMuuid	getUId (const boost::typeindex::type_index &class_idx) const
	Get interface Id for class name. More...

Detailed Description

Managing BitRefLevels.

Examples

bernstein_bezier_generate_base.cpp, build_problems.cpp, continuity_check_on_skeleton_3d.cpp, dm_build_partitioned_mesh.cpp, dm_create_subdm.cpp, dm_partitioned_no_field.cpp, elasticity.cpp, elasticity_mixed_formulation.cpp, ep.cpp, field_axpy_atom_test.cpp, field_to_vertices.cpp, forces_and_sources_testing_edge_element.cpp, forces_and_sources_testing_flat_prism_element.cpp, forces_and_sources_testing_users_base.cpp, hcurl_divergence_operator_2d.cpp, mesh_cut.cpp, mesh_insert_interface_atom.cpp, mesh_smoothing.cpp, minimal_surface_area.cpp, prism_elements_from_surface.cpp, prism_polynomial_approximation.cpp, quad_polynomial_approximation.cpp, Remodeling.cpp, remove_entities_from_problem.cpp, split_sideset.cpp, and unsaturated_transport.cpp.

Definition at line 34 of file BitRefManager.hpp.

Constructor & Destructor Documentation

BitRefManager()

MoFEM::BitRefManager::BitRefManager

(

const MoFEM::Core &

core

)

Definition at line 34 of file BitRefManager.cpp.

    : cOre(const_cast<MoFEM::Core &>(core)), dEbug(false) {}

~BitRefManager()

MoFEM::BitRefManager::~BitRefManager

(

)

Destructor.

Definition at line 36 of file BitRefManager.cpp.

{}

Member Function Documentation

filterEntitiesByRefLevel()

MoFEMErrorCode MoFEM::BitRefManager::filterEntitiesByRefLevel	(	const BitRefLevel	bit,
		const BitRefLevel	mask,
		Range &	ents,
		int	verb = QUIET
	)		const

filter entities by bit ref level

Parameters

bit
mask
ents
QUIET

Returns

MoFEMErrorCode

Definition at line 609 of file BitRefManager.cpp.

                                                                       {
  MoFEM::Interface &m_field = cOre;
  moab::Interface &moab(m_field.get_moab());
  MoFEMFunctionBeginHot;

  std::vector<EntityHandle> ents_vec;
  ents_vec.reserve(ents.size());

  std::vector<BitRefLevel *> tags_bits_ptr_vec(ents.size());

  Range swap_ents;
  auto hint = swap_ents.begin();

  for (Range::pair_iterator p_eit = ents.pair_begin(); p_eit != ents.pair_end();
       ++p_eit) {

    EntityHandle f = p_eit->first;
    const EntityHandle s = p_eit->second;

    // get bits on entities
    rval = moab.tag_get_by_ptr(cOre.get_th_RefBitLevel(), Range(f, s),
                             (const void **)(&*tags_bits_ptr_vec.begin()));

    if (rval == MB_SUCCESS) {

      auto bit_it = tags_bits_ptr_vec.begin();

      auto check = [&bit, &mask](const auto &entity_bit) -> bool {
        return

            (entity_bit & bit).any() &&

            ((entity_bit & mask) == entity_bit);
      };

      while (f != s + 1) {

        while (f != s + 1 && !check(**bit_it)) {
          ++bit_it;
          ++f;
        }

        if (f != s + 1) {

          const EntityHandle start = f;

          while (f != (s + 1) && check(**bit_it)) {
            ++bit_it;
            ++f;
          };

          hint = swap_ents.insert(hint, start, f - 1);
        }

      }
    }
  }

  ents.swap(swap_ents);

  MoFEMFunctionReturnHot(0);
}

filterEntitiesNotInDatabase()

MoFEMErrorCode MoFEM::BitRefManager::filterEntitiesNotInDatabase

(

Range &

ents

)

const

Get entities not in database.

Parameters

ents

Returns

MoFEMErrorCode

Definition at line 774 of file BitRefManager.cpp.

                                                                           {
  MoFEM::Interface &m_field = cOre;
  const RefEntity_multiIndex *ref_ents_ptr;
  MoFEMFunctionBeginHot;
  ierr = m_field.get_ref_ents(&ref_ents_ptr);
  CHKERRG(ierr);
  Range::iterator eit = ents.begin();
  for (; eit != ents.end();) {
    RefEntity_multiIndex::index<Ent_mi_tag>::type::iterator rit;
    rit = ref_ents_ptr->get<Ent_mi_tag>().find(*eit);
    if (rit != ref_ents_ptr->get<Ent_mi_tag>().end()) {
      eit = ents.erase(eit);
    } else {
      eit++;
    }
  }
  MoFEMFunctionReturnHot(0);
}

getAllEntitiesNotInDatabase()

MoFEMErrorCode MoFEM::BitRefManager::getAllEntitiesNotInDatabase

(

Range &

ents

)

const

Get all entities not in database.

Parameters

ents

Returns

MoFEMErrorCode

Definition at line 762 of file BitRefManager.cpp.

                                                                           {
  MoFEM::Interface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  MoFEMFunctionBeginHot;
  rval = moab.get_entities_by_handle(0, ents, false);
  CHKERRG(rval);
  ents = subtract(ents, ents.subset_by_type(MBENTITYSET));
  ierr = filterEntitiesNotInDatabase(ents);
  CHKERRG(ierr);
  MoFEMFunctionReturnHot(0);
}

getEntitiesByParentType()

MoFEMErrorCode MoFEM::BitRefManager::getEntitiesByParentType	(	const BitRefLevel	bit,
		const BitRefLevel	mask,
		const EntityType	type,
		Range &	ents,
		const int	verb = QUIET
	)		const

get entities by bit ref level and type of parent

Note

Entities have to be added to MoFEM database

Parameters

BitRefLevel	bitLevel
BitRefLevel	mask
type	of parent
ents	returned ents

Returns

error code

Definition at line 737 of file BitRefManager.cpp.

                                                                            {
  MoFEM::Interface &m_field = cOre;
  const RefEntity_multiIndex *ref_ents_ptr;
  MoFEMFunctionBegin;
  CHKERR m_field.get_ref_ents(&ref_ents_ptr);
  auto &ref_ents = ref_ents_ptr->get<ParentEntType_mi_tag>();
  auto it = ref_ents.lower_bound(type);
  auto hi_it = ref_ents.upper_bound(type);
  std::vector<EntityHandle> ents_vec;
  ents_vec.reserve(std::distance(it, hi_it));
  for (; it != hi_it; it++) {
    const BitRefLevel &ent_bit = it->get()->getBitRefLevel();
    if ((ent_bit & mask) == ent_bit && (ent_bit & bit).any())
      ents_vec.emplace_back(it->get()->getRefEnt());
  }
  ents.insert_list(ents_vec.begin(), ents_vec.end());
  if (verb > NOISY)
    cerr << "getEntitiesByParentType: " << ents << endl;
  MoFEMFunctionReturn(0);
}

query_interface()

MoFEMErrorCode MoFEM::BitRefManager::query_interface ( const MOFEMuuid &  uuid, UnknownInterface **  iface  ) const

virtual

Implements MoFEM::UnknownInterface.

Definition at line 22 of file BitRefManager.cpp.

                                                                              {
  MoFEMFunctionBeginHot;
  *iface = NULL;
  if (uuid == IDD_MOFEMBitRefManager) {
    *iface = const_cast<BitRefManager *>(this);
    MoFEMFunctionReturnHot(0);
  }
  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "unknown interface");
  MoFEMFunctionReturnHot(0);
}

writeBitLevelByType()

MoFEMErrorCode MoFEM::BitRefManager::writeBitLevelByType	(	const BitRefLevel	bit,
		const BitRefLevel	mask,
		const EntityType	type,
		const char *	file_name,
		const char *	file_type,
		const char *	options,
		const bool	check_for_empty = true
	)		const

Write bit ref level to file.

Parameters

bit	bit ref level
mask	mask of bit ref level
type	type of entity
file_name	file name (see moab documentation)
file_type	file type (see moab documentation)
options	file options (see moab documentation)

Returns

error code

Definition at line 548 of file BitRefManager.cpp.

                                      {
  MoFEM::Interface &m_field = cOre;
  moab::Interface &moab(m_field.get_moab());
  MoFEMFunctionBegin;
  Range ents;
  CHKERR getEntitiesByTypeAndRefLevel(bit, mask, type, ents);
  if (check_for_empty && ents.empty())
    MoFEMFunctionReturnHot(0);
  EntityHandle meshset;
  CHKERR moab.create_meshset(MESHSET_SET, meshset);
  CHKERR moab.add_entities(meshset, ents);
  CHKERR moab.write_file(file_name, file_type, options, &meshset, 1);
  CHKERR moab.delete_entities(&meshset, 1);
  MoFEMFunctionReturn(0);
}

writeEntitiesAllBitLevelsByType()

MoFEMErrorCode MoFEM::BitRefManager::writeEntitiesAllBitLevelsByType	(	const BitRefLevel	mask,
		const EntityType	type,
		const char *	file_name,
		const char *	file_type,
		const char *	options
	)

Write all entities by bit levels and type.

Parameters

mask
type
file_name
file_type
options

Returns

MoFEMErrorCode

Definition at line 585 of file BitRefManager.cpp.

                                                {
  MoFEMFunctionBegin;
  for (int ll = 0; ll != BITREFLEVEL_SIZE; ++ll) {
    std::string name = boost::lexical_cast<std::string>(ll) + "_" + file_name;
    CHKERR writeBitLevelByType(BitRefLevel().set(ll), mask, type, name.c_str(),
                               file_type, options, true);
  }
  MoFEMFunctionReturn(0);
}

writeEntitiesNotInDatabase()

MoFEMErrorCode MoFEM::BitRefManager::writeEntitiesNotInDatabase	(	const char *	file_name,
		const char *	file_type,
		const char *	options,
		const bool	check_for_empty = true
	)		const

Write ents not in database.

Parameters

file_name
file_type	for example "VTK"
options
check_for_empty

Returns

MoFEMErrorCode

Definition at line 567 of file BitRefManager.cpp.

                                      {
  MoFEM::Interface &m_field = cOre;
  moab::Interface &moab(m_field.get_moab());
  MoFEMFunctionBegin;
  EntityHandle meshset;
  Range ents;
  CHKERR getAllEntitiesNotInDatabase(ents);
  if (check_for_empty && ents.empty())
    MoFEMFunctionReturnHot(0);
  CHKERR moab.create_meshset(MESHSET_SET, meshset);
  CHKERR moab.add_entities(meshset, ents);
  CHKERR moab.write_file(file_name, file_type, options, &meshset, 1);
  CHKERR moab.delete_entities(&meshset, 1);
  MoFEMFunctionReturn(0);
}

Member Data Documentation

cOre

MoFEM::Core& MoFEM::BitRefManager::cOre

Definition at line 39 of file BitRefManager.hpp.

dEbug

bool MoFEM::BitRefManager::dEbug

Definition at line 40 of file BitRefManager.hpp.

---

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

• src/interfaces/BitRefManager.hpp
• src/interfaces/impl/BitRefManager.cpp