v0.8.17
Classes | Public Member Functions | Private Member Functions | Private Attributes | Static Private Attributes | List of all members
MoFEM::Core Struct Reference

Core (interface) class. More...

#include <src/interfaces/Core.hpp>

Inheritance diagram for MoFEM::Core:
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Collaboration diagram for MoFEM::Core:
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Classes

struct  WrapMPIComm
 

Public Member Functions

 Core (moab::Interface &moab, MPI_Comm comm=PETSC_COMM_WORLD, const int verbose=VERBOSE, const bool distributed_mesh=true)
 
 ~Core ()
 
- Public Member Functions inherited from MoFEM::DeprecatedCoreInterface
template<class IFace >
DEPRECATED MoFEMErrorCode query_interface (IFace *&ptr) const
 
template<class IFace >
DEPRECATED IFace * query_interface () const
 
virtual DEPRECATED MoFEMErrorCode seed_ref_level_2D (const EntityHandle meshset, const BitRefLevel &bit, int verb=-1)
 seed 2D entities (Triangles entities only) in the meshset and their adjacencies (only TRIs adjacencies) in a particular BitRefLevel More...
 
DEPRECATED MoFEMErrorCode seed_ref_level_3D (const EntityHandle meshset, const BitRefLevel &bit, int verb=-1)
 seed 2D entities in the meshset and their adjacencies (only TETs adjacencies) in a particular BitRefLevel More...
 
DEPRECATED MoFEMErrorCode seed_ref_level (const Range &ents, const BitRefLevel &bit, const bool only_tets=true, int verb=-1)
 seed entities in the range and their adjacencies in a particular BitRefLevel More...
 
DEPRECATED MoFEMErrorCode seed_ref_level_MESHSET (const EntityHandle meshset, const BitRefLevel &bit, int verb=-1)
 
DEPRECATED MoFEMErrorCode seed_finite_elements (const EntityHandle meshset, int verb=-1)
 
DEPRECATED MoFEMErrorCode seed_finite_elements (const Range &entities, int verb=-1)
 
DEPRECATED MoFEMErrorCode get_entities_by_type_and_ref_level (const BitRefLevel &bit, const BitRefLevel &mask, const EntityType type, const EntityHandle meshset, int verb=-1)
 add all ents from ref level given by bit to meshset More...
 
DEPRECATED MoFEMErrorCode get_entities_by_type_and_ref_level (const BitRefLevel &bit, const BitRefLevel &mask, const EntityType type, Range &ents, int verb=-1)
 add all ents from ref level given by bit to meshset More...
 
DEPRECATED MoFEMErrorCode get_entities_by_ref_level (const BitRefLevel &bit, const BitRefLevel &mask, const EntityHandle meshset)
 add all ents from ref level given by bit to meshset More...
 
DEPRECATED MoFEMErrorCode get_entities_by_ref_level (const BitRefLevel &bit, const BitRefLevel &mask, Range &ents)
 add all ents from ref level given by bit to meshset More...
 
DEPRECATED bool check_msId_meshset (const int msId, const CubitBCType cubit_bc_type)
 check for CUBIT Id and CUBIT type More...
 
DEPRECATED MoFEMErrorCode add_cubit_msId (const CubitBCType cubit_bc_tyep, const int msId, const std::string name="")
 add cubit meshset More...
 
DEPRECATED MoFEMErrorCode set_cubit_msId_attribites (const CubitBCType cubit_bc_type, const int ms_id, const std::vector< double > &attributes, const std::string name="")
 set attributes to cubit meshset More...
 
DEPRECATED MoFEMErrorCode set_cubit_msId_attribites_data_structure (const CubitBCType cubit_bc_type, const int ms_id, const GenericAttributeData &data, const std::string name="")
 set (material) data structure to cubit meshset More...
 
DEPRECATED MoFEMErrorCode set_cubit_msId_bc_data_structure (const CubitBCType cubit_bc_type, const int ms_id, const GenericCubitBcData &data)
 set boundary data structure to meshset More...
 
DEPRECATED MoFEMErrorCode delete_cubit_msId (const CubitBCType cubit_bc_type, const int msId)
 delete cubit meshset More...
 
DEPRECATED MoFEMErrorCode get_cubit_msId (const int msId, const CubitBCType cubit_bc_type, const CubitMeshSets **cubit_meshset_ptr)
 get cubit meshset More...
 
DEPRECATED MoFEMErrorCode get_cubit_msId_entities_by_dimension (const int ms_id, const CubitBCType cubit_bc_type, const int dimension, Range &entities, const bool recursive=false)
 
DEPRECATED MoFEMErrorCode get_cubit_msId_entities_by_dimension (const int ms_id, const CubitBCType cubit_bc_type, Range &entities, const bool recursive=false)
 
DEPRECATED MoFEMErrorCode get_cubit_msId_entities_by_dimension (const int msId, const unsigned int cubit_bc_type, const int dimension, Range &entities, const bool recursive=false)
 get entities from CUBIT/meshset of a particular entity dimension More...
 
DEPRECATED MoFEMErrorCode get_cubit_msId_entities_by_dimension (const int msId, const unsigned int cubit_bc_type, Range &entities, const bool recursive=false)
 get entities related to CUBIT/meshset, More...
 
DEPRECATED MoFEMErrorCode get_cubit_msId_meshset (const int msId, const unsigned int cubit_bc_type, EntityHandle &meshset)
 get meshset from CUBIT Id and CUBIT type More...
 
DEPRECATED MoFEMErrorCode get_cubit_meshsets (const unsigned int cubit_bc_type, Range &meshsets)
 get all CUBIT meshsets by CUBIT type More...
 
DEPRECATED MoFEMErrorCode print_cubit_displacement_set () const
 
DEPRECATED MoFEMErrorCode print_cubit_pressure_set () const
 
DEPRECATED MoFEMErrorCode print_cubit_force_set () const
 
DEPRECATED MoFEMErrorCode print_cubit_materials_set () const
 
DEPRECATED MoFEMErrorCode update_meshset_by_entities_children (const EntityHandle parent, const BitRefLevel &child_bit, const EntityHandle child, EntityType child_type, const bool recursive=false, int verb=-1)
 Get child entities form meshset containing parent entities. More...
 
DEPRECATED MoFEMErrorCode update_field_meshset_by_entities_children (const BitRefLevel &child_bit, int verb=-1)
 update fields meshesets by child entities More...
 
DEPRECATED MoFEMErrorCode update_field_meshset_by_entities_children (const std::string name, const BitRefLevel &child_bit, int verb=-1)
 update field mesheset by child entities More...
 
DEPRECATED MoFEMErrorCode update_finite_element_meshset_by_entities_children (const std::string name, const BitRefLevel &child_bit, const EntityType fe_ent_type, int verb=-1)
 update finite element mesheset by child entities More...
 
DEPRECATED MoFEMErrorCode shift_right_bit_ref (const int shift, int verb=-1)
 right shift bit ref level More...
 
DEPRECATED MoFEMErrorCode build_problem (const std::string &name, const bool square_matrix, int verb=-1)
 build problem data structures More...
 
DEPRECATED MoFEMErrorCode build_problem (Problem *problem_ptr, const bool square_matrix, int verb=-1)
 build problem data structures More...
 
DEPRECATED MoFEMErrorCode build_problem_on_distributed_mesh (const std::string &name, const bool square_matrix=true, int verb=-1)
 build problem data structures, assuming that mesh is distributed (collective) More...
 
DEPRECATED MoFEMErrorCode build_problem_on_distributed_mesh (Problem *problem_ptr, const bool square_matrix=true, int verb=-1)
 build problem data structures, assuming that mesh is distributed (collective) More...
 
DEPRECATED MoFEMErrorCode partition_mesh (const Range &ents, const int dim, const int adj_dim, const int n_parts, int verb=-1)
 Set partition tag to each finite element in the problem. More...
 
DEPRECATED MoFEMErrorCode partition_simple_problem (const std::string &name, int verb=-1)
 partition problem dofs More...
 
DEPRECATED MoFEMErrorCode partition_problem (const std::string &name, int verb=-1)
 partition problem dofs (collective) More...
 
DEPRECATED MoFEMErrorCode partition_compose_problem (const std::string &name, const std::string &problem_for_rows, const bool copy_rows, const std::string &problem_for_cols, const bool copy_cols, int verb=-1)
 build indexing and partition problem inheriting indexing and partitioning from two other problems More...
 
DEPRECATED MoFEMErrorCode build_sub_problem (const std::string &out_name, const std::vector< std::string > &fields_row, const std::vector< std::string > &fields_col, const std::string &main_problem, const bool square_matrix=true, int verb=-1)
 build sub problem More...
 
DEPRECATED MoFEMErrorCode partition_ghost_dofs (const std::string &name, int verb=-1)
 determine ghost nodes More...
 
DEPRECATED MoFEMErrorCode partition_finite_elements (const std::string &name, bool part_from_moab=false, int low_proc=-1, int hi_proc=-1, int verb=-1)
 partition finite elements More...
 
DEPRECATED MoFEMErrorCode get_problem_elements_layout (const std::string &name, const std::string &fe_name, PetscLayout *layout, int verb=-1)
 Get layout of elements in the problemIn layout is stored information how many elements is on each processor, for more information look int petsc documentation http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/IS/PetscLayoutCreate.html#PetscLayoutCreate More...
 
DEPRECATED MoFEMErrorCode VecCreateSeq (const std::string &name, RowColData rc, Vec *V) const
 create local vector for problem More...
 
DEPRECATED MoFEMErrorCode VecCreateGhost (const std::string &name, RowColData rc, Vec *V) const
 create ghost vector for problem (collective)collective - need to be run on all processors in communicator More...
 
DEPRECATED MoFEMErrorCode ISCreateFromProblemFieldToOtherProblemField (const std::string &x_problem, const std::string &x_field_name, RowColData x_rc, const std::string &y_problem, const std::string &y_field_name, RowColData y_rc, std::vector< int > &idx, std::vector< int > &idy, int verb=-1) const
 create IS for give two problems and field More...
 
DEPRECATED MoFEMErrorCode ISCreateFromProblemFieldToOtherProblemField (const std::string &x_problem, const std::string &x_field_name, RowColData x_rc, const std::string &y_problem, const std::string &y_field_name, RowColData y_rc, IS *ix, IS *iy, int verb=-1) const
 create IS for give two problems and field More...
 
DEPRECATED MoFEMErrorCode ISCreateProblemOrder (const std::string &problem, RowColData rc, int min_order, int max_order, IS *is, int verb=-1) const
 create IS for given order range (collective) More...
 
DEPRECATED MoFEMErrorCode ISCreateProblemFieldAndRank (const std::string &problem, RowColData rc, const std::string &field, int min_coeff_idx, int max_coeff_idx, IS *is, int verb=-1) const
 create IS for given problem, field and rank range (collective) More...
 
DEPRECATED MoFEMErrorCode VecScatterCreate (Vec xin, const std::string &x_problem, const std::string &x_field_name, RowColData x_rc, Vec yin, const std::string &y_problem, const std::string &y_field_name, RowColData y_rc, VecScatter *newctx, int verb=-1) const
 create scatter for vectors form one to another problem (collective)User specify what name of field on one problem is scattered to another. More...
 
DEPRECATED MoFEMErrorCode VecScatterCreate (Vec xin, const std::string &x_problem, RowColData x_rc, Vec yin, const std::string &y_problem, RowColData y_rc, VecScatter *newctx, int verb=-1) const
 create scatter for vectors form one to another problem (collective) More...
 
DEPRECATED MoFEMErrorCode set_local_ghost_vector (const Problem *problem_ptr, RowColData rc, Vec V, InsertMode mode, ScatterMode scatter_mode) const
 set values of vector from/to meshdatabase More...
 
DEPRECATED MoFEMErrorCode set_local_ghost_vector (const std::string &name, RowColData rc, Vec V, InsertMode mode, ScatterMode scatter_mode) const
 set values of vector from/to meshdatabase More...
 
DEPRECATED MoFEMErrorCode set_global_ghost_vector (const Problem *problem_ptr, RowColData rc, Vec V, InsertMode mode, ScatterMode scatter_mode) const
 set values of vector from/to mesh database (collective)collective - need tu be run on all processors in communicator More...
 
DEPRECATED MoFEMErrorCode set_global_ghost_vector (const std::string &name, RowColData rc, Vec V, InsertMode mode, ScatterMode scatter_mode) const
 set values of vector from/to mesh database (collective)collective - need tu be run on all processors in communicator More...
 
DEPRECATED MoFEMErrorCode set_other_local_ghost_vector (const Problem *problem_ptr, const std::string &fiel_name, const std::string &cpy_field_name, RowColData rc, Vec V, InsertMode mode, ScatterMode scatter_mode, int verb=-1)
 Copy vector to field which is not part of the problem. More...
 
DEPRECATED MoFEMErrorCode set_other_local_ghost_vector (const std::string &name, const std::string &field_name, const std::string &cpy_field_name, RowColData rc, Vec V, InsertMode mode, ScatterMode scatter_mode, int verb=-1)
 Copy vector to field which is not part of the problem. More...
 
DEPRECATED MoFEMErrorCode set_other_global_ghost_vector (const Problem *problem_ptr, const std::string &field_name, const std::string &cpy_field_name, RowColData rc, Vec V, InsertMode mode, ScatterMode scatter_mode, int verb=-1)
 Copy vector to field which is not part of the problem (collective)collective - need tu be run on all processors in communicator. More...
 
DEPRECATED MoFEMErrorCode set_other_global_ghost_vector (const std::string &name, const std::string &field_name, const std::string &cpy_field_name, RowColData rc, Vec V, InsertMode mode, ScatterMode scatter_mode, int verb=-1)
 Copy vector to field which is not part of the problem (collective)collective - need tu be run on all processors in communicator. More...
 
DEPRECATED MoFEMErrorCode field_axpy (const double alpha, const std::string &fiel_name_x, const std::string &field_name_y, bool error_if_missing=false, bool creat_if_missing=false)
 axpy fields More...
 
DEPRECATED MoFEMErrorCode field_scale (const double alpha, const std::string &field_name)
 scale field More...
 
DEPRECATED MoFEMErrorCode set_field (const double val, const EntityType type, const std::string &field_name)
 use FieldBlas More...
 
DEPRECATED MoFEMErrorCode set_field (const double val, const EntityType type, const Range &ents, const std::string &field_name)
 set field More...
 
DEPRECATED MoFEMErrorCode get_adjacencies_equality (const EntityHandle from_entiti, const int to_dimension, Range &adj_entities) const
 Get the adjacencies associated with a entity to entities of a specified dimension. \
separate interface, i.e. BitLevelManager. More...
 
DEPRECATED MoFEMErrorCode get_adjacencies_any (const EntityHandle from_entiti, 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...
 
DEPRECATED MoFEMErrorCode get_adjacencies (const Problem *problem_ptr, const EntityHandle *from_entities, const int num_netities, 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. \
separate interface, i.e. BitLevelManage. More...
 
DEPRECATED MoFEMErrorCode get_adjacencies (const BitRefLevel &bit, const EntityHandle *from_entities, const int num_netities, 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. \
separate interface, i.e. BitLevelManage. More...
 
DEPRECATED MoFEMErrorCode clear_dofs_fields (const BitRefLevel &bit, const BitRefLevel &mask, int verb=-1)
 
DEPRECATED MoFEMErrorCode clear_ents_fields (const BitRefLevel &bit, const BitRefLevel &mask, int verb=-1)
 
DEPRECATED MoFEMErrorCode clear_finite_elements (const BitRefLevel &bit, const BitRefLevel &mask, int verb=-1)
 
DEPRECATED MoFEMErrorCode add_ents_to_field_by_VERTICEs (const Range &nodes, const std::string &name, int verb=-1)
 set field entities on verticesThe lower dimension entities are added depending on the space type More...
 
DEPRECATED MoFEMErrorCode add_ents_to_field_by_VERTICEs (const EntityHandle meshset, const std::string &name, int verb=-1)
 set field entities on verticesThe lower dimension entities are added depending on the space type More...
 
DEPRECATED MoFEMErrorCode add_ents_to_field_by_EDGEs (const Range &edges, const std::string &name, int verb=-1)
 set field entities form adjacencies of edgesThe lower dimension entities are added depending on the space type More...
 
DEPRECATED MoFEMErrorCode add_ents_to_field_by_EDGEs (const EntityHandle meshset, const std::string &name, int verb=-1)
 set field entities form adjacencies of edgesThe lower dimension entities are added depending on the space type More...
 
DEPRECATED MoFEMErrorCode add_ents_to_field_by_TRIs (const EntityHandle meshset, const std::string &name, int verb=-1)
 set field entities form adjacencies of trianglesThe lower dimension entities are added depending on the space type More...
 
DEPRECATED MoFEMErrorCode add_ents_to_field_by_TRIs (const Range &tris, const std::string &name, int verb=-1)
 set field entities form adjacencies of trianglesThe lower dimension entities are added depending on the space type More...
 
DEPRECATED MoFEMErrorCode add_ents_to_field_by_TETs (const EntityHandle meshset, const std::string &name, int verb=-1)
 set field entities from adjacencies of tetrahedronThe lower dimension entities are added depending on the space type More...
 
DEPRECATED MoFEMErrorCode add_ents_to_field_by_TETs (const Range &tets, const std::string &name, int verb=-1)
 set field entities from adjacencies of tetrahedronThe lower dimension entities are added depending on the space type More...
 
DEPRECATED MoFEMErrorCode add_ents_to_field_by_QUADs (const Range &quads, const std::string &name, int verb=-1)
 set field entities from adjacencies of quadsThe lower dimension entities are added depending on the space type More...
 
DEPRECATED MoFEMErrorCode add_ents_to_field_by_QUADs (EntityHandle meshset, const std::string &name, int verb=-1)
 set field entities from adjacencies of quadsThe lower dimension entities are added depending on the space type More...
 
DEPRECATED MoFEMErrorCode add_ents_to_field_by_PRISMs (const Range &prisms, const std::string &name, int verb=-1)
 set field entities from adjacencies of prismsThe lower dimension entities are added depending on the space type More...
 
DEPRECATED MoFEMErrorCode add_ents_to_field_by_PRISMs (EntityHandle meshset, const std::string &name, int verb=-1)
 set field entities from adjacencies of prismsThe lower dimension entities are added depending on the space type More...
 
- Public Member Functions inherited from MoFEM::CoreInterface
template<typename DIT >
MoFEMErrorCode get_field_dof_data (const std::string &name, const EntityHandle *ent, const int num_ents, DIT dit, int *count=NULL)
 get field data from entity and fieldthis function is not recommended to be used in finite element implementation More...
 
template<typename DIT >
MoFEMErrorCode get_field_dof_data (const std::string &name, const Range &ents, DIT dit, int *count=NULL)
 get field data from entity and fieldthis function is not recommended to be used in finite element implementation 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 ()
 
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
 

Private Member Functions

MoFEMErrorCode addProblem (const BitProblemId id, const std::string &name, int verb=DEFAULT_VERBOSITY)
 add problem More...
 
MoFEMErrorCode getTags (int verb=DEFAULT_VERBOSITY)
 Get tag handles. More...
 
MoFEMErrorCode clearMap ()
 Cleaning database. More...
 
MoFEMErrorCode registerSubInterfaces ()
 Register insterfaces. More...
 
BitFieldId getFieldShift ()
 Return unique field Id. More...
 
BitFEId getFEShift ()
 Return unique finite element Id. More...
 
BitProblemId getProblemShift ()
 Return unique problem Id. More...
 
MoFEMErrorCode initialiseDatabaseFromMesh (int verb=DEFAULT_VERBOSITY)
 Initialize database getting information on mesh. More...
 
MoFEMErrorCode getOptions (int verb=DEFAULT_VERBOSITY)
 Get core options from command line. More...
 
template<class IFACE >
MoFEMErrorCode regSubInterface (const MOFEMuuid &uid)
 

Private Attributes

boost::shared_ptr< WrapMPICommwrapMPIComm
 
int verbose
 Verbosity level. More...
 
intfShift
 Ptr to tag handle storing last set bit in field ID. More...
 
intfeShift
 Ptr to tag handle storing last set bit in finite element ID. More...
 
intpShift
 Ptr to tag handle storing last set bit in problem ID. More...
 
boost::ptr_map< unsigned long, UnknownInterfaceiFaces
 Hash map of pointers to interfaces. More...
 
intbuildMoFEM
 keeps flags/semaphores for different stages More...
 
std::string optionsPrefix
 Prefix for options on command line. More...
 
PetscBool initaliseAndBuildField
 
PetscBool initaliseAndBuildFiniteElements
 

Static Private Attributes

static bool isGloballyInitialised = false
 Core base globally initialized. More...
 

Global initialisation and finalisation

static MoFEMErrorCode Initialize (int *argc, char ***args, const char file[], const char help[])
 Initializes the MoFEM database PETSc, MOAB and MPI. More...
 
static MoFEMErrorCode Finalize ()
 Checks for options to be called at the conclusion of the program. More...
 

Assessing interfaces

MoFEMErrorCode query_interface (const MOFEMuuid &uuid, UnknownInterface **iface) const
 Getting interface of core database. More...
 

Get tag handles to data on the mesh

Tag get_th_RefParentHandle () const
 
Tag get_th_RefBitLevel () const
 
Tag get_th_RefBitEdge () const
 
Tag get_th_RefType () const
 

Auxiliary data and functions

enum  SemaphoresBuildMofem {
  BUILD_FIELD = 1 << 0, BUILD_FE = 1 << 1, BUILD_ADJ = 1 << 2, BUILD_PROBLEM = 1 << 3,
  PARTITION_PROBLEM = 1 << 4, PARTITION_FE = 1 << 5, PARTITION_GHOST_DOFS = 1 << 6, PARTITION_MESH = 1 << 7
}
 
intgetBuildMoFEM () const
 Get flags/semaphores for different stages. More...
 
MoFEMErrorCode addPrismToDatabase (const EntityHandle prism, int verb=DEFAULT_VERBOSITY)
 add prim element More...
 

Tags to data on mesh and entities

Tag th_Part
 Tag for partition number. More...
 
Tag th_RefParentHandle
 
Tag th_RefBitLevel
 
Tag th_RefBitLevel_Mask
 
Tag th_RefBitEdge
 
Tag th_RefFEMeshset
 
Tag th_RefType
 
Tag th_FieldId
 
Tag th_FieldName
 
Tag th_FieldName_DataNamePrefix
 
Tag th_FieldSpace
 
Tag th_FieldBase
 
Tag th_FEId
 
Tag th_FEName
 
Tag th_FEIdCol
 
Tag th_FEIdRow
 
Tag th_FEIdData
 
Tag th_ProblemId
 
Tag th_ProblemName
 
Tag th_ProblemFEId
 
Tag th_ProblemNbDofsRow
 
Tag th_ProblemNbDofsCol
 
Tag th_ProblemLocalNbDofRow
 
Tag th_ProblemGhostNbDofRow
 
Tag th_ProblemLocalNbDofCol
 
Tag th_ProblemGhostNbDofCol
 
Tag th_ProblemShift
 
Tag th_FieldShift
 
Tag th_FEShift
 
Tag th_ElemType
 Needed for VTK files. More...
 
Tag th_MoFEMBuild
 
boost::shared_ptr< BasicEntityDatabasicEntityDataPtr
 
boost::shared_ptr< BasicEntityData > & get_basic_entity_data_ptr ()
 Get pointer to basic entity data. More...
 

Multi-Indices accessing data on the mesh

RefEntity_multiIndex refinedEntities
 refined entities More...
 
RefElement_multiIndex refinedFiniteElements
 refined elements More...
 
Field_multiIndex fIelds
 fields More...
 
FieldEntity_multiIndex entsFields
 entities on fields More...
 
DofEntity_multiIndex dofsField
 dofs on fields More...
 
FiniteElement_multiIndex finiteElements
 finite elements More...
 
EntFiniteElement_multiIndex entsFiniteElements
 finite element entities More...
 
FieldEntityEntFiniteElementAdjacencyMap_multiIndex entFEAdjacencies
 adjacencies of elements to dofs More...
 
Problem_multiIndex pRoblems
 problems multi-index More...
 

Get moab database

std::reference_wrapper< moab::Interface > moab
 moab database More...
 
moab::Interface & get_moab ()
 
const moab::Interface & get_moab () const
 
MoFEMErrorCode set_moab_interface (moab::Interface &new_moab, int verb=VERBOSE, const bool distributed_mesh=true)
 Set the moab interface object. More...
 

Check database consistency

MoFEMErrorCode check_number_of_ents_in_ents_field (const std::string &name) const
 check data consistency in entitiesPtr More...
 
MoFEMErrorCode check_number_of_ents_in_ents_field () const
 check data consistency in entitiesPtr More...
 
MoFEMErrorCode check_number_of_ents_in_ents_finite_element (const std::string &name) const
 check data consistency in entsFiniteElements More...
 
MoFEMErrorCode check_number_of_ents_in_ents_finite_element () const
 check data consistency in entsFiniteElements More...
 

Clear database

MoFEMErrorCode clear_database (int verb=DEFAULT_VERBOSITY)
 Clear database. More...
 
MoFEMErrorCode rebuild_database (int verb=DEFAULT_VERBOSITY)
 Clear database and initialize it once again. More...
 

Getting access to meshset manager

MeshsetsManagerget_meshsets_manager_ptr ()
 get MeshsetsManager pointer More...
 
const MeshsetsManagerget_meshsets_manager_ptr () const
 get MeshsetsManager pointer More...
 
MeshsetsManagerget_meshsets_manager ()
 get MeshsetsManager pointer More...
 
const MeshsetsManagerget_meshsets_manager () const
 get MeshsetsManager pointer More...
 

Remove and delete entities

MoFEMErrorCode remove_parents_by_ents (const Range &ents, int verb=DEFAULT_VERBOSITY)
 Remove parents from entities. More...
 
MoFEMErrorCode remove_parents_by_by_bit_ref (const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode remove_parents_by_parents (const Range &ents, int verb=DEFAULT_VERBOSITY)
 Remove paremts from entities having parents in passed range. More...
 
MoFEMErrorCode remove_ents (const Range &ents, int verb=DEFAULT_VERBOSITY)
 remove entities form mofem database More...
 
MoFEMErrorCode remove_ents_by_bit_ref (const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
 remove entities form mofem database More...
 
MoFEMErrorCode delete_ents_by_bit_ref (const BitRefLevel &bit, const BitRefLevel &mask, const bool remove_parent=false, int verb=DEFAULT_VERBOSITY)
 delete entities form mofem and moab database More...
 

Synchronize entities (Following functions in future will be

deprecated)

MoFEMErrorCode synchronise_entities (Range &ent, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode synchronise_field_entities (const BitFieldId id, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode synchronise_field_entities (const std::string &name, int verb=DEFAULT_VERBOSITY)
 

Fields

MoFEMErrorCode add_field (const std::string &name, const FieldSpace space, const FieldApproximationBase base, const FieldCoefficientsNumber nb_coefficients, const TagType tag_type=MB_TAG_SPARSE, const enum MoFEMTypes bh=MF_EXCL, int verb=DEFAULT_VERBOSITY)
 Add filed. More...
 
MoFEMErrorCode addEntsToFieldByDim (const Range &ents, const int dim, const std::string &name, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode add_ents_to_field_by_dim (const Range &ents, const int dim, const std::string &name, int verb=DEFAULT_VERBOSITY)
 Add entities to field meshset. More...
 
MoFEMErrorCode add_ents_to_field_by_type (const Range &ents, const EntityType type, const std::string &name, int verb=DEFAULT_VERBOSITY)
 Add entities to field meshset. More...
 
MoFEMErrorCode add_ents_to_field_by_dim (const EntityHandle meshset, const int dim, const std::string &name, const bool recursive=true, int verb=DEFAULT_VERBOSITY)
 Add entities to field meshsetcollective. More...
 
MoFEMErrorCode add_ents_to_field_by_type (const EntityHandle meshset, const EntityType type, const std::string &name, const bool recursive=true, int verb=DEFAULT_VERBOSITY)
 Add entities to field meshset. More...
 

Set approximation order

MoFEMErrorCode set_field_order (const Range &ents, const BitFieldId id, const ApproximationOrder order, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode set_field_order (const EntityHandle meshset, const EntityType type, const BitFieldId id, const ApproximationOrder order, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode set_field_order (const Range &ents, const std::string &name, const ApproximationOrder order, int verb=DEFAULT_VERBOSITY)
 Set order approximation of the entities in the field. More...
 
MoFEMErrorCode set_field_order (const EntityHandle meshset, const EntityType type, const std::string &name, const ApproximationOrder order, int verb=DEFAULT_VERBOSITY)
 Set order approximation of the entities in the field. More...
 
MoFEMErrorCode set_field_order_by_entity_type_and_bit_ref (const BitRefLevel &bit, const BitRefLevel &mask, const EntityType type, const BitFieldId id, const ApproximationOrder order, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode set_field_order_by_entity_type_and_bit_ref (const BitRefLevel &bit, const BitRefLevel &mask, const EntityType type, const std::string &name, const ApproximationOrder order, int verb=DEFAULT_VERBOSITY)
 Set order approximation of the entities in the field. More...
 

Build fields

MoFEMErrorCode buildFieldForNoField (const BitFieldId id, std::map< EntityType, int > &dof_counter, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode buildFieldForL2H1HcurlHdiv (const BitFieldId id, std::map< EntityType, int > &dof_counter, std::map< EntityType, int > &inactive_dof_counter, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode buildField (const boost::shared_ptr< Field > &field, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode build_fields (int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode build_field (const std::string field_name, int verb=DEFAULT_VERBOSITY)
 build field by name More...
 

Clear DOFs

MoFEMErrorCode clear_inactive_dofs (int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode clear_dofs_fields_by_bit_ref (const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode clear_dofs_fields (const Range &ents, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode clear_dofs_fields (const std::string &name, const Range &ents, int verb=DEFAULT_VERBOSITY)
 

Clear ENTs

MoFEMErrorCode clear_ents_fields_by_bit_ref (const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode clear_ents_fields (const Range &ents, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode clear_ents_fields (const std::string &name, const Range &ents, int verb=DEFAULT_VERBOSITY)
 

Remove field entities

MoFEMErrorCode remove_ents_from_field_by_bit_ref (const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
 remove entities from field More...
 
MoFEMErrorCode remove_ents_from_field (const std::string &name, const EntityHandle meshset, const EntityType type, int verb=DEFAULT_VERBOSITY)
 remove entities from field More...
 
MoFEMErrorCode remove_ents_from_field (const std::string &name, const Range &ents, int verb=DEFAULT_VERBOSITY)
 remove entities from field More...
 
MoFEMErrorCode remove_ents_from_field (const Range &ents, int verb=DEFAULT_VERBOSITY)
 remove entities from all fields More...
 

Other auxiliary functions for fields

MoFEMErrorCode list_dofs_by_field_name (const std::string &name) const
 
MoFEMErrorCode list_fields () const
 list entities in the field More...
 
BitFieldId getBitFieldId (const std::string &name) const
 
EntityHandle get_field_meshset (const BitFieldId id) const
 
EntityHandle get_field_meshset (const std::string &name) const
 get field meshset More...
 
MoFEMErrorCode get_field_entities_by_dimension (const std::string name, int dim, Range &ents) const
 get entities in the field by dimension More...
 
MoFEMErrorCode get_field_entities_by_type (const std::string name, EntityType type, Range &ents) const
 get entities in the field by type More...
 
MoFEMErrorCode get_field_entities_by_handle (const std::string name, Range &ents) const
 get entities in the field by handle More...
 
bool check_field (const std::string &name) const
 check if field is in database More...
 
const Fieldget_field_structure (const std::string &name)
 get field structure More...
 

Finite elements

bool check_finite_element (const std::string &name) const
 Check if finite element is in database. More...
 
MoFEMErrorCode add_finite_element (const std::string &fe_name, enum MoFEMTypes bh=MF_EXCL, int verb=DEFAULT_VERBOSITY)
 add finite element More...
 
MoFEMErrorCode modify_finite_element_adjacency_table (const std::string &fe_name, const EntityType type, ElementAdjacencyFunct function)
 modify finite element table, only for advanced user More...
 
MoFEMErrorCode modify_finite_element_add_field_data (const std::string &fe_name, const std::string &name_filed)
 set finite element field data More...
 
MoFEMErrorCode modify_finite_element_add_field_row (const std::string &fe_name, const std::string &name_row)
 set field row which finite element use More...
 
MoFEMErrorCode modify_finite_element_add_field_col (const std::string &fe_name, const std::string &name_col)
 set field col which finite element use More...
 
MoFEMErrorCode modify_finite_element_off_field_data (const std::string &fe_name, const std::string &name_filed)
 unset finite element field data More...
 
MoFEMErrorCode modify_finite_element_off_field_row (const std::string &fe_name, const std::string &name_row)
 unset field row which finite element use More...
 
MoFEMErrorCode modify_finite_element_off_field_col (const std::string &fe_name, const std::string &name_col)
 unset field col which finite element use More...
 
MoFEMErrorCode add_ents_to_finite_element_by_type (const EntityHandle meshset, const EntityType type, const std::string &name, const bool recursive=true)
 add entities to finite element More...
 
MoFEMErrorCode add_ents_to_finite_element_by_dim (const EntityHandle meshset, const int dim, const std::string &name, const bool recursive=true)
 add entities to finite element More...
 
MoFEMErrorCode add_ents_to_finite_element_by_type (const Range &ents, const EntityType type, const std::string &name)
 add entities to finite elements More...
 
MoFEMErrorCode add_ents_to_finite_element_by_dim (const Range &ents, const int dim, const std::string &name)
 add entities to finite elements More...
 
MoFEMErrorCode add_ents_to_finite_element_by_bit_ref (const BitRefLevel &bit, const BitRefLevel &mask, const std::string &name, EntityType type, int verb=DEFAULT_VERBOSITY)
 add TET entities from given refinement level to finite element database given by name More...
 
MoFEMErrorCode add_ents_to_finite_element_by_MESHSET (const EntityHandle meshset, const std::string &name, const bool recursive=false)
 add MESHSET element to finite element database given by name More...
 
DEPRECATED MoFEMErrorCode add_ents_to_finite_element_by_VERTICEs (const Range &vert, const std::string &name)
 add VERTICES entities from range to finite element database given by name More...
 
DEPRECATED MoFEMErrorCode add_ents_to_finite_element_by_EDGEs (const Range &vert, const std::string &name)
 add EDGES entities from range to finite element database given by name More...
 
DEPRECATED MoFEMErrorCode add_ents_to_finite_element_by_EDGEs (const EntityHandle meshset, const std::string &name, const bool recursive=false)
 add EDGES finite elements More...
 
DEPRECATED MoFEMErrorCode add_ents_to_finite_element_by_TRIs (const Range &tris, const std::string &name)
 add TRI entities from range to finite element database given by name More...
 
DEPRECATED MoFEMErrorCode add_ents_to_finite_element_by_TRIs (const EntityHandle meshset, const std::string &name, const bool recursive=false)
 add TRI entities from meshset to finite element database given by name More...
 
DEPRECATED MoFEMErrorCode add_ents_to_finite_element_by_TETs (const Range &tets, const std::string &name)
 add TET entities from range to finite element database given by name More...
 
DEPRECATED MoFEMErrorCode add_ents_to_finite_element_by_TETs (const EntityHandle meshset, const std::string &name, const bool recursive=false)
 add TET entities from meshset to finite element database given by name More...
 
DEPRECATED MoFEMErrorCode add_ents_to_finite_element_by_PRISMs (const Range &prims, const BitFEId id)
 
DEPRECATED MoFEMErrorCode add_ents_to_finite_element_by_PRISMs (const Range &prims, const std::string &name)
 add PRISM entities from meshset to finite element database given by name More...
 
DEPRECATED MoFEMErrorCode add_ents_to_finite_element_by_PRISMs (const EntityHandle meshset, const std::string &name, const bool recursive=false)
 add TET entities from meshset to finite element database given by name More...
 
DEPRECATED MoFEMErrorCode add_ents_to_finite_element_EntType_by_bit_ref (const BitRefLevel &bit, const std::string &name, EntityType type, int verb=DEFAULT_VERBOSITY)
 add TET elements from given refinement level to finite element database given by name More...
 
DEPRECATED MoFEMErrorCode add_ents_to_finite_element_EntType_by_bit_ref (const BitRefLevel &bit, const BitRefLevel &mask, const std::string &name, EntityType type, int verb=DEFAULT_VERBOSITY)
 add TET entities from given refinement level to finite element database given by name More...
 
MoFEMErrorCode remove_ents_from_finite_element_by_bit_ref (const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
 remove elements from given refinement level to finite element database More...
 
MoFEMErrorCode remove_ents_from_finite_element (const std::string &name, const EntityHandle meshset, const EntityType type, int verb=DEFAULT_VERBOSITY)
 remove entities from given refinement level to finite element database More...
 
MoFEMErrorCode remove_ents_from_finite_element (const std::string &name, const Range &ents, int verb=DEFAULT_VERBOSITY)
 remove entities from finite element database More...
 
MoFEMErrorCode remove_ents_from_finite_element (const Range &ents, int verb=DEFAULT_VERBOSITY)
 remove entities from finite elements in database More...
 
MoFEMErrorCode delete_finite_element (const std::string name, int verb=DEFAULT_VERBOSITY)
 delete finite element from mofem database More...
 
BitFEId getBitFEId (const std::string &name) const
 Get field Id. More...
 
std::string getBitFEIdName (const BitFEId id) const
 Get field name. More...
 
EntityHandle get_finite_element_meshset (const BitFEId id) const
 
EntityHandle get_finite_element_meshset (const std::string &name) const
 
MoFEMErrorCode get_finite_element_entities_by_dimension (const std::string name, int dim, Range &ents) const
 get entities in the finite element by dimension More...
 
MoFEMErrorCode get_finite_element_entities_by_type (const std::string name, EntityType type, Range &ents) const
 get entities in the finite element by type More...
 
MoFEMErrorCode get_finite_element_entities_by_handle (const std::string name, Range &ents) const
 get entities in the finite element by handle More...
 
MoFEMErrorCode list_finite_elements () const
 list finite elements in database More...
 

Problems

MoFEMErrorCode add_problem (const std::string &name, enum MoFEMTypes bh=MF_EXCL, int verb=DEFAULT_VERBOSITY)
 Add problem. More...
 
bool check_problem (const std::string name)
 check if problem exist More...
 
MoFEMErrorCode delete_problem (const std::string name)
 Delete problem. More...
 
MoFEMErrorCode modify_problem_add_finite_element (const std::string &name_problem, const std::string &MoFEMFiniteElement_name)
 add finite element to problem, this add entities assigned to finite element to a particular problem More...
 
MoFEMErrorCode modify_problem_unset_finite_element (const std::string &name_problem, const std::string &MoFEMFiniteElement_name)
 unset finite element from problem, this remove entities assigned to finite element to a particular problemNote: If problem is build, it need to be cleaned to make this effective More...
 
MoFEMErrorCode modify_problem_ref_level_add_bit (const std::string &name_problem, const BitRefLevel &bit)
 add ref level to problem
More...
 
MoFEMErrorCode modify_problem_ref_level_set_bit (const std::string &name_problem, const BitRefLevel &bit)
 set ref level for problem More...
 
MoFEMErrorCode modify_problem_mask_ref_level_add_bit (const std::string &name_problem, const BitRefLevel &bit)
 set dof mask ref level for problem More...
 
MoFEMErrorCode modify_problem_mask_ref_level_set_bit (const std::string &name_problem, const BitRefLevel &bit)
 set dof mask ref level for problem More...
 
BitProblemId getBitProblemId (const std::string &name) const
 
MoFEMErrorCode list_problem () const
 list problems More...
 
MoFEMErrorCode clear_problem (const std::string &name, int verb=DEFAULT_VERBOSITY)
 clear problem More...
 
MoFEMErrorCode clear_problems (int verb=DEFAULT_VERBOSITY)
 clear problems More...
 
MoFEMErrorCode build_finite_elements (int verb=DEFAULT_VERBOSITY)
 Build finite elementsBuild finite element data structures. Have to be run before problem and adjacencies are constructed. More...
 
MoFEMErrorCode build_finite_elements (const BitRefLevel &bit, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode build_finite_elements (const string fe_name, const Range *ents_ptr=NULL, int verb=DEFAULT_VERBOSITY)
 Build finite elementsBuild finite element data structures. Have to be run before problem and adjacencies are constructed. More...
 
MoFEMErrorCode buildFiniteElements (const boost::shared_ptr< FiniteElement > &fe, const Range *ents_ptr=NULL, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode clear_finite_elements_by_bit_ref (const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode clear_finite_elements (const Range &ents, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode clear_finite_elements (const std::string &name, const Range &ents, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode resolve_shared_ents (const Problem *problem_ptr, const std::string &fe_name, int verb=DEFAULT_VERBOSITY)
 resolve shared entities for finite elements in the problem More...
 
MoFEMErrorCode resolve_shared_ents (const std::string &name, const std::string &fe_name, int verb=DEFAULT_VERBOSITY)
 resolve shared entities for finite elements in the problem More...
 
MoFEMErrorCode get_problem_finite_elements_entities (const std::string &name, const std::string &fe_name, const EntityHandle meshset)
 add finite elements to the meshset More...
 
DEPRECATED MoFEMErrorCode build_problem_on_distributed_mesh (int verb=DEFAULT_VERBOSITY)
 build problem data structures, assuming that mesh is distributed (collective) More...
 
DEPRECATED MoFEMErrorCode build_problems (int verb=DEFAULT_VERBOSITY)
 build problem data structures More...
 
MoFEMErrorCode partition_check_matrix_fill_in (const std::string &problem_name, int row, int col, int verb)
 check if matrix fill in correspond to finite element indices More...
 

Adjacencies

MoFEMErrorCode build_adjacencies (const Range &ents, int verb=DEFAULT_VERBOSITY)
 build adjacencies More...
 
MoFEMErrorCode build_adjacencies (const BitRefLevel &bit, int verb=DEFAULT_VERBOSITY)
 build adjacencies More...
 
MoFEMErrorCode build_adjacencies (const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
 build adjacencies More...
 
MoFEMErrorCode clear_adjacencies_entities (const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
 clear adjacency map for entities on given bit level More...
 
MoFEMErrorCode clear_adjacencies_entities (const Range &ents, int verb=DEFAULT_VERBOSITY)
 clear adjacencies for field entities by entities More...
 
MoFEMErrorCode clear_adjacencies_entities (const std::string &name, const Range &ents, int verb=DEFAULT_VERBOSITY)
 clear adjacencies for field entities by entities and field namd More...
 
MoFEMErrorCode clear_adjacencies_finite_elements (const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
 clear adjacency map for finite elements on given bit level More...
 
MoFEMErrorCode clear_adjacencies_finite_elements (const Range &ents, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode clear_adjacencies_finite_elements (const std::string &name, const Range &ents, int verb=DEFAULT_VERBOSITY)
 
MoFEMErrorCode list_adjacencies () const
 list adjacencies More...
 

Create matrices (will be moved to independent interface)

MoFEMErrorCode MatCreateMPIAIJWithArrays (const std::string &name, Mat *Aij, int verb=DEFAULT_VERBOSITY)
 create Mat (MPIAIJ) for problem (collective) More...
 
MoFEMErrorCode MatCreateMPIAdj_with_Idx_mi_tag (const std::string &name, Mat *Adj, int verb=DEFAULT_VERBOSITY)
 Create Adj matrix. More...
 
MoFEMErrorCode MatCreateSeqAIJWithArrays (const std::string &name, Mat *Aij, PetscInt **i, PetscInt **j, PetscScalar **v, int verb=DEFAULT_VERBOSITY)
 create Mat (AIJ) for problem More...
 

Methods for preforming operations on elements

MoFEMErrorCode problem_basic_method_preProcess (const Problem *problem_ptr, BasicMethod &method, int verb=DEFAULT_VERBOSITY)
 Set data for BasicMethod. More...
 
MoFEMErrorCode problem_basic_method_preProcess (const std::string &problem_name, BasicMethod &method, int verb=DEFAULT_VERBOSITY)
 Set data for BasicMethod. More...
 
MoFEMErrorCode problem_basic_method_postProcess (const Problem *problem_ptr, BasicMethod &method, int verb=DEFAULT_VERBOSITY)
 Set data for BasicMethodThis function set data about problem, adjacencies and other multi-indices in database. This function can be used a special case when user need to do some pre- and post-processing before matrix or vector is initiated, or to assemble matrix for group of FEMethods. Is used by classes SnesCtx and TsCtx. Look for more details there. More...
 
MoFEMErrorCode problem_basic_method_postProcess (const std::string &problem_name, BasicMethod &method, int verb=DEFAULT_VERBOSITY)
 Set data for BasicMethodThis function set data about problem, adjacencies and other multi-indices in database. This function can be used a special case when user need to do some pre- and post-processing before matrix or vector is initiated, or to assemble matrix for group of FEMethods. Is used by classes SnesCtx and TsCtx. Look for more details there. More...
 
MoFEMErrorCode loop_finite_elements (const Problem *problem_ptr, const std::string &fe_name, FEMethod &method, int lower_rank, int upper_rank, MoFEMTypes bh=MF_EXIST, int verb=DEFAULT_VERBOSITY)
 Make a loop over finite elements on partitions from upper to lower rank. More...
 
MoFEMErrorCode loop_finite_elements (const std::string &problem_name, const std::string &fe_name, FEMethod &method, int lower_rank, int upper_rank, MoFEMTypes bh=MF_EXIST, int verb=DEFAULT_VERBOSITY)
 Make a loop over finite elements on partitions from upper to lower rank. More...
 
MoFEMErrorCode loop_finite_elements (const std::string &problem_name, const std::string &fe_name, FEMethod &method, MoFEMTypes bh=MF_EXIST, int verb=DEFAULT_VERBOSITY)
 Make a loop over finite elements. More...
 
MoFEMErrorCode loop_dofs (const Problem *problem_ptr, const std::string &field_name, RowColData rc, DofMethod &method, int lower_rank, int upper_rank, int verb=DEFAULT_VERBOSITY)
 Make a loop over dofs. More...
 
MoFEMErrorCode loop_dofs (const std::string &problem_name, const std::string &field_name, RowColData rc, DofMethod &method, int lower_rank, int upper_rank, int verb=DEFAULT_VERBOSITY)
 Make a loop over dofs. More...
 
MoFEMErrorCode loop_dofs (const std::string &problem_name, const std::string &field_name, RowColData rc, DofMethod &method, int verb=DEFAULT_VERBOSITY)
 Make a loop over dofs. More...
 
MoFEMErrorCode loop_dofs (const std::string &field_name, DofMethod &method, int verb=DEFAULT_VERBOSITY)
 Make a loop over dofs. More...
 
MoFEMErrorCode loop_entities (const std::string &field_name, EntityMethod &method, int verb=DEFAULT_VERBOSITY)
 Make a loop over entities. More...
 

Accessing multi-indices

MoFEMErrorCode get_fields (const Field_multiIndex **fields_ptr) const
 Get fields multi-index from database. More...
 
MoFEMErrorCode get_ref_ents (const RefEntity_multiIndex **refined_entities_ptr) const
 Get ref entities multi-index from database. More...
 
MoFEMErrorCode get_ref_finite_elements (const RefElement_multiIndex **refined_finite_elements_ptr) const
 Get ref finite elements multi-index form database. More...
 
MoFEMErrorCode get_finite_elements (const FiniteElement_multiIndex **fe_ptr) const
 Get finite elements multi-index. More...
 
MoFEMErrorCode get_ents_finite_elements (const EntFiniteElement_multiIndex **fe_ent_ptr) const
 Get entities finite elements multi-index. More...
 
MoFEMErrorCode get_field_ents (const FieldEntity_multiIndex **field_ents) const
 Get field multi index. More...
 
MoFEMErrorCode get_dofs (const DofEntity_multiIndex **dofs_ptr) const
 Get dofs multi index. More...
 
MoFEMErrorCode get_problem (const std::string &problem_name, const Problem **problem_ptr) const
 Get problem database (data structure) More...
 
MoFEMErrorCode get_problems (const Problem_multiIndex **problems_ptr) const
 Get pointer to problems multi-index. More...
 
FieldEntityByFieldName::iterator get_ent_field_by_name_begin (const std::string &field_name) const
 get begin iterator of filed ents of given name (instead you can use IT_GET_ENT_FIELD_BY_NAME_FOR_LOOP(MFIELD,NAME,IT) More...
 
FieldEntityByFieldName::iterator get_ent_field_by_name_end (const std::string &field_name) const
 get begin iterator of filed dofs of given name (instead you can use IT_GET_ENT_FIELD_BY_NAME_FOR_LOOP(MFIELD,NAME,IT)for(IT_GET_ENT_FIELD_BY_NAME_FOR_LOOP(MFIELD,NAME,IT)) { ... } More...
 
DofEntityByFieldName::iterator get_dofs_by_name_begin (const std::string &field_name) const
 get begin iterator of filed dofs of given name (instead you can use IT_GET_DOFS_FIELD_BY_NAME_FOR_LOOP(MFIELD,NAME,IT)for(IT_GET_DOFS_FIELD_BY_NAME_FOR_LOOP(MFIELD,NAME,IT)) { ... } More...
 
DofEntityByFieldName::iterator get_dofs_by_name_end (const std::string &field_name) const
 get begin iterator of filed dofs of given name (instead you can use IT_GET_DOFS_FIELD_BY_NAME_FOR_LOOP(MFIELD,NAME,IT)for(IT_GET_DOFS_FIELD_BY_NAME_FOR_LOOP(MFIELD,NAME,IT)) { ... } More...
 
DofEntityByNameAndEnt::iterator get_dofs_by_name_and_ent_begin (const std::string &field_name, const EntityHandle ent) const
 get begin iterator of filed dofs of given name and ent(instead you can use IT_GET_DOFS_FIELD_BY_NAME_FOR_LOOP(MFIELD,NAME,ENT,IT) More...
 
DofEntityByNameAndEnt::iterator get_dofs_by_name_and_ent_end (const std::string &field_name, const EntityHandle ent) const
 get begin iterator of filed dofs of given name and ent (instead you can use IT_GET_DOFS_FIELD_BY_NAME_FOR_LOOP(MFIELD,NAME,ENT,IT)for(IT_GET_DOFS_FIELD_BY_NAME_AND_ENT_FOR_LOOP(MFIELD,NAME,ENT,IT)) { ... } More...
 
DofEntityByNameAndType::iterator get_dofs_by_name_and_type_begin (const std::string &field_name, const EntityType type) const
 get begin iterator of filed dofs of given name and ent type (instead you can use IT_GET_DOFS_FIELD_BY_NAME_FOR_LOOP(MFIELD,NAME,TYPE,IT) More...
 
DofEntityByNameAndType::iterator get_dofs_by_name_and_type_end (const std::string &field_name, const EntityType ent) const
 get begin iterator of filed dofs of given name end ent type(instead you can use IT_GET_DOFS_FIELD_BY_NAME_FOR_LOOP(MFIELD,NAME,TYPE,IT) More...
 
EntFiniteElementByName::iterator get_fe_by_name_begin (const std::string &fe_name) const
 get begin iterator of finite elements of given name (instead you can use IT_GET_FES_BY_NAME_FOR_LOOP(MFIELD,NAME,IT) More...
 
EntFiniteElementByName::iterator get_fe_by_name_end (const std::string &fe_name) const
 get end iterator of finite elements of given name (instead you can use IT_GET_FES_BY_NAME_FOR_LOOP(MFIELD,NAME,IT) More...
 

Log events

PetscLogEvent MOFEM_EVENT_preProcess
 Event for preProcess finite element. More...
 
PetscLogEvent MOFEM_EVENT_operator
 Event for evaluating operator of finite element. More...
 
PetscLogEvent MOFEM_EVENT_postProcess
 Event for postProcess finite element. More...
 
PetscLogEvent MOFEM_EVENT_createMat
 

Communicator

MPI_Comm cOmm
 MoFEM communicator. More...
 
ParallelComm * pComm
 MOAB communicator structure. More...
 
int sIze
 MoFEM communicator size. More...
 
int rAnk
 MOFEM communicator rank. More...
 
MPI_Comm & get_comm () const
 
int get_comm_size () const
 
int get_comm_rank () const
 

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

Core (interface) class.

This is the implementation of abstract MoFEM::Interface class. Similarly to the convention used in MoAB, we use small letters to name function of purely abstract classes. This is an exception used only here. For more details about naming functions see Coding practice

This class is not used directly by the user. For internal use only. It is database with basic functions to access data. Abstraction of this is MoFEM Interface structure.

Such deign to hide complexities for users and allow low development without interfering with users modules programmer work.

Todo:
Implement static functions for Initialization and Finalization of MoFEM. Those functions should keep all static variables and initialize/finalize other libs like PETSc. Moreover initialization functions should set error handlers, etc.
Examples:
analytical_nonlinear_poisson.cpp, analytical_poisson.cpp, analytical_poisson_field_split.cpp, bone_adaptation.cpp, cell_forces.cpp, cubit_bc_test.cpp, delete_ho_nodes.cpp, elasticity.cpp, elasticity_mixed_formulation.cpp, field_to_vertices.cpp, forces_and_sources_testing_edge_element.cpp, forces_and_sources_testing_users_base.cpp, hello_world.cpp, magnetostatic.cpp, mesh_cut.cpp, mesh_smoothing.cpp, minimal_surface_area.cpp, simple_elasticity.cpp, simple_interface.cpp, split_sideset.cpp, testing_jacobian_of_hook_element.cpp, and unsaturated_transport.cpp.

Definition at line 50 of file Core.hpp.

Member Enumeration Documentation

◆ SemaphoresBuildMofem

Is used to check consistency. I n future properly this will be removed and replaced by other solution. It is only for internal use.

Enumerator
BUILD_FIELD 
BUILD_FE 
BUILD_ADJ 
BUILD_PROBLEM 
PARTITION_PROBLEM 
PARTITION_FE 
PARTITION_GHOST_DOFS 
PARTITION_MESH 

Definition at line 165 of file Core.hpp.

Constructor & Destructor Documentation

◆ Core()

MoFEM::Core::Core ( moab::Interface &  moab,
MPI_Comm  comm = PETSC_COMM_WORLD,
const int  verbose = VERBOSE,
const bool  distributed_mesh = true 
)

Construct core database

Parameters
moabMoAB interface
commMPI communicator
verboseVerbosity level
distributed_meshUId of entities and dofs depends on owing processor, assumed that mesh is distributed. Otherwise is assumed that all processors have the same meshes and same entity handlers.

Definition at line 78 of file Core.cpp.

80  : moab(moab), cOmm(0), verbose(verbose),
81  initaliseAndBuildField(PETSC_FALSE),
82  initaliseAndBuildFiniteElements(PETSC_FALSE) {
83 
84  // This is deprecated ONE should use MoFEM::Core::Initialize
85  if (!isGloballyInitialised) {
86  PetscPushErrorHandler(mofem_error_handler, PETSC_NULL);
87  isGloballyInitialised = true;
88  }
89 
90  // Register interfaces for this implementation
91  ierr = registerInterface<UnknownInterface>(IDD_MOFEMUnknown);
92  CHKERRABORT(comm, ierr);
93  ierr = registerInterface<CoreInterface>(IDD_MOFEMCoreInterface);
94  CHKERRABORT(comm, ierr);
95  ierr = registerInterface<DeprecatedCoreInterface>(
97  CHKERRABORT(comm, ierr);
98 
99  // Register sub-interfaces
101  CHKERRABORT(PETSC_COMM_SELF, ierr);
102 
103  // Register MOFEM events in PETSc
104  PetscLogEventRegister("FE_preProcess", 0, &MOFEM_EVENT_preProcess);
105  PetscLogEventRegister("FE_operator", 0, &MOFEM_EVENT_operator);
106  PetscLogEventRegister("FE_postProcess", 0, &MOFEM_EVENT_postProcess);
107  PetscLogEventRegister("MoFEMCreateMat", 0, &MOFEM_EVENT_createMat);
108 
109  // Create duplicate communicator
110  wrapMPIComm = boost::make_shared<WrapMPIComm>(comm,cOmm);
111  MPI_Comm_size(cOmm, &sIze);
112  MPI_Comm_rank(cOmm, &rAnk);
113  // CHeck if moab has set communicator if not set communicator interbally
114  ParallelComm *pComm = ParallelComm::get_pcomm(&moab, MYPCOMM_INDEX);
115  if (pComm == NULL) {
116  pComm = new ParallelComm(&moab, cOmm);
117  }
118 
119  // Initialize database
120  ierr = getTags();
121  CHKERRABORT(cOmm, ierr);
122  ierr = clearMap();
123  CHKERRABORT(cOmm, ierr);
124 
125  basicEntityDataPtr = boost::make_shared<BasicEntityData>(moab);
126  if (distributed_mesh)
127  basicEntityDataPtr->setDistributedMesh();
128  else
129  basicEntityDataPtr->unSetDistributedMesh();
130 
132  CHKERRABORT(cOmm, ierr);
134  CHKERRABORT(cOmm, ierr);
135 
136  // Print version
137  if (verbose > QUIET) {
138  char petsc_version[255];
139  ierr = PetscGetVersion(petsc_version, 255);
140  CHKERRABORT(cOmm, ierr);
141  ierr = PetscPrintf(cOmm, "MoFEM version %d.%d.%d (%s %s) \n",
142  MoFEM_VERSION_MAJOR, MoFEM_VERSION_MINOR,
143  MoFEM_VERSION_BUILD, MOAB_VERSION_STRING, petsc_version);
144  CHKERRABORT(cOmm, ierr);
145  ierr = PetscPrintf(cOmm, "git commit id %s\n", GIT_SHA1_NAME);
146  CHKERRABORT(cOmm, ierr);
147  }
148 }
MoFEMErrorCode clearMap()
Cleaning database.
Definition: Core.cpp:216
static const MOFEMuuid IDD_MOFEMCoreInterface
Definition: Interface.hpp:24
int sIze
MoFEM communicator size.
Definition: Core.hpp:866
MoFEMErrorCode initialiseDatabaseFromMesh(int verb=DEFAULT_VERBOSITY)
Initialize database getting information on mesh.
Definition: Core.cpp:544
PetscLogEvent MOFEM_EVENT_postProcess
Event for postProcess finite element.
Definition: Core.hpp:854
boost::shared_ptr< WrapMPIComm > wrapMPIComm
Definition: Core.hpp:902
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
PetscLogEvent MOFEM_EVENT_operator
Event for evaluating operator of finite element.
Definition: Core.hpp:852
static const MOFEMuuid IDD_MOFEMUnknown
PetscLogEvent MOFEM_EVENT_createMat
Definition: Core.hpp:855
MoFEMErrorCode registerSubInterfaces()
Register insterfaces.
Definition: Core.cpp:161
std::reference_wrapper< moab::Interface > moab
moab database
Definition: Core.hpp:265
PetscLogEvent MOFEM_EVENT_preProcess
Event for preProcess finite element.
Definition: Core.hpp:850
PetscBool initaliseAndBuildField
Definition: Core.hpp:920
static MoFEMErrorCodeGeneric< PetscErrorCode > ierr
Definition: Common.hpp:80
int rAnk
MOFEM communicator rank.
Definition: Core.hpp:867
MoFEMErrorCode getOptions(int verb=DEFAULT_VERBOSITY)
Get core options from command line.
Definition: Core.cpp:519
MoFEMErrorCode getTags(int verb=DEFAULT_VERBOSITY)
Get tag handles.
Definition: Core.cpp:265
static bool isGloballyInitialised
Core base globally initialized.
Definition: Core.hpp:916
PetscBool initaliseAndBuildFiniteElements
Definition: Core.hpp:923
boost::shared_ptr< BasicEntityData > basicEntityDataPtr
Definition: Core.hpp:225
#define MYPCOMM_INDEX
default communicator number PCOMM
Definition: definitions.h:282
static PetscErrorCode mofem_error_handler(MPI_Comm comm, int line, const char *fun, const char *file, PetscErrorCode n, PetscErrorType p, const char *mess, void *ctx)
ParallelComm * pComm
MOAB communicator structure.
Definition: Core.hpp:864
int verbose
Verbosity level.
Definition: Core.hpp:904
static const MOFEMuuid IDD_MOFEMDeprecatedCoreInterface
Definition: Interface.hpp:26

◆ ~Core()

MoFEM::Core::~Core ( )

Definition at line 150 of file Core.cpp.

150  {
151  PetscBool is_finalized;
152  PetscFinalized(&is_finalized);
153  // Destroy interfaces
154  iFaces.clear();
155  // This is deprecated ONE should use MoFEM::Core::Initialize
156  if (isGloballyInitialised && is_finalized) {
157  isGloballyInitialised = false;
158  }
159 }
static bool isGloballyInitialised
Core base globally initialized.
Definition: Core.hpp:916
boost::ptr_map< unsigned long, UnknownInterface > iFaces
Hash map of pointers to interfaces.
Definition: Core.hpp:913

Member Function Documentation

◆ add_ents_to_field_by_dim() [1/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_field_by_dim ( const Range &  ents,
const int  dim,
const std::string &  name,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Add entities to field meshset.

Note
not collective

The lower dimension entities are added depending on the space type

Parameters
entsrange of entities
dimdimension of entities
namename of field
verbverbosity level
Returns
error code

Implements MoFEM::CoreInterface.

Definition at line 269 of file FieldCore.cpp.

271  {
272  Range ents_dim = ents.subset_by_dimension(dim);
273  return addEntsToFieldByDim(ents_dim, dim, name, verb);
274 }
MoFEMErrorCode addEntsToFieldByDim(const Range &ents, const int dim, const std::string &name, int verb=DEFAULT_VERBOSITY)
Definition: FieldCore.cpp:190

◆ add_ents_to_field_by_dim() [2/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_field_by_dim ( const EntityHandle  meshset,
const int  dim,
const std::string &  name,
const bool  recursive = true,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Add entities to field meshsetcollective.

The lower dimension entities are added depending on the space type

Parameters
meshset
dimdimension
namename of field
recursivetake entities recursively from embedded entities
verbverbosity level
Returns
error code

Implements MoFEM::CoreInterface.

Definition at line 289 of file FieldCore.cpp.

292  {
294  Range ents;
295  CHKERR get_moab().get_entities_by_dimension(meshset, dim, ents, recursive);
296  CHKERR addEntsToFieldByDim(ents, dim, name, verb);
298 }
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode addEntsToFieldByDim(const Range &ents, const int dim, const std::string &name, int verb=DEFAULT_VERBOSITY)
Definition: FieldCore.cpp:190

◆ add_ents_to_field_by_type() [1/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_field_by_type ( const Range &  ents,
const EntityType  type,
const std::string &  name,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Add entities to field meshset.

Note
not collective

The lower dimension entities are added depending on the space type

Parameters
entsrange of entities
typetype of entities
namename of field
verbverbosity level
Returns
error code

Implements MoFEM::CoreInterface.

Definition at line 276 of file FieldCore.cpp.

279  {
281  Range ents_type = ents.subset_by_type(type);
282  if (!ents_type.empty()) {
283  const int dim = get_moab().dimension_from_handle(ents_type[0]);
284  CHKERR addEntsToFieldByDim(ents_type, dim, name, verb);
285  }
287 }
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode addEntsToFieldByDim(const Range &ents, const int dim, const std::string &name, int verb=DEFAULT_VERBOSITY)
Definition: FieldCore.cpp:190
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_field_by_type() [2/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_field_by_type ( const EntityHandle  meshset,
const EntityType  type,
const std::string &  name,
const bool  recursive = true,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Add entities to field meshset.

Note
not collective

The lower dimension entities are added depending on the space type

Parameters
meshset
typeof entities
namename of field
recursivetake entities recursively from embedded entities
verbverbosity level
Returns
error code

Implements MoFEM::CoreInterface.

Definition at line 300 of file FieldCore.cpp.

303  {
305  Range ents;
306  CHKERR get_moab().get_entities_by_type(meshset, type, ents, recursive);
307  if (!ents.empty()) {
308  const int dim = get_moab().dimension_from_handle(ents[0]);
309  CHKERR addEntsToFieldByDim(ents, dim, name, verb);
310  }
312 }
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode addEntsToFieldByDim(const Range &ents, const int dim, const std::string &name, int verb=DEFAULT_VERBOSITY)
Definition: FieldCore.cpp:190
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_bit_ref()

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_bit_ref ( const BitRefLevel bit,
const BitRefLevel mask,
const std::string &  name,
EntityType  type,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

add TET entities from given refinement level to finite element database given by name

Note
not collective
Parameters
BitRefLevelbit
BitRefLevelmask
finiteelement name
finiteelement type
verboselevel

Implements MoFEM::CoreInterface.

Definition at line 483 of file FECore.cpp.

485  {
487 
488  if (verb == -1)
489  verb = verbose;
490  *buildMoFEM &= 1 << 0;
491  const BitFEId id = getBitFEId(name);
493  typedef RefElement_multiIndex::index<EntType_mi_tag>::type refMoabFE_by_type;
494  refMoabFE_by_type &ref_MoFEMFiniteElement =
495  refinedFiniteElements.get<EntType_mi_tag>();
496  refMoabFE_by_type::iterator miit = ref_MoFEMFiniteElement.lower_bound(type);
497  refMoabFE_by_type::iterator hi_miit =
498  ref_MoFEMFiniteElement.upper_bound(type);
499  if (verb > 1) {
500  PetscSynchronizedPrintf(cOmm, "nb. ref elements in database %d\n",
501  std::distance(miit, hi_miit));
502  }
503  int nb_add_FEs = 0;
504  for (; miit != hi_miit; miit++) {
505  BitRefLevel bit2 = miit->get()->getBitRefLevel();
506  if ((bit2 & mask) != bit2)
507  continue;
508  if ((bit2 & bit).any()) {
509  EntityHandle ent = miit->get()->getRefEnt();
510  CHKERR get_moab().add_entities(idm, &ent, 1);
511  nb_add_FEs++;
512  }
513  }
514  if (verb > 0) {
515  std::ostringstream ss;
516  ss << "Add Nb. FEs " << nb_add_FEs << " form BitRef " << bit << std::endl;
517  PetscSynchronizedPrintf(cOmm, "%s", ss.str().c_str());
518  PetscSynchronizedFlush(cOmm, PETSC_STDOUT);
519  }
520 
522 }
EntityHandle get_finite_element_meshset(const BitFEId id) const
Definition: FECore.cpp:282
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
std::bitset< BITFEID_SIZE > BitFEId
Definition: Common.hpp:150
BitFEId getBitFEId(const std::string &name) const
Get field Id.
Definition: FECore.cpp:260
std::bitset< BITREFLEVEL_SIZE > BitRefLevel
Bit structure attached to each entity identifying to what mesh entity is attached.
Definition: Common.hpp:147
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
RefElement_multiIndex refinedFiniteElements
refined elements
Definition: Core.hpp:245
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_dim() [1/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_dim ( const EntityHandle  entities,
const int  dim,
const std::string &  name,
const bool  recursive = true 
)
protectedvirtual

add entities to finite element

Note
not collective
Parameters
entitiesmeshset or range form were entities taken
dimdimension
namename of field
recursivetake entities from meshsets in meshset
Returns
error code

Implements MoFEM::CoreInterface.

Definition at line 364 of file FECore.cpp.

366  {
367  EntityHandle idm = no_handle;
368  *buildMoFEM &= 1 << 0;
371  Range ents;
372  CHKERR get_moab().get_entities_by_dimension(meshset, dim, ents, recursive);
373  CHKERR getInterface<BitRefManager>()->setElementsBitRefLevel(ents);
374  CHKERR get_moab().add_entities(idm, ents);
376 }
EntityHandle get_finite_element_meshset(const BitFEId id) const
Definition: FECore.cpp:282
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
const EntityHandle no_handle
Definition: Common.hpp:133
BitFEId getBitFEId(const std::string &name) const
Get field Id.
Definition: FECore.cpp:260
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
#define CHKERR
Inline error check.
Definition: definitions.h:586
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_dim() [2/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_dim ( const Range &  ents,
const int  dim,
const std::string &  name 
)
protectedvirtual

add entities to finite elements

Note
not collective
Parameters
entsrange of entities
dimdimension of entities
namename of finite element
Returns
error code

Implements MoFEM::CoreInterface.

Definition at line 391 of file FECore.cpp.

392  {
393  EntityHandle idm = no_handle;
394  *buildMoFEM &= 1 << 0;
397  CHKERR getInterface<BitRefManager>()->setElementsBitRefLevel(
398  ents.subset_by_dimension(dim));
399  CHKERR get_moab().add_entities(idm, ents.subset_by_dimension(dim));
401 }
EntityHandle get_finite_element_meshset(const BitFEId id) const
Definition: FECore.cpp:282
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
const EntityHandle no_handle
Definition: Common.hpp:133
BitFEId getBitFEId(const std::string &name) const
Get field Id.
Definition: FECore.cpp:260
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
#define CHKERR
Inline error check.
Definition: definitions.h:586
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_EDGEs() [1/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_EDGEs ( const Range &  edge,
const std::string &  name 
)
protectedvirtual

add EDGES entities from range to finite element database given by name

Deprecated:
use add_ents_to_finite_element_by_type
Parameters
rangecontains tetrahedron
nameFinite Element name

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 410 of file FECore.cpp.

411  {
413  CHKERR add_ents_to_finite_element_by_type(edges, MBEDGE, name);
415 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode add_ents_to_finite_element_by_type(const EntityHandle meshset, const EntityType type, const std::string &name, const bool recursive=true)
add entities to finite element
Definition: FECore.cpp:347
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_EDGEs() [2/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_EDGEs ( const EntityHandle  meshset,
const std::string &  name,
const bool  recursive = false 
)
protectedvirtual

add EDGES finite elements

Deprecated:
use add_ents_to_finite_element_by_type
Parameters
meshset
namename of finite element
recursivetake entities from meshsets in meshset
Returns
error code

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 403 of file FECore.cpp.

404  {
406  CHKERR add_ents_to_finite_element_by_type(meshset, MBEDGE, name, recursive);
408 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode add_ents_to_finite_element_by_type(const EntityHandle meshset, const EntityType type, const std::string &name, const bool recursive=true)
add entities to finite element
Definition: FECore.cpp:347
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_MESHSET()

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_MESHSET ( const EntityHandle  meshset,
const std::string &  name,
const bool  recursive = false 
)
protectedvirtual

add MESHSET element to finite element database given by name

Note
not collective
Parameters
meshsetcontains all entities that could be used for finite element
nameFinite Element name

Implements MoFEM::CoreInterface.

Definition at line 524 of file FECore.cpp.

525  {
527  *buildMoFEM &= 1 << 0;
528  const BitFEId id = getBitFEId(name);
530  if (recursive == false) {
531  CHKERR get_moab().add_entities(idm, &meshset, 1);
532  } else {
533  Range meshsets;
534  CHKERR get_moab().get_entities_by_type(meshset, MBENTITYSET, meshsets,
535  false);
536  CHKERR get_moab().add_entities(idm, meshsets);
537  }
539 }
EntityHandle get_finite_element_meshset(const BitFEId id) const
Definition: FECore.cpp:282
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
std::bitset< BITFEID_SIZE > BitFEId
Definition: Common.hpp:150
BitFEId getBitFEId(const std::string &name) const
Get field Id.
Definition: FECore.cpp:260
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
#define CHKERR
Inline error check.
Definition: definitions.h:586
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_PRISMs() [1/3]

DEPRECATED MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_PRISMs ( const Range &  prims,
const BitFEId  id 
)
protected

◆ add_ents_to_finite_element_by_PRISMs() [2/3]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_PRISMs ( const Range &  prims,
const std::string &  name 
)
protectedvirtual

add PRISM entities from meshset to finite element database given by name

Deprecated:
use add_ents_to_finite_element_by_type
Parameters
rangecontains tetrahedron
nameFinite Element name

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 450 of file FECore.cpp.

451  {
453  CHKERR add_ents_to_finite_element_by_type(prims, MBPRISM, name);
455 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode add_ents_to_finite_element_by_type(const EntityHandle meshset, const EntityType type, const std::string &name, const bool recursive=true)
add entities to finite element
Definition: FECore.cpp:347
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_PRISMs() [3/3]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_PRISMs ( const EntityHandle  meshset,
const std::string &  name,
const bool  recursive = false 
)
protectedvirtual

add TET entities from meshset to finite element database given by name

Deprecated:
use add_ents_to_finite_element_by_type
Parameters
meshsetcontains tetrahedron
nameFinite Element name
recursiveif true parent meshset is searched recursively

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 456 of file FECore.cpp.

457  {
459  CHKERR add_ents_to_finite_element_by_type(meshset, MBPRISM, name, recursive);
461 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode add_ents_to_finite_element_by_type(const EntityHandle meshset, const EntityType type, const std::string &name, const bool recursive=true)
add entities to finite element
Definition: FECore.cpp:347
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_TETs() [1/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_TETs ( const Range &  tets,
const std::string &  name 
)
protectedvirtual

add TET entities from range to finite element database given by name

Deprecated:
use add_ents_to_finite_element_by_type
Parameters
rangecontains tetrahedron
nameFinite Element name

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 437 of file FECore.cpp.

438  {
440  CHKERR add_ents_to_finite_element_by_type(tets, MBTET, name);
442 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode add_ents_to_finite_element_by_type(const EntityHandle meshset, const EntityType type, const std::string &name, const bool recursive=true)
add entities to finite element
Definition: FECore.cpp:347
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_TETs() [2/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_TETs ( const EntityHandle  meshset,
const std::string &  name,
const bool  recursive = false 
)
protectedvirtual

add TET entities from meshset to finite element database given by name

Deprecated:
use add_ents_to_finite_element_by_type
Parameters
meshsetcontains tetrahedron
nameFinite Element name
recursiveif true parent meshset is searched recursively

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 443 of file FECore.cpp.

444  {
446  CHKERR add_ents_to_finite_element_by_type(meshset, MBTET, name, recursive);
448 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode add_ents_to_finite_element_by_type(const EntityHandle meshset, const EntityType type, const std::string &name, const bool recursive=true)
add entities to finite element
Definition: FECore.cpp:347
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_TRIs() [1/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_TRIs ( const Range &  tris,
const std::string &  name 
)
protectedvirtual

add TRI entities from range to finite element database given by name

Deprecated:
use add_ents_to_finite_element_by_type
Parameters
rangecontains tetrahedron
nameFinite Element name

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 424 of file FECore.cpp.

425  {
427  CHKERR add_ents_to_finite_element_by_type(tris, MBTRI, name);
429 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode add_ents_to_finite_element_by_type(const EntityHandle meshset, const EntityType type, const std::string &name, const bool recursive=true)
add entities to finite element
Definition: FECore.cpp:347
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_TRIs() [2/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_TRIs ( const EntityHandle  meshset,
const std::string &  name,
const bool  recursive = false 
)
protectedvirtual

add TRI entities from meshset to finite element database given by name

Deprecated:
use add_ents_to_finite_element_by_type
Parameters
rangecontains tetrahedron
nameFinite Element name
recursiveif true parent meshset is searched recursively

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 430 of file FECore.cpp.

431  {
433  CHKERR add_ents_to_finite_element_by_type(meshset, MBTRI, name, recursive);
435 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode add_ents_to_finite_element_by_type(const EntityHandle meshset, const EntityType type, const std::string &name, const bool recursive=true)
add entities to finite element
Definition: FECore.cpp:347
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_type() [1/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_type ( const EntityHandle  entities,
const EntityType  type,
const std::string &  name,
const bool  recursive = true 
)
protectedvirtual

add entities to finite element

Note
not collective
Parameters
entitiesmeshset or range form were entities taken
typetype of entity
namename of field
recursivetake entities from meshsets in meshset
Returns
error code

Implements MoFEM::CoreInterface.

Definition at line 347 of file FECore.cpp.

349  {
350  *buildMoFEM &= 1 << 0;
351  EntityHandle idm = no_handle;
353 
355  Range ents;
356  CHKERR get_moab().get_entities_by_type(meshset, type, ents, recursive);
357  CHKERR getInterface<BitRefManager>()->setElementsBitRefLevel(ents);
358  CHKERR get_moab().add_entities(idm, ents);
359 
361 }
EntityHandle get_finite_element_meshset(const BitFEId id) const
Definition: FECore.cpp:282
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
const EntityHandle no_handle
Definition: Common.hpp:133
BitFEId getBitFEId(const std::string &name) const
Get field Id.
Definition: FECore.cpp:260
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
#define CHKERR
Inline error check.
Definition: definitions.h:586
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_type() [2/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_type ( const Range &  ents,
const EntityType  type,
const std::string &  name 
)
protectedvirtual

add entities to finite elements

Note
not collective
Parameters
entsrange of entities
typetype of entity (MBVERTEX, MBEDGE, MBTRI, ...)
namename of finite element
Returns
error code

Implements MoFEM::CoreInterface.

Definition at line 378 of file FECore.cpp.

379  {
380  EntityHandle idm = no_handle;
381  *buildMoFEM &= 1 << 0;
384  CHKERR getInterface<BitRefManager>()->setElementsBitRefLevel(
385  ents.subset_by_type(type));
386  CHKERR get_moab().add_entities(idm, ents.subset_by_type(type));
388 } // namespace MoFEM
EntityHandle get_finite_element_meshset(const BitFEId id) const
Definition: FECore.cpp:282
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
const EntityHandle no_handle
Definition: Common.hpp:133
BitFEId getBitFEId(const std::string &name) const
Get field Id.
Definition: FECore.cpp:260
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
#define CHKERR
Inline error check.
Definition: definitions.h:586
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_by_VERTICEs()

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_by_VERTICEs ( const Range &  vert,
const std::string &  name 
)
protectedvirtual

add VERTICES entities from range to finite element database given by name

Deprecated:
use add_ents_to_finite_element_by_type
Parameters
rangecontains tetrahedron
nameFinite Element name

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 417 of file FECore.cpp.

418  {
420  CHKERR add_ents_to_finite_element_by_type(vert, MBVERTEX, name);
422 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode add_ents_to_finite_element_by_type(const EntityHandle meshset, const EntityType type, const std::string &name, const bool recursive=true)
add entities to finite element
Definition: FECore.cpp:347
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_EntType_by_bit_ref() [1/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_EntType_by_bit_ref ( const BitRefLevel bit,
const std::string &  name,
EntityType  type,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

add TET elements from given refinement level to finite element database given by name

Deprecated:
use add_ents_to_finite_element_by_bit_ref with mask explicitly given
Parameters
BitRefLevelbit
finiteelement name
finiteelenent type
verrboselevel

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 464 of file FECore.cpp.

466  {
469  type, verb);
470 
472 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
MoFEMErrorCode add_ents_to_finite_element_by_bit_ref(const BitRefLevel &bit, const BitRefLevel &mask, const std::string &name, EntityType type, int verb=DEFAULT_VERBOSITY)
add TET entities from given refinement level to finite element database given by name ...
Definition: FECore.cpp:483
std::bitset< BITREFLEVEL_SIZE > BitRefLevel
Bit structure attached to each entity identifying to what mesh entity is attached.
Definition: Common.hpp:147
#define CHKERR
Inline error check.
Definition: definitions.h:586
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_ents_to_finite_element_EntType_by_bit_ref() [2/2]

MoFEMErrorCode MoFEM::Core::add_ents_to_finite_element_EntType_by_bit_ref ( const BitRefLevel bit,
const BitRefLevel mask,
const std::string &  name,
EntityType  type,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

add TET entities from given refinement level to finite element database given by name

Deprecated:
use add_ents_to_finite_element_by_bit_ref with mask explicitly given
Parameters
BitRefLevelbit
BitRefLevelmask
finiteelement name
finiteelement type
verrboselevel

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 474 of file FECore.cpp.

476  {
478  CHKERR add_ents_to_finite_element_by_bit_ref(bit, mask, name, type, verb);
479 
481 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
MoFEMErrorCode add_ents_to_finite_element_by_bit_ref(const BitRefLevel &bit, const BitRefLevel &mask, const std::string &name, EntityType type, int verb=DEFAULT_VERBOSITY)
add TET entities from given refinement level to finite element database given by name ...
Definition: FECore.cpp:483
#define CHKERR
Inline error check.
Definition: definitions.h:586
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_field()

MoFEMErrorCode MoFEM::Core::add_field ( const std::string &  name,
const FieldSpace  space,
const FieldApproximationBase  base,
const FieldCoefficientsNumber  nb_coefficients,
const TagType  tag_type = MB_TAG_SPARSE,
const enum MoFEMTypes  bh = MF_EXCL,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Add filed.

Parameters
nameField name
spaceSpace L2,H1,Hdiv,Hcurl
baseApproximation base AINSWORTH_LEGENDRE_BASE, AINSWORTH_BERNSTEIN_BEZIER_BASE ...
nb_coefficientsNumber of field coefficients
tag_typeTag type, MB_TAG_DENSE or MB_TAG_SPARSE (default)
bhControl behavior, if MF_EXCL throws error if exist
verbVerbosity level
Returns
Return error code

TODO:

Todo:
MB_TAG_DENSE will not work properly in general case. It is need to separate field tags for each entity separately. That will allow for HO orders but homogenous approx. order on each entity. Need some discussion what is optimal solution. MB_TAG_SPARSE gives flexibility, but it not memory efficient. MB_TAG_DENSE uses memory more efficient and in principle allow for better efficiency if properly utilized.

FIXME:

Bug:
Need to resolve problem of dense tags at this stage of development will make only problems

Implements MoFEM::CoreInterface.

Definition at line 91 of file FieldCore.cpp.

95  {
97  if (verb == -1)
98  verb = verbose;
99  *buildMoFEM = 0;
100  auto fit = fIelds.get<FieldName_mi_tag>().find(name);
101  if (fit != fIelds.get<FieldName_mi_tag>().end()) {
102  if (bh == MF_EXCL) {
103  SETERRQ1(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
104  "field is <%s> in database", name.c_str());
105  }
106  } else {
107  EntityHandle meshset;
108  CHKERR get_moab().create_meshset(MESHSET_SET | MESHSET_TRACK_OWNER,
109  meshset);
110  // id
111  BitFieldId id = getFieldShift();
112  CHKERR get_moab().tag_set_data(th_FieldId, &meshset, 1, &id);
113  // space
114  CHKERR get_moab().tag_set_data(th_FieldSpace, &meshset, 1, &space);
115  // base
116  CHKERR get_moab().tag_set_data(th_FieldBase, &meshset, 1, &base);
117 
118  // name
119  void const *tag_data[] = {name.c_str()};
120  int tag_sizes[1];
121  tag_sizes[0] = name.size();
122  CHKERR get_moab().tag_set_by_ptr(th_FieldName, &meshset, 1, tag_data,
123  tag_sizes);
124  // name data prefix
125  const std::string name_data_prefix("_App_Data");
126  void const *tag_prefix_data[] = {name_data_prefix.c_str()};
127  int tag_prefix_sizes[1];
128  tag_prefix_sizes[0] = name_data_prefix.size();
129  CHKERR get_moab().tag_set_by_ptr(th_FieldName_DataNamePrefix, &meshset, 1,
130  tag_prefix_data, tag_prefix_sizes);
131  Tag th_app_order, th_field_data, th_rank;
132  // data
133  std::string tag_data_name = name_data_prefix + name;
134  const int def_len = 0;
135  CHKERR get_moab().tag_get_handle(
136  tag_data_name.c_str(), def_len, MB_TYPE_OPAQUE, th_field_data,
137  MB_TAG_CREAT | MB_TAG_BYTES | MB_TAG_VARLEN | MB_TAG_SPARSE, NULL);
138  std::string tag_data_name_verts = name_data_prefix + name + "V";
139  VectorDouble def_vert_data(nb_of_coefficients);
140  def_vert_data.clear();
141  CHKERR get_moab().tag_get_handle(
142  tag_data_name_verts.c_str(), nb_of_coefficients, MB_TYPE_DOUBLE,
143  th_field_data, MB_TAG_CREAT | tag_type, &*def_vert_data.begin());
144  // order
145  ApproximationOrder def_ApproximationOrder = -1;
146  const std::string Tag_ApproximationOrder_name = "_App_Order_" + name;
147  CHKERR get_moab().tag_get_handle(
148  Tag_ApproximationOrder_name.c_str(), sizeof(ApproximationOrder),
149  MB_TYPE_OPAQUE, th_app_order,
150  MB_TAG_CREAT | MB_TAG_BYTES | MB_TAG_SPARSE, &def_ApproximationOrder);
151  // rank
152  int def_rank = 1;
153  const std::string tag_rank_name = "_Field_Rank_" + name;
154  CHKERR get_moab().tag_get_handle(
155  tag_rank_name.c_str(), sizeof(FieldCoefficientsNumber), MB_TYPE_OPAQUE,
156  th_rank, MB_TAG_CREAT | MB_TAG_BYTES | MB_TAG_SPARSE, &def_rank);
157  CHKERR get_moab().tag_set_data(th_rank, &meshset, 1, &nb_of_coefficients);
158 
159  // add meshset
160  std::pair<Field_multiIndex::iterator, bool> p;
161  CoordSystemsManager *cs_manger_ptr;
162  CHKERR getInterface(cs_manger_ptr);
163  boost::shared_ptr<CoordSys> undefined_cs_ptr;
164  CHKERR cs_manger_ptr->getCoordSysPtr("UNDEFINED", undefined_cs_ptr);
165  int sys_name_size[1];
166  sys_name_size[0] = undefined_cs_ptr->getName().size();
167  void const *sys_name[] = {&*undefined_cs_ptr->getNameRef().begin()};
168  CHKERR get_moab().tag_set_by_ptr(cs_manger_ptr->get_th_CoordSysName(),
169  &meshset, 1, sys_name, sys_name_size);
170  EntityHandle coord_sys_id = undefined_cs_ptr->getMeshset();
171  CHKERR get_moab().add_entities(coord_sys_id, &meshset, 1);
172  p = fIelds.insert(
173  boost::make_shared<Field>(moab, meshset, undefined_cs_ptr));
174  if (bh == MF_EXCL) {
175  if (!p.second)
176  SETERRQ1(PETSC_COMM_SELF, MOFEM_NOT_FOUND,
177  "field not inserted %s (top tip, it could be already there)",
178  Field(moab, meshset, undefined_cs_ptr).getName().c_str());
179  }
180  if (verb > QUIET) {
181  std::ostringstream ss;
182  ss << "add: " << **p.first << std::endl;
183  PetscPrintf(cOmm, ss.str().c_str());
184  }
185  }
186 
188 }
int FieldCoefficientsNumber
Number of field coefficients.
Definition: Common.hpp:132
Tag th_FieldSpace
Definition: Core.hpp:204
Tag th_FieldName_DataNamePrefix
Definition: Core.hpp:204
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
IFACE getInterface() const
Get interface pointer to pointer of interface.
std::bitset< BITFIELDID_SIZE > BitFieldId
Definition: Common.hpp:149
Tag th_FieldId
Definition: Core.hpp:204
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
Tag th_FieldBase
Definition: Core.hpp:204
ublas::vector< double, DoubleAllocator > VectorDouble
Definition: Common.hpp:211
Tag th_FieldName
Definition: Core.hpp:204
#define CHKERR
Inline error check.
Definition: definitions.h:586
Field_multiIndex fIelds
fields
Definition: Core.hpp:247
int ApproximationOrder
Approximation on the entity.
Definition: Common.hpp:131
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404
BitFieldId getFieldShift()
Return unique field Id.
Definition: Core.cpp:194

◆ add_finite_element()

MoFEMErrorCode MoFEM::Core::add_finite_element ( const std::string &  fe_name,
enum MoFEMTypes  bh = MF_EXCL,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

add finite element

Parameters
namefinite element name
Note
add_file is a collective, should be executed on all processors. Otherwise could lead to deadlock.

Example

CHKERR mField.add_finite_element("ELASTIC");
CHKERR mField.add_finite_element("PLASTIC");

Implements MoFEM::CoreInterface.

Definition at line 45 of file FECore.cpp.

46  {
48  *buildMoFEM &= 1 << 0;
49  if (verb == -1) {
50  verb = verbose;
51  }
52  typedef FiniteElement_multiIndex::index<FiniteElement_name_mi_tag>::type
53  FiniteElements_by_name;
54  FiniteElements_by_name &finite_element_name_set =
55  finiteElements.get<FiniteElement_name_mi_tag>();
56  FiniteElements_by_name::iterator it_fe =
57  finite_element_name_set.find(fe_name);
58  if (bh == MF_EXCL) {
59  if (it_fe != finite_element_name_set.end()) {
60  SETERRQ1(cOmm, MOFEM_NOT_FOUND, "this < %s > is there", fe_name.c_str());
61  }
62  } else {
63  if (it_fe != finite_element_name_set.end())
65  }
66  EntityHandle meshset;
67  CHKERR get_moab().create_meshset(MESHSET_SET | MESHSET_TRACK_OWNER, meshset);
68 
69  // id
70  BitFEId id = getFEShift();
71  CHKERR get_moab().tag_set_data(th_FEId, &meshset, 1, &id);
72 
73  // id name
74  void const *tag_data[] = {fe_name.c_str()};
75  int tag_sizes[1];
76  tag_sizes[0] = fe_name.size();
77  CHKERR get_moab().tag_set_by_ptr(th_FEName, &meshset, 1, tag_data, tag_sizes);
78 
79  // add FiniteElement
80  std::pair<FiniteElement_multiIndex::iterator, bool> p = finiteElements.insert(
81  boost::shared_ptr<FiniteElement>(new FiniteElement(moab, meshset)));
82  if (!p.second)
83  SETERRQ(cOmm, MOFEM_OPERATION_UNSUCCESSFUL, "FiniteElement not inserted");
84  if (verb > 0) {
85  std::ostringstream ss;
86  ss << "add finite element: " << fe_name << std::endl;
87  PetscPrintf(cOmm, ss.str().c_str());
88  // list_finiteElements();
89  }
91 }
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
std::bitset< BITFEID_SIZE > BitFEId
Definition: Common.hpp:150
Tag th_FEName
Definition: Core.hpp:206
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
BitFEId getFEShift()
Return unique finite element Id.
Definition: Core.cpp:206
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
FiniteElement_multiIndex finiteElements
finite elements
Definition: Core.hpp:251
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
Tag th_FEId
Definition: Core.hpp:206
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ add_problem()

MoFEMErrorCode MoFEM::Core::add_problem ( const std::string &  name,
enum MoFEMTypes  bh = MF_EXCL,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Add problem.

Note
add_file is a collective, should be executed on all processors. Otherwise could lead to deadlock.

Implements MoFEM::CoreInterface.

Definition at line 55 of file ProblemsCore.cpp.

56  {
58  if (verb == -1)
59  verb = verbose;
60  auto miit = pRoblems.get<Problem_mi_tag>().find(name);
61  if (miit == pRoblems.get<Problem_mi_tag>().end()) {
63  CHKERR addProblem(id, name, verb);
64  } else if (bh == MF_EXCL) {
65  SETERRQ1(PETSC_COMM_SELF, MOFEM_NOT_FOUND, "problem is in database %s",
66  name.c_str());
67  }
69 }
std::bitset< BITPROBLEMID_SIZE > BitProblemId
Definition: Common.hpp:151
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
BitProblemId getProblemShift()
Return unique problem Id.
Definition: Core.cpp:211
MoFEMErrorCode addProblem(const BitProblemId id, const std::string &name, int verb=DEFAULT_VERBOSITY)
add problem
Problem_multiIndex pRoblems
problems multi-index
Definition: Core.hpp:257
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ addEntsToFieldByDim()

MoFEMErrorCode MoFEM::Core::addEntsToFieldByDim ( const Range &  ents,
const int  dim,
const std::string &  name,
int  verb = DEFAULT_VERBOSITY 
)
protected

Definition at line 190 of file FieldCore.cpp.

191  {
192 
193  *buildMoFEM = 0;
194  EntityHandle idm = no_handle;
195  if (verb == -1)
196  verb = verbose;
198  idm = get_field_meshset(name);
199  FieldSpace space;
200  CHKERR get_moab().tag_get_data(th_FieldSpace, &idm, 1, &space);
201  std::vector<int> nb_ents_on_dim(3, 0);
202  switch (space) {
203  case L2:
204  CHKERR get_moab().add_entities(idm, ents);
205  if (verb >= VERY_VERBOSE) {
206  std::ostringstream ss;
207  ss << "add entities to field " << name;
208  ss << " nb. add ents " << ents.size();
209  ss << std::endl;
210  PetscSynchronizedPrintf(cOmm, ss.str().c_str());
211  }
212  break;
213  case H1:
214  CHKERR get_moab().add_entities(idm, ents);
215  for (int dd = 0; dd != dim; ++dd) {
216  Range adj_ents;
217  CHKERR get_moab().get_adjacencies(ents, dd, false, adj_ents,
218  moab::Interface::UNION);
219  if (dd == 0) {
220  Range topo_nodes;
221  CHKERR get_moab().get_connectivity(ents, topo_nodes, true);
222  Range mid_nodes;
223  CHKERR get_moab().get_connectivity(ents, mid_nodes, false);
224  mid_nodes = subtract(mid_nodes, topo_nodes);
225  adj_ents = subtract(adj_ents, mid_nodes);
226  }
227  CHKERR get_moab().add_entities(idm, adj_ents);
228  nb_ents_on_dim[dd] = adj_ents.size();
229  }
230  break;
231  case HCURL:
232  CHKERR get_moab().add_entities(idm, ents);
233  for (int dd = 1; dd != dim; ++dd) {
234  Range adj_ents;
235  CHKERR get_moab().get_adjacencies(ents, dd, false, adj_ents,
236  moab::Interface::UNION);
237  CHKERR get_moab().add_entities(idm, adj_ents);
238  nb_ents_on_dim[dd] = adj_ents.size();
239  }
240  break;
241  case HDIV:
242  CHKERR get_moab().add_entities(idm, ents);
243  if (dim > 2) {
244  Range adj_ents;
245  CHKERR get_moab().get_adjacencies(ents, 2, false, adj_ents,
246  moab::Interface::UNION);
247  CHKERR get_moab().add_entities(idm, adj_ents);
248  nb_ents_on_dim[2] = adj_ents.size();
249  }
250  break;
251  default:
252  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
253  "sorry, unknown space added to entity");
254  }
255  if (verb >= VERY_VERBOSE) {
256  std::ostringstream ss;
257  ss << "add entities to field " << name;
258  ss << " nb. add ents " << ents.size();
259  ss << " nb. add faces " << nb_ents_on_dim[2];
260  ss << " nb. add edges " << nb_ents_on_dim[1];
261  ss << " nb. add nodes " << nb_ents_on_dim[0];
262  ss << std::endl;
263  PetscSynchronizedPrintf(cOmm, ss.str().c_str());
264  PetscSynchronizedFlush(cOmm, PETSC_STDOUT);
265  }
267 }
Tag th_FieldSpace
Definition: Core.hpp:204
field with continuous normal traction
Definition: definitions.h:170
const Tensor2_symmetric_Expr< const ddTensor0< T, Dim, i, j >, typename promote< T, double >::V, Dim, i, j > dd(const Tensor0< T *> &a, const Index< i, Dim > index1, const Index< j, Dim > index2, const Tensor1< int, Dim > &d_ijk, const Tensor1< double, Dim > &d_xyz)
Definition: ddTensor0.hpp:33
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
const EntityHandle no_handle
Definition: Common.hpp:133
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
field with continuous tangents
Definition: definitions.h:169
FieldSpace
approximation spaces
Definition: definitions.h:165
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
EntityHandle get_field_meshset(const BitFieldId id) const
Definition: FieldCore.cpp:31
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404
continuous field
Definition: definitions.h:168
field with C-1 continuity
Definition: definitions.h:171

◆ addPrismToDatabase()

MoFEMErrorCode MoFEM::Core::addPrismToDatabase ( const EntityHandle  prism,
int  verb = DEFAULT_VERBOSITY 
)

add prim element

FIXME: This is dirt solution, need to be fixed

Parameters
prismprim handle
verbverbosity level
Returns
error code

Definition at line 236 of file Core.cpp.

236  {
238  if (verb == -1)
239  verb = verbose;
240  std::pair<RefEntity_multiIndex::iterator, bool> p_ent;
241  p_ent = refinedEntities.insert(
242  boost::make_shared<RefEntity>(basicEntityDataPtr, prism));
243  if (p_ent.second) {
244  std::pair<RefElement_multiIndex::iterator, bool> p;
245  p = refinedFiniteElements.insert(
246  boost::shared_ptr<RefElement>(new RefElement_PRISM(*p_ent.first)));
247  int num_nodes;
248  const EntityHandle *conn;
249  CHKERR get_moab().get_connectivity(prism, conn, num_nodes, true);
250  Range face_side3, face_side4;
251  CHKERR get_moab().get_adjacencies(conn, 3, 2, false, face_side3);
252  CHKERR get_moab().get_adjacencies(&conn[3], 3, 2, false, face_side4);
253  if (face_side3.size() != 1)
254  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
255  "prism don't have side face 3");
256  if (face_side4.size() != 1)
257  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
258  "prims don't have side face 4");
259  p.first->get()->getSideNumberPtr(*face_side3.begin());
260  p.first->get()->getSideNumberPtr(*face_side4.begin());
261  }
263 }
RefEntity_multiIndex refinedEntities
refined entities
Definition: Core.hpp:244
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
RefElement_multiIndex refinedFiniteElements
refined elements
Definition: Core.hpp:245
#define CHKERR
Inline error check.
Definition: definitions.h:586
boost::shared_ptr< BasicEntityData > basicEntityDataPtr
Definition: Core.hpp:225
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ addProblem()

MoFEMErrorCode MoFEM::Core::addProblem ( const BitProblemId  id,
const std::string &  name,
int  verb = DEFAULT_VERBOSITY 
)
private

add problem

Parameters
idproblem id
nameproblem name
verbverbosity level
Returns
MoFEMErrorCode

Definition at line 30 of file ProblemsCore.cpp.

31  {
33  if (verb == -1)
34  verb = verbose;
35  EntityHandle meshset;
36  CHKERR get_moab().create_meshset(MESHSET_SET | MESHSET_TRACK_OWNER, meshset);
37  CHKERR get_moab().tag_set_data(th_ProblemId, &meshset, 1, &id);
38  void const *tag_data[] = {name.c_str()};
39  int tag_sizes[1];
40  tag_sizes[0] = name.size();
41  CHKERR get_moab().tag_set_by_ptr(th_ProblemName, &meshset, 1, tag_data, tag_sizes);
42  // create entry
43  std::pair<Problem_multiIndex::iterator, bool> p =
44  pRoblems.insert(Problem(moab, meshset));
45  NOT_USED(p);
46  assert(p.second);
47  if (verb > 0) {
48  std::ostringstream ss;
49  ss << "add problem: " << name << std::endl;
50  PetscPrintf(cOmm, ss.str().c_str());
51  }
53 }
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
Tag th_ProblemName
Definition: Core.hpp:208
Tag th_ProblemId
Definition: Core.hpp:208
Problem_multiIndex pRoblems
problems multi-index
Definition: Core.hpp:257
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404
#define NOT_USED(x)
Definition: definitions.h:300

◆ build_adjacencies() [1/3]

MoFEMErrorCode MoFEM::Core::build_adjacencies ( const Range &  ents,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

build adjacencies

Parameters
listof entities

This function will get information of adjacent finite elements and fields of all entities. If this is not executed, partitioning the problem is not possible. Adjacency map is based on degrees of freedom adjacent to elements. This linked to geometric element connectivity.

If new degrees of freedom or new finite elements are added to the database, adjacency map has to be rebuild.

Implements MoFEM::CoreInterface.

Definition at line 848 of file FECore.cpp.

848  {
850  if (verb == -1)
851  verb = verbose;
852  if (!((*buildMoFEM) & BUILD_FIELD))
853  SETERRQ(cOmm, MOFEM_NOT_FOUND, "field not build");
854  if (!((*buildMoFEM) & BUILD_FE))
855  SETERRQ(cOmm, MOFEM_NOT_FOUND, "fe not build");
856  for (Range::const_pair_iterator peit = ents.pair_begin();
857  peit != ents.pair_end(); ++peit) {
858  EntFiniteElement_multiIndex::index<Ent_mi_tag>::type::iterator fit, hi_fit;
859  fit = entsFiniteElements.get<Ent_mi_tag>().lower_bound(peit->first);
860  hi_fit = entsFiniteElements.get<Ent_mi_tag>().upper_bound(peit->second);
861  for (; fit != hi_fit; ++fit) {
862  if ((*fit)->getBitFieldIdRow().none() &&
863  (*fit)->getBitFieldIdCol().none() &&
864  (*fit)->getBitFieldIdData().none())
865  continue;
866  int by = BYROW;
867  if ((*fit)->getBitFieldIdRow() != (*fit)->getBitFieldIdCol())
868  by |= BYCOL;
869  if ((*fit)->getBitFieldIdRow() != (*fit)->getBitFieldIdData())
870  by |= BYDATA;
871  FieldEntityEntFiniteElementAdjacencyMap_change_ByWhat modify_row(by);
872  UId ent_uid = UId(0);
873  for (DofEntity_multiIndex_uid_view::iterator rvit =
874  (*fit)->row_dof_view->begin();
875  rvit != (*fit)->row_dof_view->end(); ++rvit) {
876  if (ent_uid == (*rvit)->getFieldEntityPtr()->getGlobalUniqueId())
877  continue;
878  ent_uid = (*rvit)->getFieldEntityPtr()->getGlobalUniqueId();
879  std::pair<FieldEntityEntFiniteElementAdjacencyMap_multiIndex::iterator,
880  bool>
881  p;
882  p = entFEAdjacencies.insert(FieldEntityEntFiniteElementAdjacencyMap(
883  (*rvit)->getFieldEntityPtr(), *fit));
884  bool success = entFEAdjacencies.modify(p.first, modify_row);
885  if (!success)
887  "modification unsuccessful");
888  }
889  if ((*fit)->getBitFieldIdRow() != (*fit)->getBitFieldIdCol()) {
890  int by = BYCOL;
891  if ((*fit)->getBitFieldIdCol() != (*fit)->getBitFieldIdData())
892  by |= BYDATA;
893  FieldEntityEntFiniteElementAdjacencyMap_change_ByWhat modify_col(by);
894  ent_uid = UId(0);
895  for (DofEntity_multiIndex_uid_view::iterator cvit =
896  (*fit)->col_dof_view->begin();
897  cvit != (*fit)->col_dof_view->end(); cvit++) {
898  if (ent_uid == (*cvit)->getFieldEntityPtr()->getGlobalUniqueId())
899  continue;
900  ent_uid = (*cvit)->getFieldEntityPtr()->getGlobalUniqueId();
901  std::pair<
902  FieldEntityEntFiniteElementAdjacencyMap_multiIndex::iterator,
903  bool>
904  p;
905  p = entFEAdjacencies.insert(FieldEntityEntFiniteElementAdjacencyMap(
906  (*cvit)->getFieldEntityPtr(), *fit));
907  bool success = entFEAdjacencies.modify(p.first, modify_col);
908  if (!success)
910  "modification unsuccessful");
911  }
912  }
913  if ((*fit)->getBitFieldIdRow() != (*fit)->getBitFieldIdData() ||
914  (*fit)->getBitFieldIdCol() != (*fit)->getBitFieldIdData()) {
915  FieldEntityEntFiniteElementAdjacencyMap_change_ByWhat modify_data(
916  BYDATA);
917  ent_uid = UId(0);
918  for (FEDofEntity_multiIndex::iterator dvit = (*fit)->data_dofs->begin();
919  dvit != (*fit)->data_dofs->end(); dvit++) {
920  if (ent_uid == (*dvit)->getFieldEntityPtr()->getGlobalUniqueId())
921  continue;
922  ent_uid = (*dvit)->getFieldEntityPtr()->getGlobalUniqueId();
923  std::pair<
924  FieldEntityEntFiniteElementAdjacencyMap_multiIndex::iterator,
925  bool>
926  p;
927  p = entFEAdjacencies.insert(FieldEntityEntFiniteElementAdjacencyMap(
928  (*dvit)->getFieldEntityPtr(), *fit));
929  bool success = entFEAdjacencies.modify(p.first, modify_data);
930  if (!success)
932  "modification unsuccessful");
933  }
934  }
935  }
936  }
937  if (verb >= VERY_NOISY) {
939  }
940  if (verb >= VERBOSE) {
941  PetscSynchronizedPrintf(cOmm, "Nb. entFEAdjacencies %u\n",
942  entFEAdjacencies.size());
943  PetscSynchronizedFlush(cOmm, PETSC_STDOUT);
944  }
945  *buildMoFEM |= 1 << 2;
947 }
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
uint128_t UId
Unique Id.
Definition: Common.hpp:136
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
FieldEntityEntFiniteElementAdjacencyMap_multiIndex entFEAdjacencies
adjacencies of elements to dofs
Definition: Core.hpp:255
int verbose
Verbosity level.
Definition: Core.hpp:904
EntFiniteElement_multiIndex entsFiniteElements
finite element entities
Definition: Core.hpp:252
MoFEMErrorCode list_adjacencies() const
list adjacencies
Definition: FieldCore.cpp:912

◆ build_adjacencies() [2/3]

MoFEMErrorCode MoFEM::Core::build_adjacencies ( const BitRefLevel bit,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

build adjacencies

Parameters
bitadjacencies for refine level

This function will get information of adjacent finite elements and fields of all entities. If this is not executed, partitioning the problem is not possible. Adjacency map is based on degrees of freedom adjacent to elements. This linked to geometric element connectivity.

If new degrees of freedom or new finite elements are added to the database, adjacency map has to be rebuild.

Implements MoFEM::CoreInterface.

Definition at line 961 of file FECore.cpp.

961  {
963  if (verb == -1)
964  verb = verbose;
965  CHKERR build_adjacencies(bit, BitRefLevel().set(), verb);
966 
968 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
MoFEMErrorCode build_adjacencies(const Range &ents, int verb=DEFAULT_VERBOSITY)
build adjacencies
Definition: FECore.cpp:848
std::bitset< BITREFLEVEL_SIZE > BitRefLevel
Bit structure attached to each entity identifying to what mesh entity is attached.
Definition: Common.hpp:147
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ build_adjacencies() [3/3]

MoFEMErrorCode MoFEM::Core::build_adjacencies ( const BitRefLevel bit,
const BitRefLevel mask,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

build adjacencies

Parameters
bitadjacencies for refine level
maskmask for bit level

This function will get information of adjacent finite elements and fields of all entities. If this is not executed, partitioning the problem is not possible. Adjacency map is based on degrees of freedom adjacent to elements. This linked to geometric element connectivity.

If new degrees of freedom or new finite elements are added to the database, adjacency map has to be rebuild.

Implements MoFEM::CoreInterface.

Definition at line 949 of file FECore.cpp.

950  {
952  if (verb == -1)
953  verb = verbose;
954  Range ents;
955  CHKERR BitRefManager(*this).getEntitiesByRefLevel(bit, mask, ents);
956 
957  CHKERR build_adjacencies(ents, verb);
958 
960 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
MoFEMErrorCode build_adjacencies(const Range &ents, int verb=DEFAULT_VERBOSITY)
build adjacencies
Definition: FECore.cpp:848
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ build_field()

MoFEMErrorCode MoFEM::Core::build_field ( const std::string  field_name,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

build field by name

Parameters
field_name
verbm
Returns
MoFEMErrorCode

Implements MoFEM::CoreInterface.

Definition at line 857 of file FieldCore.cpp.

857  {
859  auto miit = fIelds.get<FieldName_mi_tag>().find(field_name);
860  if (miit == fIelds.get<FieldName_mi_tag>().end()) {
861  SETERRQ1(PETSC_COMM_SELF, MOFEM_NOT_FOUND, "Field < %s > not found",
862  field_name.c_str());
863  }
864  CHKERR buildField((*miit), verb);
865  PetscSynchronizedFlush(cOmm, PETSC_STDOUT);
867 }
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
Field_multiIndex fIelds
fields
Definition: Core.hpp:247
MoFEMErrorCode buildField(const boost::shared_ptr< Field > &field, int verb=DEFAULT_VERBOSITY)
Definition: FieldCore.cpp:776
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ build_fields()

MoFEMErrorCode MoFEM::Core::build_fields ( int  verb = DEFAULT_VERBOSITY)
protectedvirtual

build fields

Implements MoFEM::CoreInterface.

Definition at line 869 of file FieldCore.cpp.

869  {
871  if (verb == -1)
872  verb = verbose;
873  auto &set_id = fIelds.get<BitFieldId_mi_tag>();
874  for (auto miit = set_id.begin(); miit != set_id.end(); miit++) {
875  CHKERR buildField((*miit), verb);
876  }
877  *buildMoFEM = 1 << 0;
878  if (verb > QUIET) {
879  PetscSynchronizedPrintf(cOmm, "Nb. dofs %u\n", dofsField.size());
880  }
881  PetscSynchronizedFlush(cOmm, PETSC_STDOUT);
883  // return 0;
884 }
DofEntity_multiIndex dofsField
dofs on fields
Definition: Core.hpp:249
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
#define CHKERR
Inline error check.
Definition: definitions.h:586
Field_multiIndex fIelds
fields
Definition: Core.hpp:247
MoFEMErrorCode buildField(const boost::shared_ptr< Field > &field, int verb=DEFAULT_VERBOSITY)
Definition: FieldCore.cpp:776
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ build_finite_elements() [1/3]

MoFEMErrorCode MoFEM::Core::build_finite_elements ( int  verb = DEFAULT_VERBOSITY)
protectedvirtual

Build finite elementsBuild finite element data structures. Have to be run before problem and adjacencies are constructed.

Parameters
verbVerbosity level
Returns
Error code

Implements MoFEM::CoreInterface.

Definition at line 765 of file FECore.cpp.

765  {
767  if (verb == -1)
768  verb = verbose;
769 
770  FiniteElement_multiIndex::iterator fe_miit = finiteElements.begin();
771 
772  // loop Finite Elements
773  for (; fe_miit != finiteElements.end(); fe_miit++) {
774  if (verb > 0)
775  PetscPrintf(cOmm, "Build Finite Elements %s\n",
776  (*fe_miit)->getName().c_str());
777  CHKERR buildFiniteElements(*fe_miit, NULL, verb);
778  }
779 
780  if (verb > 0) {
781  PetscSynchronizedPrintf(cOmm, "Nb. FEs %u\n", entsFiniteElements.size());
782  PetscSynchronizedFlush(cOmm, PETSC_STDOUT);
783  typedef EntFiniteElement_multiIndex::index<BitFEId_mi_tag>::type
784  FiniteElementById;
785  FiniteElementById &finite_elements_by_id =
786  entsFiniteElements.get<BitFEId_mi_tag>();
787  FiniteElement_multiIndex::iterator fe_id_it = finiteElements.begin();
788  for (; fe_id_it != finiteElements.end(); fe_id_it++) {
789  FiniteElementById::iterator miit =
790  finite_elements_by_id.lower_bound((*fe_id_it)->getId());
791  FiniteElementById::iterator hi_miit =
792  finite_elements_by_id.upper_bound((*fe_id_it)->getId());
793  int count = std::distance(miit, hi_miit);
794  std::ostringstream ss;
795  ss << *(*fe_id_it) << " Nb. FEs " << count << std::endl;
796  PetscSynchronizedPrintf(cOmm, ss.str().c_str());
797  PetscSynchronizedFlush(cOmm, PETSC_STDOUT);
798  }
799  }
800 
801  *buildMoFEM |= 1 << 1;
803 }
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
FiniteElement_multiIndex finiteElements
finite elements
Definition: Core.hpp:251
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
MoFEMErrorCode buildFiniteElements(const boost::shared_ptr< FiniteElement > &fe, const Range *ents_ptr=NULL, int verb=DEFAULT_VERBOSITY)
Definition: FECore.cpp:542
EntFiniteElement_multiIndex entsFiniteElements
finite element entities
Definition: Core.hpp:252

◆ build_finite_elements() [2/3]

MoFEMErrorCode MoFEM::Core::build_finite_elements ( const BitRefLevel bit,
int  verb = DEFAULT_VERBOSITY 
)
protected

Definition at line 805 of file FECore.cpp.

805  {
807  SETERRQ(cOmm, MOFEM_NOT_IMPLEMENTED, "Not yet implemented");
809 }
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498

◆ build_finite_elements() [3/3]

MoFEMErrorCode MoFEM::Core::build_finite_elements ( const string  fe_name,
const Range *  ents_ptr = NULL,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Build finite elementsBuild finite element data structures. Have to be run before problem and adjacencies are constructed.

Parameters
fe_nameName of finite element
ents_ptrPointer to range of finite elements
verbVerbosity level
Returns
Error code

Implements MoFEM::CoreInterface.

Definition at line 811 of file FECore.cpp.

812  {
814  if (verb == -1)
815  verb = verbose;
816 
817  FiniteElement_multiIndex::index<FiniteElement_name_mi_tag>::type::iterator
818  fe_miit = finiteElements.get<FiniteElement_name_mi_tag>().find(fe_name);
819  if (fe_miit == finiteElements.get<FiniteElement_name_mi_tag>().end()) {
820  SETERRQ1(cOmm, MOFEM_NOT_FOUND, "Finite element <%s> not found",
821  fe_name.c_str());
822  }
823 
824  if (verb >= VERBOSE)
825  PetscPrintf(cOmm, "Build Finite Elements %s\n", fe_name.c_str());
826  CHKERR buildFiniteElements(*fe_miit, ents_ptr, verb);
827 
828  if (verb >= VERBOSE) {
829  typedef EntFiniteElement_multiIndex::index<BitFEId_mi_tag>::type
830  FiniteElementById;
831  FiniteElementById &finite_elements_by_id =
832  entsFiniteElements.get<BitFEId_mi_tag>();
833  FiniteElementById::iterator miit =
834  finite_elements_by_id.lower_bound((*fe_miit)->getId());
835  FiniteElementById::iterator hi_miit =
836  finite_elements_by_id.upper_bound((*fe_miit)->getId());
837  int count = std::distance(miit, hi_miit);
838  std::ostringstream ss;
839  ss << *(*fe_miit) << " Nb. FEs " << count << std::endl;
840  PetscSynchronizedPrintf(cOmm, ss.str().c_str());
841  PetscSynchronizedFlush(cOmm, PETSC_STDOUT);
842  }
843 
844  *buildMoFEM |= 1 << 1;
846 }
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
FiniteElement_multiIndex finiteElements
finite elements
Definition: Core.hpp:251
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
MoFEMErrorCode buildFiniteElements(const boost::shared_ptr< FiniteElement > &fe, const Range *ents_ptr=NULL, int verb=DEFAULT_VERBOSITY)
Definition: FECore.cpp:542
EntFiniteElement_multiIndex entsFiniteElements
finite element entities
Definition: Core.hpp:252

◆ build_problem_on_distributed_mesh()

MoFEMErrorCode MoFEM::Core::build_problem_on_distributed_mesh ( int  verb = DEFAULT_VERBOSITY)
protectedvirtual

build problem data structures, assuming that mesh is distributed (collective)

Deprecated:
Use ProblemsManager to build and partition problems

Mesh is distributed, that means that each processor keeps only own part of the mesh and shared entities.

Collective - need to be run on all processors in communicator, i.e. each function has to call this function.

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 230 of file ProblemsCore.cpp.

230  {
232  if (verb == -1)
233  verb = verbose;
234  DofEntity_multiIndex_active_view dofs_rows, dofs_cols;
235  Problem_multiIndex::iterator p_miit = pRoblems.begin();
236  for (; p_miit != pRoblems.end(); p_miit++) {
237  ierr = getInterface<ProblemsManager>()->buildProblemOnDistributedMesh(
238  const_cast<Problem *>(&*p_miit), verb);
239  CHKERRG(ierr);
240  }
242 }
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define CHKERRG(n)
Check error code of MoFEM/MOAB/PETSc function.
Definition: definitions.h:534
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
static MoFEMErrorCodeGeneric< PetscErrorCode > ierr
Definition: Common.hpp:80
Problem_multiIndex pRoblems
problems multi-index
Definition: Core.hpp:257
int verbose
Verbosity level.
Definition: Core.hpp:904
multi_index_container< boost::shared_ptr< DofEntity >, indexed_by< ordered_unique< const_mem_fun< DofEntity, UId, &DofEntity::getGlobalUniqueId > >, ordered_non_unique< const_mem_fun< DofEntity, char, &DofEntity::getActive > > > > DofEntity_multiIndex_active_view
multi-index view on DofEntity activity

◆ build_problems()

MoFEMErrorCode MoFEM::Core::build_problems ( int  verb = DEFAULT_VERBOSITY)
protectedvirtual

build problem data structures

Deprecated:
Use MoFEM::Interface::build_problem(const std::string &name,const bool square_matrix,int verb = -1) instead. This function not allows to Control if problem is structurally symmetric.

Implements MoFEM::DeprecatedCoreInterface.

Definition at line 292 of file ProblemsCore.cpp.

292  {
294  if (verb == -1)
295  verb = verbose;
296  if (!((*buildMoFEM) & BUILD_FIELD))
297  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "fields not build");
298  if (!((*buildMoFEM) & BUILD_FE))
299  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "FEs not build");
300  if (!((*buildMoFEM) & BUILD_ADJ))
301  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "adjacencies not build");
302  // iterate problems
303  Problem_multiIndex::iterator p_miit = pRoblems.begin();
304  for (; p_miit != pRoblems.end(); p_miit++) {
305  Problem *problem_ptr = const_cast<Problem *>(&*p_miit);
306  ierr = build_problem(problem_ptr, false, verb);
307  CHKERRG(ierr);
308  }
311 }
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define CHKERRG(n)
Check error code of MoFEM/MOAB/PETSc function.
Definition: definitions.h:534
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
static MoFEMErrorCodeGeneric< PetscErrorCode > ierr
Definition: Common.hpp:80
int * buildMoFEM
keeps flags/semaphores for different stages
Definition: Core.hpp:915
DEPRECATED MoFEMErrorCode build_problem(const std::string &name, const bool square_matrix, int verb=-1)
build problem data structures
Problem_multiIndex pRoblems
problems multi-index
Definition: Core.hpp:257
int verbose
Verbosity level.
Definition: Core.hpp:904

◆ buildField()

MoFEMErrorCode MoFEM::Core::buildField ( const boost::shared_ptr< Field > &  field,
int  verb = DEFAULT_VERBOSITY 
)
protected

Definition at line 776 of file FieldCore.cpp.

777  {
779  if (verb == -1)
780  verb = verbose;
781  if (verb > QUIET) {
782  PetscSynchronizedPrintf(cOmm, "Build Field %s (rank %d)\n",
783  field->getName().c_str(), rAnk);
784  }
785  std::map<EntityType, int> dof_counter;
786  std::map<EntityType, int> inactive_dof_counter;
787 
788  switch (field->getSpace()) {
789  case NOFIELD:
790  CHKERR buildFieldForNoField(field->getId(), dof_counter, verb);
791  break;
792  case L2:
793  case H1:
794  case HCURL:
795  case HDIV:
796  CHKERR buildFieldForL2H1HcurlHdiv(field->getId(), dof_counter,
797  inactive_dof_counter, verb);
798  break;
799  default:
800  SETERRQ(PETSC_COMM_SELF, MOFEM_NOT_IMPLEMENTED, "not implemented");
801  }
802 
803  if (verb > QUIET) {
804  int nb_added_dofs = 0;
805  int nb_inactive_added_dofs = 0;
806  for (auto const &it : dof_counter) {
807  switch (it.first) {
808  case MBVERTEX:
809  PetscSynchronizedPrintf(cOmm,
810  "nb added dofs (vertices) %d (inactive %d)\n",
811  it.second, inactive_dof_counter[it.first]);
812  break;
813  case MBEDGE:
814  PetscSynchronizedPrintf(cOmm,
815  "nb added dofs (edges) %d (inactive %d)\n",
816  it.second, inactive_dof_counter[it.first]);
817  break;
818  case MBTRI:
819  PetscSynchronizedPrintf(cOmm,
820  "nb added dofs (triangles) %d (inactive %d)\n",
821  it.second, inactive_dof_counter[it.first]);
822  break;
823  case MBQUAD:
824  PetscSynchronizedPrintf(cOmm,
825  "nb added dofs (quads) %d (inactive %d)\n",
826  it.second, inactive_dof_counter[it.first]);
827  break;
828  case MBTET:
829  PetscSynchronizedPrintf(cOmm, "nb added dofs (tets) %d (inactive %d)\n",
830  it.second, inactive_dof_counter[it.first]);
831  break;
832  case MBPRISM:
833  PetscSynchronizedPrintf(cOmm,
834  "nb added dofs (prisms) %d (inactive %d)\n",
835  it.second, inactive_dof_counter[it.first]);
836  break;
837  case MBENTITYSET:
838  PetscSynchronizedPrintf(cOmm,
839  "nb added dofs (meshsets) %d (inactive %d)\n",
840  it.second, inactive_dof_counter[it.first]);
841  break;
842  default:
843  SETERRQ(PETSC_COMM_SELF, MOFEM_NOT_IMPLEMENTED, "not implemented");
844  }
845  nb_added_dofs += it.second;
846  nb_inactive_added_dofs += inactive_dof_counter[it.first];
847  }
848  if (verb > QUIET) {
849  PetscSynchronizedPrintf(cOmm,
850  "nb added dofs %d (number of inactive dofs %d)\n",
851  nb_added_dofs, nb_inactive_added_dofs);
852  }
853  }
855 }
field with continuous normal traction
Definition: definitions.h:170
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
scalar or vector of scalars describe (no true field)
Definition: definitions.h:167
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
int rAnk
MOFEM communicator rank.
Definition: Core.hpp:867
field with continuous tangents
Definition: definitions.h:169
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode buildFieldForL2H1HcurlHdiv(const BitFieldId id, std::map< EntityType, int > &dof_counter, std::map< EntityType, int > &inactive_dof_counter, int verb=DEFAULT_VERBOSITY)
Definition: FieldCore.cpp:670
int verbose
Verbosity level.
Definition: Core.hpp:904
MoFEMErrorCode buildFieldForNoField(const BitFieldId id, std::map< EntityType, int > &dof_counter, int verb=DEFAULT_VERBOSITY)
Definition: FieldCore.cpp:589
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404
continuous field
Definition: definitions.h:168
field with C-1 continuity
Definition: definitions.h:171

◆ buildFieldForL2H1HcurlHdiv()

MoFEMErrorCode MoFEM::Core::buildFieldForL2H1HcurlHdiv ( const BitFieldId  id,
std::map< EntityType, int > &  dof_counter,
std::map< EntityType, int > &  inactive_dof_counter,
int  verb = DEFAULT_VERBOSITY 
)
protected

Definition at line 670 of file FieldCore.cpp.

672  {
674  if (verb == -1)
675  verb = verbose;
676 
677  // Find field
678  auto &set_id = fIelds.get<BitFieldId_mi_tag>();
679  auto field_it = set_id.find(id);
680  if (field_it == set_id.end()) {
681  SETERRQ(PETSC_COMM_SELF, MOFEM_NOT_FOUND, "Field not found");
682  }
683  const int rank = field_it->get()->getNbOfCoeffs();
684  const boost::string_ref &field_name = field_it->get()->getNameRef();
685 
686  // Ents in the field meshset
687  Range ents_of_id_meshset;
688  CHKERR get_moab().get_entities_by_handle((*field_it)->meshSet,
689  ents_of_id_meshset, false);
690  if (verb > VERY_NOISY) {
691  PetscSynchronizedPrintf(PETSC_COMM_SELF, "Ents in field %s meshset %d\n",
692  (*field_it)->getName().c_str(),
693  ents_of_id_meshset.size());
694  }
695 
696  for (auto p_eit = ents_of_id_meshset.pair_begin();
697  p_eit != ents_of_id_meshset.pair_end(); ++p_eit) {
698 
699  const EntityHandle first = p_eit->first;
700  const EntityHandle second = p_eit->second;
701 
702  auto feit = entsFields.get<Composite_Name_And_Ent_mi_tag>().lower_bound(
703  boost::make_tuple(field_name, first));
704  if (feit == entsFields.get<Composite_Name_And_Ent_mi_tag>().end())
705  continue;
706  auto hi_feit = entsFields.get<Composite_Name_And_Ent_mi_tag>().upper_bound(
707  boost::make_tuple(field_name, second));
708 
709  // If there are DOFs in that range is more pragmatic to remove them rather
710  // than to find sub-ranges or make them inactive
711  auto dit = dofsField.get<Composite_Name_And_Ent_mi_tag>().lower_bound(
712  boost::make_tuple(field_name, first));
713  auto hi_dit = dofsField.get<Composite_Name_And_Ent_mi_tag>().upper_bound(
714  boost::make_tuple(field_name, second));
715  dofsField.get<Composite_Name_And_Ent_mi_tag>().erase(dit, hi_dit);
716 
717  // Add vertices DOFs by bulk
718  boost::shared_ptr<std::vector<DofEntity>> dofs_array =
719  boost::make_shared<std::vector<DofEntity>>(std::vector<DofEntity>());
720  // Add Sequence of DOFs to sequence container as weak_ptr
721  int nb_dofs_on_ents = 0;
722  for (auto tmp_feit = feit; tmp_feit != hi_feit; ++tmp_feit) {
723  nb_dofs_on_ents += rank * tmp_feit->get()->getOrderNbDofs(
724  tmp_feit->get()->getMaxOrder());
725  }
726  // Add Sequence of DOFs to sequence container as weak_ptr
727  dofs_array->reserve(nb_dofs_on_ents);
728  for (; feit != hi_feit; ++feit) {
729  // Create dofs instances and shared pointers
730  int DD = 0;
731  // Loop orders (loop until max entity order is set)
732  for (int oo = 0; oo <= feit->get()->getMaxOrder(); ++oo) {
733  // Loop nb. dofs at order oo
734  for (int dd = 0; dd < feit->get()->getOrderNbDofsDiff(oo); ++dd) {
735  // Loop rank
736  for (int rr = 0; rr < rank; ++rr, ++DD) {
737  dofs_array->emplace_back(*feit, oo, rr, DD, true);
738  ++dof_counter[feit->get()->getEntType()];
739  }
740  }
741  }
742  if (DD > feit->get()->getNbDofsOnEnt()) {
743  std::ostringstream ss;
744  ss << "rank " << rAnk << " ";
745  ss << **feit << std::endl;
746  SETERRQ3(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
747  "Expected number of DOFs on entity not equal to number added "
748  "to database (DD = %d != %d = "
749  "feit->get()->getNbDofsOnEnt())\n"
750  "%s",
751  DD, feit->get()->getNbDofsOnEnt(), ss.str().c_str());
752  }
753  }
754  // Insert into Multi-Index container
755  int dofs_field_size0 = dofsField.size();
756  auto hint = dofsField.end();
757  for (auto &v : *dofs_array) {
758  hint = dofsField.emplace_hint(hint, dofs_array, &v);
759  }
760  field_it->get()->getDofSequenceContainer()->push_back(dofs_array);
761  if (PetscUnlikely(static_cast<int>(dofs_array.use_count()) !=
762  static_cast<int>(dofs_array->size() + 1))) {
763  SETERRQ2(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
764  "Wrong use count %d != %d", dofs_array.use_count(),
765  dofs_array->size() + 1);
766  }
767  if (dofs_field_size0 + dofs_array->size() != dofsField.size()) {
768  SETERRQ2(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
769  "Wrong number of inserted DOFs %d != %d", dofs_array->size(),
770  dofsField.size() - dofs_field_size0);
771  }
772  }
774 }
DofEntity_multiIndex dofsField
dofs on fields
Definition: Core.hpp:249
const Tensor2_symmetric_Expr< const ddTensor0< T, Dim, i, j >, typename promote< T, double >::V, Dim, i, j > dd(const Tensor0< T *> &a, const Index< i, Dim > index1, const Index< j, Dim > index2, const Tensor1< int, Dim > &d_ijk, const Tensor1< double, Dim > &d_xyz)
Definition: ddTensor0.hpp:33
FieldEntity_multiIndex entsFields
entities on fields
Definition: Core.hpp:248
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
int rAnk
MOFEM communicator rank.
Definition: Core.hpp:867
#define CHKERR
Inline error check.
Definition: definitions.h:586
Field_multiIndex fIelds
fields
Definition: Core.hpp:247
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ buildFieldForNoField()

MoFEMErrorCode MoFEM::Core::buildFieldForNoField ( const BitFieldId  id,
std::map< EntityType, int > &  dof_counter,
int  verb = DEFAULT_VERBOSITY 
)
protected

Definition at line 589 of file FieldCore.cpp.

590  {
592  if (verb == -1)
593  verb = verbose;
594  // field it
595  auto &set_id = fIelds.get<BitFieldId_mi_tag>();
596  // find fiels
597  auto miit = set_id.find(id);
598  if (miit == set_id.end()) {
599  SETERRQ(PETSC_COMM_SELF, MOFEM_NOT_FOUND, "field not found");
600  }
601 
602  // ents in the field meshset
603  Range ents_of_id_meshset;
604  CHKERR get_moab().get_entities_by_handle((*miit)->meshSet, ents_of_id_meshset,
605  false);
606  if (verb > VERY_NOISY) {
607  PetscSynchronizedPrintf(cOmm, "ents in field %s meshset %d\n",
608  (*miit)->getName().c_str(),
609  ents_of_id_meshset.size());
610  }
611  for (Range::iterator eit = ents_of_id_meshset.begin();
612  eit != ents_of_id_meshset.end(); eit++) {
613  // serch if field meshset is in database
614  RefEntity_multiIndex::index<Ent_mi_tag>::type::iterator miit_ref_ent;
615  miit_ref_ent = refinedEntities.get<Ent_mi_tag>().find(*eit);
616  if (miit_ref_ent == refinedEntities.get<Ent_mi_tag>().end()) {
617  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
618  "Entity is not in MoFEM database, entities in field meshset need "
619  "to be seeded (i.e. bit ref level add to them)");
620  }
621  std::pair<FieldEntity_multiIndex::iterator, bool> e_miit;
622  // create database entity
623  e_miit = entsFields.insert(
624  boost::make_shared<FieldEntity>(*miit, *miit_ref_ent));
625  // this is nor real field in space (set order to zero)
626  bool success = entsFields.modify(e_miit.first, FieldEntity_change_order(0));
627  if (!success)
628  SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
629  "modification unsuccessful");
630  FieldCoefficientsNumber rank = 0;
631  // create dofs on this entity (nb. of dofs is equal to rank)
632  for (; rank < (*e_miit.first)->getNbOfCoeffs(); rank++) {
633  std::pair<DofEntity_multiIndex::iterator, bool> d_miit;
634  // check if dof is in darabase
635  d_miit.first = dofsField.project<0>(dofsField.get<Unique_mi_tag>().find(
636  DofEntity::getGlobalUniqueIdCalculate(rank, *(e_miit.first))));
637  // if dof is not in database
638  if (d_miit.first == dofsField.end()) {
639  // insert dof
640  d_miit = dofsField.insert(
641  boost::make_shared<DofEntity>(*(e_miit.first), 0, rank, rank));
642  if (d_miit.second) {
643  dof_counter[MBENTITYSET]++; // Count entities in the meshset
644  }
645  bool success =
646  dofsField.modify(d_miit.first, DofEntity_active_change(true));
647  if (!success)
648  SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
649  "modification unsuccessful");
650  }
651  }
652  }
653  if (verb > VERY_VERBOSE) {
654  typedef DofEntity_multiIndex::index<FieldName_mi_tag>::type DofsByName;
655  DofsByName &set = dofsField.get<FieldName_mi_tag>();
656  DofsByName::iterator miit2 = set.lower_bound(miit->get()->getNameRef());
657  DofsByName::iterator hi_miit2 = set.upper_bound(miit->get()->getNameRef());
658  assert(miit2 != hi_miit2);
659  for (; miit2 != hi_miit2; miit2++) {
660  std::ostringstream ss;
661  ss << *miit2 << std::endl;
662  ;
663  PetscSynchronizedPrintf(cOmm, ss.str().c_str());
664  }
665  PetscSynchronizedFlush(cOmm, PETSC_STDOUT);
666  }
668 }
int FieldCoefficientsNumber
Number of field coefficients.
Definition: Common.hpp:132
DofEntity_multiIndex dofsField
dofs on fields
Definition: Core.hpp:249
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
RefEntity_multiIndex refinedEntities
refined entities
Definition: Core.hpp:244
FieldEntity_multiIndex entsFields
entities on fields
Definition: Core.hpp:248
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
static UId getGlobalUniqueIdCalculate(const DofIdx dof, const UId &ent_uid)
#define CHKERR
Inline error check.
Definition: definitions.h:586
Field_multiIndex fIelds
fields
Definition: Core.hpp:247
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ buildFiniteElements()

MoFEMErrorCode MoFEM::Core::buildFiniteElements ( const boost::shared_ptr< FiniteElement > &  fe,
const Range *  ents_ptr = NULL,
int  verb = DEFAULT_VERBOSITY 
)
protected

Definition at line 542 of file FECore.cpp.

543  {
545  if (verb == -1)
546  verb = verbose;
547 
548  typedef RefElement_multiIndex::index<Ent_mi_tag>::type RefFiniteElementByEnt;
549  typedef Field_multiIndex::index<BitFieldId_mi_tag>::type FieldById;
550  FieldById &fields_by_id = fIelds.get<BitFieldId_mi_tag>();
551 
552  // get id of mofem fields for row, col and data
553  enum IntLoop { ROW = 0, COL, DATA, LAST };
554  BitFieldId fe_fields[LAST] = {fe.get()->getBitFieldIdRow(),
555  fe.get()->getBitFieldIdCol(),
556  fe.get()->getBitFieldIdData()};
557 
558  // get finite element meshset
559  EntityHandle meshset = get_finite_element_meshset(fe.get()->getId());
560  // get entities from finite element meshset // if meshset
561  Range fe_ents;
562  CHKERR get_moab().get_entities_by_handle(meshset, fe_ents, false);
563 
564  if (ents_ptr)
565  fe_ents = intersect(fe_ents, *ents_ptr);
566 
567  // map entity uid to pointers
568  typedef std::vector<boost::weak_ptr<EntFiniteElement>> VecOfWeakFEPtrs;
569  typedef std::pair<const UId *, VecOfWeakFEPtrs> EntUIdAndVecOfWeakFEPtrs;
570  typedef multi_index_container<
571  EntUIdAndVecOfWeakFEPtrs,
572  indexed_by<sequenced<>,
573  hashed_non_unique<member<EntUIdAndVecOfWeakFEPtrs, const UId *,
574  &EntUIdAndVecOfWeakFEPtrs::first>>>>
575  EntUIdAndVecOfWeakFEPtrs_multi_index;
576  EntUIdAndVecOfWeakFEPtrs_multi_index ent_uid_and_fe_vec;
577 
578  std::map<EntityHandle, int> data_dofs_size;
579 
580  // loop meshset Ents and add finite elements
581  for (Range::const_pair_iterator peit = fe_ents.const_pair_begin();
582  peit != fe_ents.const_pair_end(); peit++) {
583 
584  EntityHandle first = peit->first;
585  EntityHandle second = peit->second;
586 
587  // note: iterator is a wrapper
588  // check if is in refinedFiniteElements database
589  RefFiniteElementByEnt::iterator ref_fe_miit, hi_ref_fe_miit;
590  ref_fe_miit = refinedFiniteElements.get<Ent_mi_tag>().lower_bound(first);
591  if (ref_fe_miit == refinedFiniteElements.get<Ent_mi_tag>().end()) {
592  std::ostringstream ss;
593  ss << "refinedFiniteElements not in database ent = " << first;
594  ss << " type " << get_moab().type_from_handle(first);
595  ss << " " << *fe;
596  SETERRQ(cOmm, MOFEM_DATA_INCONSISTENCY, ss.str().c_str());
597  }
598  hi_ref_fe_miit =
599  refinedFiniteElements.get<Ent_mi_tag>().upper_bound(second);
600 
601  for (; ref_fe_miit != hi_ref_fe_miit; ref_fe_miit++) {
602 
603  std::pair<EntFiniteElement_multiIndex::iterator, bool> p =
604  entsFiniteElements.insert(
605  boost::make_shared<EntFiniteElement>(*ref_fe_miit, fe));
606 
607  if (fe_fields[ROW] == fe_fields[COL]) {
608  p.first->get()->col_dof_view = p.first->get()->row_dof_view;
609  } else if (p.first->get()->col_dof_view == p.first->get()->row_dof_view) {
610  p.first->get()->col_dof_view =
611  boost::make_shared<DofEntity_multiIndex_uid_view>();
612  }
613 
614  p.first->get()->row_dof_view->clear();
615  p.first->get()->col_dof_view->clear();
616  p.first->get()->data_dofs->clear();
617 
618  for (unsigned int ii = 0; ii < BitFieldId().size(); ii++) {
619 
620  // Common field id for ROW, COL and DATA
621  BitFieldId id_common = 0;
622  // Check if the field (ii) is added to finite element
623  for (int ss = 0; ss < LAST; ss++) {
624  id_common |= fe_fields[ss] & BitFieldId().set(ii);
625  }
626  if (id_common.none())
627  continue;
628 
629  // Find in database data associated with the field (ii)
630  const BitFieldId field_id = BitFieldId().set(ii);
631  FieldById::iterator miit = fields_by_id.find(field_id);
632  if (miit == fields_by_id.end()) {
633  SETERRQ(cOmm, MOFEM_DATA_INCONSISTENCY, "Data inconsistency");
634  }
635 
636  // Entities adjacent to entities
637  Range adj_ents;
638 
639  // Resolve entities on element, those entities are used to build tag
640  // with dof uids on finite element tag
641  CHKERR p.first->get()->getElementAdjacency(*miit, adj_ents);
642 
643  // Loop over adjacencies of element and find field entities on those
644  // adjacencies, that create hash map map_uid_fe which is used later
645  const std::string field_name = miit->get()->getName();
646  const bool add_to_data =
647  (field_id & p.first->get()->getBitFieldIdData()).any();
648  FieldEntity_multiIndex::index<
649  Composite_Name_And_Ent_mi_tag>::type::iterator meit,
650  hi_meit;
651  for (Range::pair_iterator p_eit = adj_ents.pair_begin();
652  p_eit != adj_ents.pair_end(); ++p_eit) {
653  const EntityHandle first = p_eit->first;
654  const EntityHandle second = p_eit->second;
655  meit = entsFields.get<Composite_Name_And_Ent_mi_tag>().lower_bound(
656  boost::make_tuple(field_name, first));
657  if (meit == entsFields.get<Composite_Name_And_Ent_mi_tag>().end()) {
658  continue;
659  }
660  hi_meit = entsFields.get<Composite_Name_And_Ent_mi_tag>().upper_bound(
661  boost::make_tuple(field_name, second));
662  for (; meit != hi_meit; ++meit) {
663  const UId *uid_ptr = &(meit->get()->getGlobalUniqueId());
664  auto e_uid_vec_fe_it = ent_uid_and_fe_vec.get<1>().find(uid_ptr);
665  if (e_uid_vec_fe_it == ent_uid_and_fe_vec.get<1>().end()) {
666  ent_uid_and_fe_vec.insert(ent_uid_and_fe_vec.end(),
667  std::pair<const UId *, VecOfWeakFEPtrs>(
668  uid_ptr, VecOfWeakFEPtrs(1, *p.first)));
669  } else {
670  const VecOfWeakFEPtrs &vec_fe_ptrs = e_uid_vec_fe_it->second;
671  const_cast<VecOfWeakFEPtrs &>(vec_fe_ptrs).push_back(*p.first);
672  }
673 
674  if (add_to_data) {
675  data_dofs_size[p.first->get()->getEnt()] +=
676  meit->get()->getNbDofsOnEnt();
677  }
678  }
679  }
680  }
681  }
682  }
683 
684  // Reserve memory
685  std::map<EntityHandle, boost::shared_ptr<std::vector<FEDofEntity>>>
686  data_dofs_array;
687  for (std::map<EntityHandle, int>::iterator mit = data_dofs_size.begin();
688  mit != data_dofs_size.end(); mit++) {
689  if (mit->second > 0) {
690  data_dofs_array[mit->first] =
691  boost::make_shared<std::vector<FEDofEntity>>();
692  data_dofs_array[mit->first]->reserve(mit->second);
693  }
694  }
695 
696  typedef DofEntity_multiIndex::index<Unique_Ent_mi_tag>::type DofsByEntUId;
697  DofsByEntUId &dofs_by_ent_uid = dofsField.get<Unique_Ent_mi_tag>();
698 
699  // Loop over hash map, which has all entities on given elemnts
700  boost::shared_ptr<SideNumber> side_number_ptr;
701  for (EntUIdAndVecOfWeakFEPtrs_multi_index::iterator mit =
702  ent_uid_and_fe_vec.begin();
703  mit != ent_uid_and_fe_vec.end(); mit++) {
704  DofsByEntUId::iterator dit, hi_dit;
705  dit = dofs_by_ent_uid.lower_bound(*mit->first);
706  hi_dit = dofs_by_ent_uid.upper_bound(*mit->first);
707  for (; dit != hi_dit; dit++) {
708  const BitFieldId field_id = dit->get()->getId();
709  const EntityHandle dof_ent = dit->get()->getEnt();
710  std::vector<boost::weak_ptr<EntFiniteElement>>::const_iterator fe_it,
711  hi_fe_it;
712  fe_it = mit->second.begin();
713  hi_fe_it = mit->second.end();
714  for (; fe_it != hi_fe_it; fe_it++) {
715 
716  // if rows and columns of finite element are the same, then
717  // we exploit that case
718  if ((field_id & fe_it->lock().get()->getBitFieldIdRow()).any()) {
719  fe_it->lock().get()->row_dof_view->insert(
720  fe_it->lock().get()->row_dof_view->end(), *dit);
721  }
722  if (fe_it->lock().get()->col_dof_view !=
723  fe_it->lock().get()->row_dof_view) {
724  if ((field_id & fe_it->lock().get()->getBitFieldIdCol()).any()) {
725  fe_it->lock().get()->col_dof_view->insert(
726  fe_it->lock().get()->col_dof_view->end(), *dit);
727  }
728  }
729 
730  // Add FEDofEntity, first create dofs, one by one, note that memory
731  // is already reserved. Then create shared pointers and finally add
732  // th_FEName to element multi-index
733  const EntityHandle fe_ent = fe_it->lock().get()->getEnt();
734  boost::shared_ptr<std::vector<FEDofEntity>> &data_dofs_array_vec =
735  data_dofs_array[fe_ent];
736  if (data_dofs_size[fe_ent] != 0 &&
737  (field_id & fe_it->lock().get()->getBitFieldIdData()).any()) {
738 
739  // There are data dofs on this element
740  side_number_ptr = fe_it->lock().get()->getSideNumberPtr(dof_ent);
741  data_dofs_array_vec->emplace_back(side_number_ptr, *dit);
742  if (data_dofs_array_vec->size() ==
743  (unsigned int)data_dofs_size[fe_ent]) {
744  // That means that FEDofEntity vector is full, and can be added to
745  // multi-index
746 
747  // Create shared pointers vector
748  auto hint = fe_it->lock().get()->data_dofs->end();
749  for (std::vector<FEDofEntity>::iterator vit =
750  data_dofs_array_vec->begin();
751  vit != data_dofs_array_vec->end(); vit++) {
752  hint = fe_it->lock().get()->data_dofs->emplace_hint(
753  hint, data_dofs_array_vec, &(*vit));
754  }
755  fe_it->lock().get()->getDofsSequence() = data_dofs_array_vec;
756  }
757  }
758  }
759  }
760  }
761 
763 }
DofEntity_multiIndex dofsField
dofs on fields
Definition: Core.hpp:249
EntityHandle get_finite_element_meshset(const BitFEId id) const
Definition: FECore.cpp:282
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
FieldEntity_multiIndex entsFields
entities on fields
Definition: Core.hpp:248
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
std::bitset< BITFIELDID_SIZE > BitFieldId
Definition: Common.hpp:149
uint128_t UId
Unique Id.
Definition: Common.hpp:136
RefElement_multiIndex refinedFiniteElements
refined elements
Definition: Core.hpp:245
#define CHKERR
Inline error check.
Definition: definitions.h:586
Field_multiIndex fIelds
fields
Definition: Core.hpp:247
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404
EntFiniteElement_multiIndex entsFiniteElements
finite element entities
Definition: Core.hpp:252

◆ check_field()

bool MoFEM::Core::check_field ( const std::string &  name) const
protectedvirtual

check if field is in database

Parameters
namefield name
Returns
true if field exist

Implements MoFEM::CoreInterface.

Definition at line 43 of file FieldCore.cpp.

43  {
44  auto &set = fIelds.get<FieldName_mi_tag>();
45  auto miit = set.find(name);
46  if (miit == set.end())
47  return false;
48  return true;
49 }
Field_multiIndex fIelds
fields
Definition: Core.hpp:247

◆ check_finite_element()

bool MoFEM::Core::check_finite_element ( const std::string &  name) const
protectedvirtual

Check if finite element is in database.

Parameters
nameName of finite element
Returns
true if element is declared

Implements MoFEM::CoreInterface.

Definition at line 35 of file FECore.cpp.

35  {
36  typedef FiniteElement_multiIndex::index<FiniteElement_name_mi_tag>::type
37  FeSetByName;
38  const FeSetByName &set = finiteElements.get<FiniteElement_name_mi_tag>();
39  FeSetByName::iterator miit = set.find(name);
40  if (miit == set.end())
41  return false;
42  return true;
43 }
FiniteElement_multiIndex finiteElements
finite elements
Definition: Core.hpp:251

◆ check_number_of_ents_in_ents_field() [1/2]

MoFEMErrorCode MoFEM::Core::check_number_of_ents_in_ents_field ( const std::string &  name) const
protectedvirtual

check data consistency in entitiesPtr

Implements MoFEM::CoreInterface.

Definition at line 992 of file FieldCore.cpp.

992  {
994  auto it = fIelds.get<FieldName_mi_tag>().find(name);
995  if (it == fIelds.get<FieldName_mi_tag>().end()) {
996  SETERRQ1(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
997  "field not found < %s >", name.c_str());
998  }
999  EntityHandle meshset = (*it)->getMeshset();
1000  int num_entities;
1001  CHKERR get_moab().get_number_entities_by_handle(meshset, num_entities);
1002  if (entsFields.get<FieldName_mi_tag>().count((*it)->getName()) >
1003  (unsigned int)num_entities) {
1004  SETERRQ1(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
1005  "not equal number of entities in meshset and field multiindex "
1006  "< %s >",
1007  name.c_str());
1008  }
1010 }
FieldEntity_multiIndex entsFields
entities on fields
Definition: Core.hpp:248
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
#define CHKERR
Inline error check.
Definition: definitions.h:586
Field_multiIndex fIelds
fields
Definition: Core.hpp:247

◆ check_number_of_ents_in_ents_field() [2/2]

MoFEMErrorCode MoFEM::Core::check_number_of_ents_in_ents_field ( ) const
protectedvirtual

check data consistency in entitiesPtr

Implements MoFEM::CoreInterface.

Definition at line 1011 of file FieldCore.cpp.

1011  {
1013  for (auto &it : fIelds.get<FieldName_mi_tag>()) {
1014  if (it->getSpace() == NOFIELD)
1015  continue; // FIXME: should be treated properly, not test is just
1016  // skipped for this NOFIELD space
1017  EntityHandle meshset = it->getMeshset();
1018  int num_entities;
1019  CHKERR get_moab().get_number_entities_by_handle(meshset, num_entities);
1020  if (entsFields.get<FieldName_mi_tag>().count(it->getName()) >
1021  (unsigned int)num_entities) {
1022  SETERRQ1(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
1023  "not equal number of entities in meshset and field "
1024  "multiindex < %s >",
1025  it->getName().c_str());
1026  }
1027  }
1029 }
FieldEntity_multiIndex entsFields
entities on fields
Definition: Core.hpp:248
moab::Interface & get_moab()
Definition: Core.hpp:266
scalar or vector of scalars describe (no true field)
Definition: definitions.h:167
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
Field_multiIndex fIelds
fields
Definition: Core.hpp:247
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ check_number_of_ents_in_ents_finite_element() [1/2]

MoFEMErrorCode MoFEM::Core::check_number_of_ents_in_ents_finite_element ( const std::string &  name) const
protectedvirtual

check data consistency in entsFiniteElements

Implements MoFEM::CoreInterface.

Definition at line 981 of file FECore.cpp.

982  {
984  FiniteElement_multiIndex::index<FiniteElement_name_mi_tag>::type::iterator it;
985  it = finiteElements.get<FiniteElement_name_mi_tag>().find(name);
986  if (it == finiteElements.get<FiniteElement_name_mi_tag>().end()) {
987  SETERRQ1(cOmm, 1, "finite element not found < %s >", name.c_str());
988  }
989  EntityHandle meshset = (*it)->getMeshset();
990 
991  int num_entities;
992  CHKERR get_moab().get_number_entities_by_handle(meshset, num_entities);
993 
994  if (entsFiniteElements.get<FiniteElement_name_mi_tag>().count(
995  (*it)->getName().c_str()) != (unsigned int)num_entities) {
996  SETERRQ1(cOmm, 1,
997  "not equal number of entities in meshset and finite elements "
998  "multiindex < %s >",
999  (*it)->getName().c_str());
1000  }
1002 }
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
FiniteElement_multiIndex finiteElements
finite elements
Definition: Core.hpp:251
#define CHKERR
Inline error check.
Definition: definitions.h:586
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404
EntFiniteElement_multiIndex entsFiniteElements
finite element entities
Definition: Core.hpp:252

◆ check_number_of_ents_in_ents_finite_element() [2/2]

MoFEMErrorCode MoFEM::Core::check_number_of_ents_in_ents_finite_element ( ) const
protectedvirtual

check data consistency in entsFiniteElements

Implements MoFEM::CoreInterface.

Definition at line 1004 of file FECore.cpp.

1004  {
1006  FiniteElement_multiIndex::index<FiniteElement_name_mi_tag>::type::iterator it;
1007  it = finiteElements.get<FiniteElement_name_mi_tag>().begin();
1008  for (; it != finiteElements.get<FiniteElement_name_mi_tag>().end(); it++) {
1009  EntityHandle meshset = (*it)->getMeshset();
1010 
1011  int num_entities;
1012  CHKERR get_moab().get_number_entities_by_handle(meshset, num_entities);
1013 
1014  if (entsFiniteElements.get<FiniteElement_name_mi_tag>().count(
1015  (*it)->getName().c_str()) != (unsigned int)num_entities) {
1016  SETERRQ1(cOmm, 1,
1017  "not equal number of entities in meshset and finite elements "
1018  "multiindex < %s >",
1019  (*it)->getName().c_str());
1020  }
1021  }
1023 }
MPI_Comm cOmm
MoFEM communicator.
Definition: Core.hpp:863
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
FiniteElement_multiIndex finiteElements
finite elements
Definition: Core.hpp:251
#define CHKERR
Inline error check.
Definition: definitions.h:586
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404
EntFiniteElement_multiIndex entsFiniteElements
finite element entities
Definition: Core.hpp:252

◆ check_problem()

bool MoFEM::Core::check_problem ( const std::string  name)
protectedvirtual

check if problem exist

Parameters
nameproblem name
Returns
true if problem is in database

Implements MoFEM::CoreInterface.

Definition at line 21 of file ProblemsCore.cpp.

21  {
22  Problem_multiIndex::index<Problem_mi_tag>::type::iterator pit;
23  pit = pRoblems.get<Problem_mi_tag>().find(name);
24  if (pit == pRoblems.get<Problem_mi_tag>().end()) {
25  return false;
26  }
27  return true;
28 }
Problem_multiIndex pRoblems
problems multi-index
Definition: Core.hpp:257

◆ clear_adjacencies_entities() [1/3]

MoFEMErrorCode MoFEM::Core::clear_adjacencies_entities ( const BitRefLevel bit,
const BitRefLevel mask,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

clear adjacency map for entities on given bit level

Parameters
bit
mask

Implements MoFEM::CoreInterface.

Definition at line 349 of file DeleteCore.cpp.

351  {
353  if (verb == -1)
354  verb = verbose;
355  Range ents;
356  CHKERR BitRefManager(*this).getEntitiesByRefLevel(bit, mask, ents, verb);
359 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
MoFEMErrorCode clear_adjacencies_entities(const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
clear adjacency map for entities on given bit level
Definition: DeleteCore.cpp:349
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ clear_adjacencies_entities() [2/3]

MoFEMErrorCode MoFEM::Core::clear_adjacencies_entities ( const Range &  ents,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

clear adjacencies for field entities by entities

Implements MoFEM::CoreInterface.

Definition at line 361 of file DeleteCore.cpp.

361  {
363  if (verb == -1)
364  verb = verbose;
365  for (Range::const_pair_iterator p_eit = ents.pair_begin();
366  p_eit != ents.pair_end(); ++p_eit) {
367  const EntityHandle first = p_eit->first;
368  const EntityHandle second = p_eit->second;
369  FieldEntityEntFiniteElementAdjacencyMap_multiIndex::index<
370  Ent_mi_tag>::type::iterator ait,
371  hi_ait;
372  ait = entFEAdjacencies.get<Ent_mi_tag>().lower_bound(first);
373  hi_ait = entFEAdjacencies.get<Ent_mi_tag>().upper_bound(second);
374  entFEAdjacencies.get<Ent_mi_tag>().erase(ait, hi_ait);
375  }
377 }
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
FieldEntityEntFiniteElementAdjacencyMap_multiIndex entFEAdjacencies
adjacencies of elements to dofs
Definition: Core.hpp:255
int verbose
Verbosity level.
Definition: Core.hpp:904

◆ clear_adjacencies_entities() [3/3]

MoFEMErrorCode MoFEM::Core::clear_adjacencies_entities ( const std::string &  name,
const Range &  ents,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

clear adjacencies for field entities by entities and field namd

Implements MoFEM::CoreInterface.

Definition at line 379 of file DeleteCore.cpp.

380  {
382  if (verb == -1)
383  verb = verbose;
384 
385  const Field *field_ptr = get_field_structure(name);
386  int field_bit_number = field_ptr->getBitNumber();
387  bool is_distributed_mesh = basicEntityDataPtr->trueIfDistributedMesh();
388  ParallelComm *pcomm =
389  ParallelComm::get_pcomm(&get_moab(), basicEntityDataPtr->pcommID);
390 
391  for (Range::const_pair_iterator p_eit = ents.pair_begin();
392  p_eit != ents.pair_end(); p_eit++) {
393 
394  // First and last handle
395  const EntityHandle first = p_eit->first;
396  const EntityHandle second = p_eit->second;
397 
398  // Get owner proc and owner handle
399  int f_owner_proc;
400  EntityHandle f_moab_owner_handle;
401  CHKERR pcomm->get_owner_handle(first, f_owner_proc, f_moab_owner_handle);
402  int s_owner_proc;
403  EntityHandle s_moab_owner_handle;
404  CHKERR pcomm->get_owner_handle(second, s_owner_proc, s_moab_owner_handle);
405 
406  // Get UId
408  f_owner_proc, field_bit_number, f_moab_owner_handle,
409  is_distributed_mesh);
411  s_owner_proc, field_bit_number, s_moab_owner_handle,
412  is_distributed_mesh);
413 
414  // Find adjacencies
415  FieldEntityEntFiniteElementAdjacencyMap_multiIndex::index<
416  Unique_mi_tag>::type::iterator ait,
417  hi_ait;
418  ait = entFEAdjacencies.get<Unique_mi_tag>().lower_bound(first_uid);
419  hi_ait = entFEAdjacencies.get<Unique_mi_tag>().upper_bound(second_uid);
420  entFEAdjacencies.get<Unique_mi_tag>().erase(ait, hi_ait);
421  }
423 }
moab::Interface & get_moab()
Definition: Core.hpp:266
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
UId getGlobalUniqueIdCalculate() const
Calculate global UId.
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
const Field * get_field_structure(const std::string &name)
get field structure
Definition: FieldCore.cpp:51
uint128_t UId
Unique Id.
Definition: Common.hpp:136
FieldEntityEntFiniteElementAdjacencyMap_multiIndex entFEAdjacencies
adjacencies of elements to dofs
Definition: Core.hpp:255
#define CHKERR
Inline error check.
Definition: definitions.h:586
boost::shared_ptr< BasicEntityData > basicEntityDataPtr
Definition: Core.hpp:225
int verbose
Verbosity level.
Definition: Core.hpp:904

◆ clear_adjacencies_finite_elements() [1/3]

MoFEMErrorCode MoFEM::Core::clear_adjacencies_finite_elements ( const BitRefLevel bit,
const BitRefLevel mask,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

clear adjacency map for finite elements on given bit level

Parameters
bit
mask

Implements MoFEM::CoreInterface.

Definition at line 478 of file DeleteCore.cpp.

480  {
482  Range ents;
483  CHKERR BitRefManager(*this).getEntitiesByRefLevel(bit, mask, ents, verb);
486 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
MoFEMErrorCode clear_adjacencies_finite_elements(const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
clear adjacency map for finite elements on given bit level
Definition: DeleteCore.cpp:478
#define CHKERR
Inline error check.
Definition: definitions.h:586
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ clear_adjacencies_finite_elements() [2/3]

MoFEMErrorCode MoFEM::Core::clear_adjacencies_finite_elements ( const Range &  ents,
int  verb = DEFAULT_VERBOSITY 
)
protected

Definition at line 488 of file DeleteCore.cpp.

489  {
491  if (verb == -1)
492  verb = verbose;
493  for (Range::const_pair_iterator p_eit = ents.pair_begin();
494  p_eit != ents.pair_end(); p_eit++) {
495  EntityHandle first = p_eit->first;
496  EntityHandle second = p_eit->second;
497  FieldEntityEntFiniteElementAdjacencyMap_multiIndex::index<
498  FEEnt_mi_tag>::type::iterator ait,
499  hi_ait;
500  ait = entFEAdjacencies.get<FEEnt_mi_tag>().lower_bound(first);
501  hi_ait = entFEAdjacencies.get<FEEnt_mi_tag>().upper_bound(second);
502  entFEAdjacencies.get<FEEnt_mi_tag>().erase(ait, hi_ait);
503  }
505 }
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
FieldEntityEntFiniteElementAdjacencyMap_multiIndex entFEAdjacencies
adjacencies of elements to dofs
Definition: Core.hpp:255
int verbose
Verbosity level.
Definition: Core.hpp:904

◆ clear_adjacencies_finite_elements() [3/3]

MoFEMErrorCode MoFEM::Core::clear_adjacencies_finite_elements ( const std::string &  name,
const Range &  ents,
int  verb = DEFAULT_VERBOSITY 
)
protected

Definition at line 507 of file DeleteCore.cpp.

509  {
511  if (verb == -1)
512  verb = verbose;
513 
514  FiniteElement_multiIndex::index<FiniteElement_name_mi_tag>::type::iterator
515  it_fe = finiteElements.get<FiniteElement_name_mi_tag>().find(name);
516  if (it_fe != finiteElements.get<FiniteElement_name_mi_tag>().end()) {
517 
518  const int fe_bit_number = it_fe->get()->getBitNumber();
519 
520  for (Range::const_pair_iterator p_eit = ents.pair_begin();
521  p_eit != ents.pair_end(); p_eit++) {
522 
523  // First and last handle
524  const EntityHandle first = p_eit->first;
525  const EntityHandle second = p_eit->second;
526 
527  // Get UId
528  UId first_uid =
529  EntFiniteElement::getGlobalUniqueIdCalculate(first, fe_bit_number);
530  UId second_uid =
531  EntFiniteElement::getGlobalUniqueIdCalculate(second, fe_bit_number);
532 
533  // Find and remove adjacencies
534  FieldEntityEntFiniteElementAdjacencyMap_multiIndex::index<
535  FE_Unique_mi_tag>::type::iterator ait,
536  hi_ait;
537  ait = entFEAdjacencies.get<FE_Unique_mi_tag>().lower_bound(first_uid);
538  hi_ait = entFEAdjacencies.get<FE_Unique_mi_tag>().upper_bound(second_uid);
539  entFEAdjacencies.get<FE_Unique_mi_tag>().erase(ait, hi_ait);
540  }
541  }
543 }
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
UId getGlobalUniqueIdCalculate() const
Generate UId for finite element entity.
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
uint128_t UId
Unique Id.
Definition: Common.hpp:136
FieldEntityEntFiniteElementAdjacencyMap_multiIndex entFEAdjacencies
adjacencies of elements to dofs
Definition: Core.hpp:255
FiniteElement_multiIndex finiteElements
finite elements
Definition: Core.hpp:251
int verbose
Verbosity level.
Definition: Core.hpp:904

◆ clear_database()

MoFEMErrorCode MoFEM::Core::clear_database ( int  verb = DEFAULT_VERBOSITY)
protectedvirtual

Clear database.

Parameters
verbVerbosity level
Returns
Error code

Implements MoFEM::CoreInterface.

Definition at line 467 of file Core.cpp.

467  {
469  if (verb == -1)
470  verb = verbose;
471  CHKERR clearMap();
473 }
MoFEMErrorCode clearMap()
Cleaning database.
Definition: Core.cpp:216
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ clear_dofs_fields() [1/2]

MoFEMErrorCode MoFEM::Core::clear_dofs_fields ( const Range &  ents,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Clear dofs by ents

Implements MoFEM::CoreInterface.

Definition at line 78 of file DeleteCore.cpp.

78  {
80  if (verb == -1)
81  verb = verbose;
82 
83  for (Range::const_pair_iterator p_eit = ents.pair_begin();
84  p_eit != ents.pair_end(); p_eit++) {
85  EntityHandle first = p_eit->first;
86  EntityHandle second = p_eit->second;
87  // get dofs range
88  DofEntityByEnt::iterator dit, hi_dit;
89  dit = dofsField.get<Ent_mi_tag>().lower_bound(first);
90  if (dit == dofsField.get<Ent_mi_tag>().end())
91  continue;
92  hi_dit = dofsField.get<Ent_mi_tag>().upper_bound(second);
93 
94  // bool last_hi_dit;
95  // if (hi_dit == dofsField.get<Ent_mi_tag>().end()) {
96  // last_hi_dit = true;
97  // } else {
98  // last_hi_dit = false;
99  // }
100  // clear dofs in finite elements
101  // FieldEntityEntFiniteElementAdjacencyMap_multiIndex::index<
102  // Ent_mi_tag>::type::iterator ait,
103  // hi_ait;
104  // ait = entFEAdjacencies.get<Ent_mi_tag>().lower_bound(first);
105  // hi_ait = entFEAdjacencies.get<Ent_mi_tag>().upper_bound(second);
106  // for (; ait != hi_ait; ++ait) {
107  // // Delete data dofs on element
108  // {
109  // FEDofEntity_multiIndex::iterator diit, hi_diit;
110  // diit = ait->entFePtr->data_dofs->lower_bound(
111  // dit->get()->getGlobalUniqueId());
112  // if (last_hi_dit) {
113  // hi_diit = ait->entFePtr->data_dofs->end();
114  // } else {
115  // hi_diit = ait->entFePtr->data_dofs->lower_bound(
116  // hi_dit->get()->getGlobalUniqueId());
117  // }
118  // ait->entFePtr->data_dofs->erase(diit, hi_diit);
119  // }
120  // // Delete dofs view on rows and columns on elements
121  // {
122  // DofEntity_multiIndex_uid_view::iterator diit, hi_diit;
123  // diit = ait->entFePtr->row_dof_view->lower_bound(
124  // dit->get()->getGlobalUniqueId());
125  // if (last_hi_dit) {
126  // hi_diit = ait->entFePtr->row_dof_view->end();
127  // } else {
128  // hi_diit = ait->entFePtr->row_dof_view->lower_bound(
129  // hi_dit->get()->getGlobalUniqueId());
130  // }
131  // ait->entFePtr->row_dof_view->erase(diit, hi_diit);
132  // if (ait->entFePtr->row_dof_view != ait->entFePtr->col_dof_view) {
133  // diit = ait->entFePtr->col_dof_view->lower_bound(
134  // dit->get()->getGlobalUniqueId());
135  // if (last_hi_dit) {
136  // hi_diit = ait->entFePtr->col_dof_view->end();
137  // } else {
138  // hi_diit = ait->entFePtr->col_dof_view->lower_bound(
139  // hi_dit->get()->getGlobalUniqueId());
140  // }
141  // ait->entFePtr->col_dof_view->erase(diit, hi_diit);
142  // }
143  // }
144  // }
145  // finally clear dofs
146  dofsField.get<Ent_mi_tag>().erase(dit,hi_dit);
147  }
149 }
DofEntity_multiIndex dofsField
dofs on fields
Definition: Core.hpp:249
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
int verbose
Verbosity level.
Definition: Core.hpp:904

◆ clear_dofs_fields() [2/2]

MoFEMErrorCode MoFEM::Core::clear_dofs_fields ( const std::string &  name,
const Range &  ents,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Clear dofs by field name and ents

Implements MoFEM::CoreInterface.

Definition at line 151 of file DeleteCore.cpp.

152  {
154  if (verb == -1)
155  verb = verbose;
156 
157  // const Field *field_ptr = get_field_structure(name);
158  // int field_bit_number = field_ptr->getBitNumber();
159  // bool is_distributed_mesh = basicEntityDataPtr->trueIfDistributedMesh();
160  // ParallelComm *pcomm =
161  // ParallelComm::get_pcomm(&moab, basicEntityDataPtr->pcommID);
162 
163  for (Range::const_pair_iterator p_eit = ents.pair_begin();
164  p_eit != ents.pair_end(); p_eit++) {
165  EntityHandle first = p_eit->first;
166  EntityHandle second = p_eit->second;
167  DofEntityByNameAndEnt::iterator dit, hi_dit;
168  dit = dofsField.get<Composite_Name_And_Ent_mi_tag>().lower_bound(
169  boost::make_tuple(name, first));
170  hi_dit = dofsField.get<Composite_Name_And_Ent_mi_tag>().upper_bound(
171  boost::make_tuple(name, second));
172  // bool last_hi_dit;
173  // if (hi_dit == dofsField.get<Composite_Name_And_Ent_mi_tag>().end()) {
174  // last_hi_dit = true;
175  // } else {
176  // last_hi_dit = false;
177  // }
178 
179  // // Get owner proc and owner handle
180  // int f_owner_proc;
181  // EntityHandle f_moab_owner_handle;
182  // CHKERR pcomm->get_owner_handle(first, f_owner_proc, f_moab_owner_handle);
183  // int s_owner_proc;
184  // EntityHandle s_moab_owner_handle;
185  // CHKERR pcomm->get_owner_handle(second, s_owner_proc, s_moab_owner_handle);
186 
187  // // Get UId
188  // UId first_uid = FieldEntity::getGlobalUniqueIdCalculate(
189  // f_owner_proc, field_bit_number, f_moab_owner_handle,
190  // is_distributed_mesh);
191  // UId second_uid = FieldEntity::getGlobalUniqueIdCalculate(
192  // s_owner_proc, field_bit_number, s_moab_owner_handle,
193  // is_distributed_mesh);
194 
195  // FieldEntityEntFiniteElementAdjacencyMap_multiIndex::index<
196  // Unique_mi_tag>::type::iterator ait,
197  // hi_ait;
198  // ait = entFEAdjacencies.get<Unique_mi_tag>().lower_bound(
199  // first_uid);
200  // hi_ait = entFEAdjacencies.get<Unique_mi_tag>().upper_bound(
201  // second_uid);
202  // for (; ait != hi_ait; ++ait) {
203  // // Delete data dofs on element
204  // {
205  // FEDofEntity_multiIndex::iterator diit, hi_diit;
206  // diit = ait->entFePtr->data_dofs->lower_bound(
207  // dit->get()->getGlobalUniqueId());
208  // if (last_hi_dit) {
209  // hi_diit = ait->entFePtr->data_dofs->end();
210  // } else {
211  // hi_diit = ait->entFePtr->data_dofs->lower_bound(
212  // hi_dit->get()->getGlobalUniqueId());
213  // }
214  // ait->entFePtr->data_dofs->erase(diit, hi_diit);
215  // }
216  // // Delete dofs view on rows and columns on elements
217  // {
218  // DofEntity_multiIndex_uid_view::iterator diit, hi_diit;
219  // diit = ait->entFePtr->row_dof_view->lower_bound(
220  // dit->get()->getGlobalUniqueId());
221  // if (last_hi_dit) {
222  // hi_diit = ait->entFePtr->row_dof_view->end();
223  // } else {
224  // hi_diit = ait->entFePtr->row_dof_view->lower_bound(
225  // hi_dit->get()->getGlobalUniqueId());
226  // }
227  // ait->entFePtr->row_dof_view->erase(diit, hi_diit);
228  // if (ait->entFePtr->row_dof_view != ait->entFePtr->col_dof_view) {
229  // diit = ait->entFePtr->col_dof_view->lower_bound(
230  // dit->get()->getGlobalUniqueId());
231  // if (last_hi_dit) {
232  // hi_diit = ait->entFePtr->col_dof_view->end();
233  // } else {
234  // hi_diit = ait->entFePtr->col_dof_view->lower_bound(
235  // hi_dit->get()->getGlobalUniqueId());
236  // }
237  // ait->entFePtr->col_dof_view->erase(diit, hi_diit);
238  // }
239  // }
240  // }
241  dofsField.get<Composite_Name_And_Ent_mi_tag>().erase(dit, hi_dit);
242  }
244 }
DofEntity_multiIndex dofsField
dofs on fields
Definition: Core.hpp:249
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
int verbose
Verbosity level.
Definition: Core.hpp:904

◆ clear_dofs_fields_by_bit_ref()

MoFEMErrorCode MoFEM::Core::clear_dofs_fields_by_bit_ref ( const BitRefLevel bit,
const BitRefLevel mask,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Clear dofs by bit level

Implements MoFEM::CoreInterface.

Definition at line 67 of file DeleteCore.cpp.

68  {
70  if (verb == -1)
71  verb = verbose;
72  Range ents;
73  CHKERR BitRefManager(*this).getEntitiesByRefLevel(bit, mask, ents, verb);
74  CHKERR clear_dofs_fields(ents, verb);
76 }
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:491
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:498
MoFEMErrorCode clear_dofs_fields(const Range &ents, int verb=DEFAULT_VERBOSITY)
Definition: DeleteCore.cpp:78
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904

◆ clear_ents_fields() [1/2]

MoFEMErrorCode MoFEM::Core::clear_ents_fields ( const Range &  ents,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Clear entities by field name

Implements MoFEM::CoreInterface.

Definition at line 259 of file DeleteCore.cpp.

259  {
261  if (verb == -1)
262  verb = verbose;
263  CHKERR clear_dofs_fields(ents, verb);
265  for (Range::const_pair_iterator p_eit = ents.pair_begin();
266  p_eit != ents.pair_end(); p_eit++) {
267  EntityHandle first = p_eit->first;
268  EntityHandle second = p_eit->second;
269  FieldEntity_multiIndex::index<Ent_mi_tag>::type::iterator dit, hi_dit;
270  dit = entsFields.get<Ent_mi_tag>().lower_bound(first);
271  hi_dit = entsFields.get<Ent_mi_tag>().upper_bound(second);
272  entsFields.get<Ent_mi_tag>().erase(dit, hi_dit);
273  }
275 }
FieldEntity_multiIndex entsFields
entities on fields
Definition: Core.hpp:248
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
MoFEMErrorCode clear_adjacencies_entities(const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
clear adjacency map for entities on given bit level
Definition: DeleteCore.cpp:349
MoFEMErrorCode clear_dofs_fields(const Range &ents, int verb=DEFAULT_VERBOSITY)
Definition: DeleteCore.cpp:78
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ clear_ents_fields() [2/2]

MoFEMErrorCode MoFEM::Core::clear_ents_fields ( const std::string &  name,
const Range &  ents,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Clear entities by field name

Implements MoFEM::CoreInterface.

Definition at line 277 of file DeleteCore.cpp.

278  {
280  if (verb == -1)
281  verb = verbose;
282  CHKERR clear_dofs_fields(name, ents, verb);
283  CHKERR clear_adjacencies_entities(name, ents, verb);
284  for (Range::const_pair_iterator p_eit = ents.pair_begin();
285  p_eit != ents.pair_end(); p_eit++) {
286  EntityHandle first = p_eit->first;
287  EntityHandle second = p_eit->second;
288  FieldEntity_multiIndex::index<Composite_Name_And_Ent_mi_tag>::type::iterator
289  dit,
290  hi_dit;
291  dit = entsFields.get<Composite_Name_And_Ent_mi_tag>().lower_bound(
292  boost::make_tuple(name, first));
293  hi_dit = entsFields.get<Composite_Name_And_Ent_mi_tag>().upper_bound(
294  boost::make_tuple(name, second));
295  entsFields.get<Composite_Name_And_Ent_mi_tag>().erase(dit, hi_dit);
296  }
298 }
FieldEntity_multiIndex entsFields
entities on fields
Definition: Core.hpp:248
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
MoFEMErrorCode clear_adjacencies_entities(const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
clear adjacency map for entities on given bit level
Definition: DeleteCore.cpp:349
MoFEMErrorCode clear_dofs_fields(const Range &ents, int verb=DEFAULT_VERBOSITY)
Definition: DeleteCore.cpp:78
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ clear_ents_fields_by_bit_ref()

MoFEMErrorCode MoFEM::Core::clear_ents_fields_by_bit_ref ( const BitRefLevel bit,
const BitRefLevel mask,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

Clear ents by bit level

Implements MoFEM::CoreInterface.

Definition at line 246 of file DeleteCore.cpp.

247  {
249  if (verb == -1)
250  verb = verbose;
251  Range ents;
252  CHKERR BitRefManager(*this).getEntitiesByRefLevel(bit, mask, ents, verb);
253  CHKERR clear_dofs_fields(ents, verb);
255  CHKERR clear_ents_fields(ents, verb);
257 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
MoFEMErrorCode clear_adjacencies_entities(const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
clear adjacency map for entities on given bit level
Definition: DeleteCore.cpp:349
MoFEMErrorCode clear_dofs_fields(const Range &ents, int verb=DEFAULT_VERBOSITY)
Definition: DeleteCore.cpp:78
#define CHKERR
Inline error check.
Definition: definitions.h:586
MoFEMErrorCode clear_ents_fields(const Range &ents, int verb=DEFAULT_VERBOSITY)
Definition: DeleteCore.cpp:259
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ clear_finite_elements() [1/2]

MoFEMErrorCode MoFEM::Core::clear_finite_elements ( const Range &  ents,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

clear finite elements

Implements MoFEM::CoreInterface.

Definition at line 437 of file DeleteCore.cpp.

437  {
439  if (verb == -1)
440  verb = verbose;
442  for (Range::const_pair_iterator p_eit = ents.pair_begin();
443  p_eit != ents.pair_end(); p_eit++) {
444  EntityHandle first = p_eit->first;
445  EntityHandle second = p_eit->second;
446  EntFiniteElement_multiIndex::index<Ent_mi_tag>::type::iterator fit, hi_fit;
447  fit = entsFiniteElements.get<Ent_mi_tag>().lower_bound(first);
448  hi_fit = entsFiniteElements.get<Ent_mi_tag>().upper_bound(second);
449  entsFiniteElements.get<Ent_mi_tag>().erase(fit, hi_fit);
450  }
452 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
MoFEMErrorCode clear_adjacencies_finite_elements(const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
clear adjacency map for finite elements on given bit level
Definition: DeleteCore.cpp:478
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404
EntFiniteElement_multiIndex entsFiniteElements
finite element entities
Definition: Core.hpp:252

◆ clear_finite_elements() [2/2]

MoFEMErrorCode MoFEM::Core::clear_finite_elements ( const std::string &  name,
const Range &  ents,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

clear finite elements

Implements MoFEM::CoreInterface.

Definition at line 454 of file DeleteCore.cpp.

455  {
457  if (verb == -1)
458  verb = verbose;
459  CHKERR clear_adjacencies_finite_elements(name, ents, verb);
460  for (Range::const_pair_iterator p_eit = ents.pair_begin();
461  p_eit != ents.pair_end(); p_eit++) {
462  EntityHandle first = p_eit->first;
463  EntityHandle second = p_eit->second;
464  EntFiniteElement_multiIndex::index<
465  Composite_Name_And_Ent_mi_tag>::type::iterator fit,
466  hi_fit;
467  fit = entsFiniteElements.get<Composite_Name_And_Ent_mi_tag>().lower_bound(
468  boost::make_tuple(name, first));
469  hi_fit =
470  entsFiniteElements.get<Composite_Name_And_Ent_mi_tag>().upper_bound(
471  boost::make_tuple(name, second));
472  fit = entsFiniteElements.get<Composite_Name_And_Ent_mi_tag>().erase(fit,
473  hi_fit);
474  }
476 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
MoFEMErrorCode clear_adjacencies_finite_elements(const BitRefLevel &bit, const BitRefLevel &mask, int verb=DEFAULT_VERBOSITY)
clear adjacency map for finite elements on given bit level
Definition: DeleteCore.cpp:478
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404
EntFiniteElement_multiIndex entsFiniteElements
finite element entities
Definition: Core.hpp:252

◆ clear_finite_elements_by_bit_ref()

MoFEMErrorCode MoFEM::Core::clear_finite_elements_by_bit_ref ( const BitRefLevel bit,
const BitRefLevel mask,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

clear finite elements

Implements MoFEM::CoreInterface.

Definition at line 425 of file DeleteCore.cpp.

427  {
429  if (verb == -1)
430  verb = verbose;
431  Range ents;
432  CHKERR BitRefManager(*this).getEntitiesByRefLevel(bit, mask, ents, verb);
433  CHKERR clear_finite_elements(ents, verb);
435 }
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
#define CHKERR
Inline error check.
Definition: definitions.h:586
int verbose
Verbosity level.
Definition: Core.hpp:904
MoFEMErrorCode clear_finite_elements(const Range &ents, int verb=DEFAULT_VERBOSITY)
Definition: DeleteCore.cpp:437
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ clear_inactive_dofs()

MoFEMErrorCode MoFEM::Core::clear_inactive_dofs ( int  verb = DEFAULT_VERBOSITY)
protectedvirtual

Clear inactive dofs

Implements MoFEM::CoreInterface.

Definition at line 34 of file DeleteCore.cpp.

34  {
36  if (verb == -1)
37  verb = verbose;
38  Range ents;
39  for (DofEntity_multiIndex::iterator dit = dofsField.begin();
40  dit != dofsField.end();) {
41  if (!dit->get()->getActive()) {
42  // FieldEntityEntFiniteElementAdjacencyMap_multiIndex::index<
43  // Unique_mi_tag>::type::iterator ait,
44  // hi_ait;
45  // ait = entFEAdjacencies.get<Unique_mi_tag>().lower_bound(
46  // (*dit)->getFieldEntityPtr()->getGlobalUniqueId());
47  // hi_ait = entFEAdjacencies.get<Unique_mi_tag>().upper_bound(
48  // (*dit)->getFieldEntityPtr()->getGlobalUniqueId());
49  // for (; ait != hi_ait; ait++) {
50  // boost::shared_ptr<EntFiniteElement> ent_fe_ptr;
51  // ent_fe_ptr = ait->entFePtr;
52  // ent_fe_ptr->row_dof_view->erase((*dit)->getGlobalUniqueId());
53  // if (ent_fe_ptr->row_dof_view != ent_fe_ptr->col_dof_view) {
54  // ent_fe_ptr->col_dof_view->erase((*dit)->getGlobalUniqueId());
55  // }
56  // ent_fe_ptr->data_dofs->get<Unique_mi_tag>().erase(
57  // (*dit)->getGlobalUniqueId());
58  // }
59  dit = dofsField.erase(dit);
60  } else {
61  ++dit;
62  }
63  }
65 }
DofEntity_multiIndex dofsField
dofs on fields
Definition: Core.hpp:249
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return() ...
Definition: definitions.h:467
int verbose
Verbosity level.
Definition: Core.hpp:904
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:404

◆ clear_problem()

MoFEMErrorCode MoFEM::Core::clear_problem ( const std::string &  name,
int  verb = DEFAULT_VERBOSITY 
)
protectedvirtual

clear problem

Implements MoFEM::CoreInterface.

Definition at line 244 of file ProblemsCore.cpp.

244  {
246  if (verb == -1)
247  verb = verbose;
248  typedef Problem_multiIndex::index<Problem_mi_tag>::type ProblemsByName;
249  ProblemsByName &prob_by_name = pRoblems.get<Problem_mi_tag>();
250  ProblemsByName::iterator p_miit = prob_by_name.find(problem_name);
251  if (p_miit == prob_by_name.end()) {
252  SETERRQ1(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
253  "problem < %s > not found, (top tip: check spelling)",
254  problem_name.c_str());
255  }
256