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#include <tet_mesh.h>
Inheritance diagram for oomph::TetMeshBase:
Public Member Functions | |
| TetMeshBase () | |
| Constructor. More... | |
| TetMeshBase (const TetMeshBase &node)=delete | |
| Broken copy constructor. More... | |
| void | operator= (const TetMeshBase &)=delete |
| Broken assignment operator. More... | |
| virtual | ~TetMeshBase () |
| Destructor (empty) More... | |
| void | assess_mesh_quality (std::ofstream &some_file) |
| Assess mesh quality: Ratio of max. edge length to min. height, so if it's very large it's BAAAAAD. More... | |
| template<class ELEMENT > | |
| void | setup_boundary_coordinates (const unsigned &b) |
| Setup boundary coordinate on boundary b which is assumed to be planar. Boundary coordinates are the x-y coordinates in the plane of that boundary, with the x-axis along the line from the (lexicographically) "lower left" to the "upper right" node. The y axis is obtained by taking the cross-product of the positive x direction with the outer unit normal computed by the face elements (or its negative if switch_normal is set to true). Doc faces in output file (if it's open). More... | |
| template<class ELEMENT > | |
| void | setup_boundary_coordinates (const unsigned &b, const bool &switch_normal) |
| Setup boundary coordinate on boundary b which is assumed to be planar. Boundary coordinates are the x-y coordinates in the plane of that boundary, with the x-axis along the line from the (lexicographically) "lower left" to the "upper right" node. The y axis is obtained by taking the cross-product of the positive x direction with the outer unit normal computed by the face elements (or its negative if switch_normal is set to true). Doc faces in output file (if it's open). More... | |
| template<class ELEMENT > | |
| void | setup_boundary_coordinates (const unsigned &b, const bool &switch_normal, std::ofstream &outfile) |
| Setup boundary coordinate on boundary b which is assumed to be planar. Boundary coordinates are the x-y coordinates in the plane of that boundary, with the x-axis along the line from the (lexicographically) "lower left" to the "upper right" node. The y axis is obtained by taking the cross-product of the positive x direction with the outer unit normal computed by the face elements (or its negative if switch_normal is set to true). Doc faces in output file (if it's open). More... | |
| template<class ELEMENT > | |
| void | setup_boundary_coordinates (const unsigned &b, std::ofstream &outfile) |
| Setup boundary coordinate on boundary b which is assumed to be planar. Boundary coordinates are the x-y coordinates in the plane of that boundary, with the x-axis along the line from the (lexicographically) "lower left" to the "upper right" node. The y axis is obtained by taking the cross-product of the positive x direction with the outer unit normal computed by the face elements (or its negative if switch_normal is set to true). Doc faces in output file (if it's open). More... | |
| unsigned | nboundary_element_in_region (const unsigned &b, const unsigned &r) const |
| Return the number of elements adjacent to boundary b in region r. More... | |
| FiniteElement * | boundary_element_in_region_pt (const unsigned &b, const unsigned &r, const unsigned &e) const |
| Return pointer to the e-th element adjacent to boundary b in region r. More... | |
| int | face_index_at_boundary_in_region (const unsigned &b, const unsigned &r, const unsigned &e) const |
| Return face index of the e-th element adjacent to boundary b in region r. More... | |
| unsigned | nregion () |
| Return the number of regions specified by attributes. More... | |
| unsigned | nregion_element (const unsigned &r) |
| Return the number of elements in region r. More... | |
| double | region_attribute (const unsigned &i) |
| Return the i-th region attribute (here only used as the (assumed to be unsigned) region id. More... | |
| FiniteElement * | region_element_pt (const unsigned &r, const unsigned &e) |
| Return the e-th element in the r-th region. More... | |
| template<class ELEMENT > | |
| void | snap_to_quadratic_surface (const Vector< unsigned > &boundary_id, const std::string &quadratic_surface_file_name, const bool &switch_normal, DocInfo &doc_info) |
| Snap boundaries specified by the IDs listed in boundary_id to a quadratric surface, specified in the file quadratic_surface_file_name. This is usually used with vmtk-based meshes for which oomph-lib's xda to poly conversion code produces the files "quadratic_fsi_boundary.dat" and "quadratic_outer_solid_boundary.dat" which specify the quadratic FSI boundary (for the fluid and the solid) and the quadratic representation of the outer boundary of the solid. When used with these files, the flag switch_normal should be set to true when calling the function for the outer boundary of the solid. The DocInfo object can be used to label optional output files. (Uses directory and label). More... | |
| template<class ELEMENT > | |
| void | snap_to_quadratic_surface (const Vector< unsigned > &boundary_id, const std::string &quadratic_surface_file_name, const bool &switch_normal) |
| Snap boundaries specified by the IDs listed in boundary_id to a quadratric surface, specified in the file quadratic_surface_file_name. This is usually used with vmtk-based meshes for which oomph-lib's xda to poly conversion code produces the files "quadratic_fsi_boundary.dat" and "quadratic_outer_solid_boundary.dat" which specify the quadratic FSI boundary (for the fluid and the solid) and the quadratic representation of the outer boundary of the solid. When used with these files, the flag switch_normal should be set to true when calling the function for the outer boundary of the solid. More... | |
| void | snap_nodes_onto_geometric_objects () |
| Move the nodes on boundaries with associated GeomObjects so that they exactly coincide with the geometric object. This requires that the boundary coordinates are set up consistently. More... | |
| template<class ELEMENT > | |
| void | split_elements_in_corners (TimeStepper *time_stepper_pt=&Mesh::Default_TimeStepper) |
| Non-Delaunay split elements that have three faces on a boundary into sons. Timestepper species timestepper for new nodes; defaults to to steady timestepper. More... | |
| void | setup_boundary_element_info () |
| Setup lookup schemes which establish which elements are located next to mesh's boundaries (wrapper to suppress doc). More... | |
| void | setup_boundary_element_info (std::ostream &outfile) |
| Setup lookup schemes which establish which elements are located next to mesh's boundaries. Doc in outfile (if it's open). More... | |
| Public Member Functions inherited from oomph::Mesh | |
| void | resize_halo_nodes () |
| Helper function that resizes halo nodes to the same size as their non-halo counterparts if required. (A discrepancy can arise if a FaceElement that introduces additional unknowns are attached to a bulk element that shares a node with a haloed element. In that case the joint node between haloed and non-haloed element is resized on that processor but not on the one that holds the halo counterpart (because no FaceElement is attached to the halo element) More... | |
| Mesh () | |
| Default constructor. More... | |
| Mesh (const Vector< Mesh * > &sub_mesh_pt) | |
| Constructor builds combined mesh from the meshes specified. Note: This simply merges the meshes' elements and nodes (ignoring duplicates; no boundary information etc. is created). More... | |
| void | merge_meshes (const Vector< Mesh * > &sub_mesh_pt) |
| Merge meshes. Note: This simply merges the meshes' elements and nodes (ignoring duplicates; no boundary information etc. is created). More... | |
| virtual void | reset_boundary_element_info (Vector< unsigned > &ntmp_boundary_elements, Vector< Vector< unsigned >> &ntmp_boundary_elements_in_region, Vector< FiniteElement * > &deleted_elements) |
| Virtual function to perform the reset boundary elements info rutines. More... | |
| template<class BULK_ELEMENT > | |
| void | doc_boundary_coordinates (const unsigned &b, std::ofstream &the_file) |
| Output boundary coordinates on boundary b – template argument specifies the bulk element type (needed to create FaceElement of appropriate type on mesh boundary). More... | |
| virtual void | scale_mesh (const double &factor) |
| Scale all nodal coordinates by given factor. Virtual so it can be overloaded in SolidMesh class where it also re-assigns the Lagrangian coordinates. More... | |
| Mesh (const Mesh &dummy)=delete | |
| Broken copy constructor. More... | |
| void | operator= (const Mesh &)=delete |
| Broken assignment operator. More... | |
| virtual | ~Mesh () |
| Virtual Destructor to clean up all memory. More... | |
| void | flush_element_and_node_storage () |
| Flush storage for elements and nodes by emptying the vectors that store the pointers to them. This is useful if a particular mesh is only built to generate a small part of a bigger mesh. Once the elements and nodes have been created, they are typically copied into the new mesh and the auxiliary mesh can be deleted. However, if we simply call the destructor of the auxiliary mesh, it will also wipe out the nodes and elements, because it still "thinks" it's in charge of these... More... | |
| void | flush_element_storage () |
| Flush storage for elements (only) by emptying the vectors that store the pointers to them. This is useful if a particular mesh is only built to generate a small part of a bigger mesh. Once the elements and nodes have been created, they are typically copied into the new mesh and the auxiliary mesh can be deleted. However, if we simply call the destructor of the auxiliary mesh, it will also wipe out the nodes and elements, because it still "thinks" it's in charge of these... More... | |
| void | flush_node_storage () |
| Flush storage for nodes (only) by emptying the vectors that store the pointers to them. More... | |
| Node *& | node_pt (const unsigned long &n) |
| Return pointer to global node n. More... | |
| Node * | node_pt (const unsigned long &n) const |
| Return pointer to global node n (const version) More... | |
| GeneralisedElement *& | element_pt (const unsigned long &e) |
| Return pointer to element e. More... | |
| GeneralisedElement * | element_pt (const unsigned long &e) const |
| Return pointer to element e (const version) More... | |
| const Vector< GeneralisedElement * > & | element_pt () const |
| Return reference to the Vector of elements. More... | |
| Vector< GeneralisedElement * > & | element_pt () |
| Return reference to the Vector of elements. More... | |
| FiniteElement * | finite_element_pt (const unsigned &e) const |
| Upcast (downcast?) to FiniteElement (needed to access FiniteElement member functions). More... | |
| Node *& | boundary_node_pt (const unsigned &b, const unsigned &n) |
| Return pointer to node n on boundary b. More... | |
| Node * | boundary_node_pt (const unsigned &b, const unsigned &n) const |
| Return pointer to node n on boundary b. More... | |
| void | set_nboundary (const unsigned &nbound) |
| Set the number of boundaries in the mesh. More... | |
| void | remove_boundary_nodes () |
| Clear all pointers to boundary nodes. More... | |
| void | remove_boundary_nodes (const unsigned &b) |
| Remove all information about nodes stored on the b-th boundary of the mesh. More... | |
| void | remove_boundary_node (const unsigned &b, Node *const &node_pt) |
| Remove a node from the boundary b. More... | |
| void | add_boundary_node (const unsigned &b, Node *const &node_pt) |
| Add a (pointer to) a node to the b-th boundary. More... | |
| void | copy_boundary_node_data_from_nodes () |
| Replace existing boundary node lookup schemes with new schemes created using the boundary data stored in the nodes. More... | |
| bool | boundary_coordinate_exists (const unsigned &i) const |
| Indicate whether the i-th boundary has an intrinsic coordinate. More... | |
| unsigned long | nelement () const |
| Return number of elements in the mesh. More... | |
| unsigned long | nnode () const |
| Return number of nodes in the mesh. More... | |
| unsigned | ndof_types () const |
| Return number of dof types in mesh. More... | |
| unsigned | elemental_dimension () const |
| Return number of elemental dimension in mesh. More... | |
| unsigned | nodal_dimension () const |
| Return number of nodal dimension in mesh. More... | |
| void | add_node_pt (Node *const &node_pt) |
| Add a (pointer to a) node to the mesh. More... | |
| void | add_element_pt (GeneralisedElement *const &element_pt) |
| Add a (pointer to) an element to the mesh. More... | |
| virtual void | node_update (const bool &update_all_solid_nodes=false) |
| Update nodal positions in response to changes in the domain shape. Uses the FiniteElement::get_x(...) function for FiniteElements and doesn't do anything for other element types. If a MacroElement pointer has been set for a FiniteElement, the MacroElement representation is used to update the nodal positions; if not get_x(...) uses the FE interpolation and thus leaves the nodal positions unchanged. Virtual, so it can be overloaded by specific meshes, such as AlgebraicMeshes or SpineMeshes. Generally, this function updates the position of all nodes in response to changes in the boundary position. However, we ignore all SolidNodes since their position is computed as part of the solution – unless the bool flag is set to true. Such calls are typically made when the initial mesh is created and/or after a mesh has been refined repeatedly before the start of the computation. More... | |
| virtual void | reorder_nodes (const bool &use_old_ordering=true) |
| Re-order nodes in the order in which they appear in elements – can be overloaded for more efficient re-ordering. More... | |
| virtual void | get_node_reordering (Vector< Node * > &reordering, const bool &use_old_ordering=true) const |
| Get a reordering of the nodes in the order in which they appear in elements – can be overloaded for more efficient re-ordering. More... | |
| template<class BULK_ELEMENT , template< class > class FACE_ELEMENT> | |
| void | build_face_mesh (const unsigned &b, Mesh *const &face_mesh_pt) |
| Constuct a Mesh of FACE_ELEMENTs along the b-th boundary of the mesh (which contains elements of type BULK_ELEMENT) More... | |
| unsigned | self_test () |
| Self-test: Check elements and nodes. Return 0 for OK. More... | |
| void | max_and_min_element_size (double &max_size, double &min_size) |
| Determine max and min area for all FiniteElements in the mesh (non-FiniteElements are ignored) More... | |
| double | total_size () |
| Determine the sum of all "sizes" of the FiniteElements in the mesh (non-FiniteElements are ignored). This gives the length/area/volume occupied by the mesh. More... | |
| void | check_inverted_elements (bool &mesh_has_inverted_elements, std::ofstream &inverted_element_file) |
| Check for inverted elements and report outcome in boolean variable. This visits all elements at their integration points and checks if the Jacobian of the mapping between local and global coordinates is positive – using the same test that would be carried out (but only in PARANOID mode) during the assembly of the elements' Jacobian matrices. Inverted elements are output in inverted_element_file (if the stream is open). More... | |
| void | check_inverted_elements (bool &mesh_has_inverted_elements) |
| Check for inverted elements and report outcome in boolean variable. This visits all elements at their integration points and checks if the Jacobian of the mapping between local and global coordinates is positive – using the same test that would be carried out (but only in PARANOID mode) during the assembly of the elements' Jacobian matrices. More... | |
| unsigned | check_for_repeated_nodes (const double &epsilon=1.0e-12) |
| Check for repeated nodes within a given spatial tolerance. Return (0/1) for (pass/fail). More... | |
| Vector< Node * > | prune_dead_nodes () |
| Prune nodes. Nodes that have been marked as obsolete are removed from the mesh (and its boundary-node scheme). Returns vector of pointers to deleted nodes. More... | |
| unsigned | nboundary () const |
| Return number of boundaries. More... | |
| unsigned long | nboundary_node (const unsigned &ibound) const |
| Return number of nodes on a particular boundary. More... | |
| FiniteElement * | boundary_element_pt (const unsigned &b, const unsigned &e) const |
| Return pointer to e-th finite element on boundary b. More... | |
| Node * | get_some_non_boundary_node () const |
| Find a node not on any boundary in mesh_pt (useful for pinning a single node in a purely Neumann problem so that it is fully determined). More... | |
| unsigned | nboundary_element (const unsigned &b) const |
| Return number of finite elements that are adjacent to boundary b. More... | |
| int | face_index_at_boundary (const unsigned &b, const unsigned &e) const |
| For the e-th finite element on boundary b, return int to indicate the face_index of the face adjacent to the boundary. This is consistent with input required during the generation of FaceElements. More... | |
| virtual void | dump (std::ofstream &dump_file, const bool &use_old_ordering=true) const |
| Dump the data in the mesh into a file for restart. More... | |
| void | dump (const std::string &dump_file_name, const bool &use_old_ordering=true) const |
| Dump the data in the mesh into a file for restart. More... | |
| virtual void | read (std::ifstream &restart_file) |
| Read solution from restart file. More... | |
| void | output_paraview (std::ofstream &file_out, const unsigned &nplot) const |
| Output in paraview format into specified file. Breaks up each element into sub-elements for plotting purposes. We assume that all elements are of the same type (fct will break break (in paranoid mode) if paraview output fcts of the elements are inconsistent). More... | |
| void | output_fct_paraview (std::ofstream &file_out, const unsigned &nplot, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt) const |
| Output in paraview format into specified file. Breaks up each element into sub-elements for plotting purposes. We assume that all elements are of the same type (fct will break break (in paranoid mode) if paraview output fcts of the elements are inconsistent). More... | |
| void | output_fct_paraview (std::ofstream &file_out, const unsigned &nplot, const double &time, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt) const |
| Output in paraview format into specified file. Breaks up each element into sub-elements for plotting purposes. We assume that all elements are of the same type (fct will break break (in paranoid mode) if paraview output fcts of the elements are inconsistent). More... | |
| void | output (std::ostream &outfile) |
| Output for all elements. More... | |
| void | output (std::ostream &outfile, const unsigned &n_plot) |
| Output at f(n_plot) points in each element. More... | |
| void | output (FILE *file_pt) |
| Output for all elements (C-style output) More... | |
| void | output (FILE *file_pt, const unsigned &nplot) |
| Output at f(n_plot) points in each element (C-style output) More... | |
| void | output (const std::string &output_filename) |
| Output for all elements. More... | |
| void | output (const std::string &output_filename, const unsigned &n_plot) |
| Output at f(n_plot) points in each element. More... | |
| void | output_fct (std::ostream &outfile, const unsigned &n_plot, FiniteElement::SteadyExactSolutionFctPt) |
| Output a given Vector function at f(n_plot) points in each element. More... | |
| void | output_fct (std::ostream &outfile, const unsigned &n_plot, const double &time, FiniteElement::UnsteadyExactSolutionFctPt) |
| Output a given time-dep. Vector function at f(n_plot) points in each element. More... | |
| void | output_boundaries (std::ostream &outfile) |
| Output the nodes on the boundaries (into separate tecplot zones) More... | |
| void | output_boundaries (const std::string &output_filename) |
| Output the nodes on the boundaries (into separate tecplot zones). Specify filename. More... | |
| void | assign_initial_values_impulsive () |
| Assign initial values for an impulsive start. More... | |
| void | shift_time_values () |
| Shift time-dependent data along for next timestep: Deal with nodal Data/positions and the element's internal Data. More... | |
| void | calculate_predictions () |
| Calculate predictions for all Data and positions associated with the mesh, usually used in adaptive time-stepping. More... | |
| void | set_nodal_and_elemental_time_stepper (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data) |
| Set the timestepper associated with all nodal and elemental data stored in the mesh. More... | |
| virtual void | set_mesh_level_time_stepper (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data) |
| Function that can be used to set any additional timestepper data stored at the Mesh (as opposed to nodal and elemental) levels. This is virtual so that it can be overloaded in the appropriate Meshes. Examples include the SpineMeshes and adaptive triangle and tet meshes. More... | |
| void | set_consistent_pinned_values_for_continuation (ContinuationStorageScheme *const &continuation_stepper_pt) |
| Set consistent values for pinned data in continuation. More... | |
| bool | does_pointer_correspond_to_mesh_data (double *const ¶meter_pt) |
| Does the double pointer correspond to any mesh data. More... | |
| void | set_nodal_time_stepper (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data) |
| Set the timestepper associated with the nodal data in the mesh. More... | |
| void | set_elemental_internal_time_stepper (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data) |
| Set the timestepper associated with the internal data stored within elements in the meah. More... | |
| virtual void | compute_norm (double &norm) |
| Compute norm of solution by summing contributions of compute_norm(...) for all constituent elements in the mesh. What that norm means depends on what's defined in the element's function; may need to take the square root afterwards if the elements compute the square of the L2 norm, say. More... | |
| virtual void | compute_norm (Vector< double > &norm) |
| Compute norm of solution by summing contributions of compute_norm(...) for all constituent elements in the mesh. What that norm means depends on what's defined in the element's function; may need to take the square root afterwards if the elements compute the square of the L2 norm, say. More... | |
| virtual void | compute_error (std::ostream &outfile, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, double &error, double &norm) |
| Plot error when compared against a given exact solution. Also returns the norm of the error and that of the exact solution. More... | |
| virtual void | compute_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, double &error, double &norm) |
| Plot error when compared against a given time-depdendent exact solution. Also returns the norm of the error and that of the exact solution. More... | |
| virtual void | compute_error (FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, double &error, double &norm) |
| Plot error when compared against a given time-dependent exact solution. Also returns the norm of the error and that of the exact solution. More... | |
| virtual void | compute_error (FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, Vector< double > &error, Vector< double > &norm) |
| Plot error when compared against a given time-dependent exact solution. Also returns the norm of the error and that of the exact solution. More... | |
| virtual void | compute_error (std::ostream &outfile, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, Vector< double > &error, Vector< double > &norm) |
| Plot error when compared against a given time-depdendent exact solution. Also returns the norm of the error and that of the exact solution. Version with vectors of norms and errors so that different variables' norms and errors can be returned individually. More... | |
| virtual void | compute_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, Vector< double > &error, Vector< double > &norm) |
| Plot error when compared against a given time-depdendent exact solution. Also returns the norm of the error and that of the exact solution. Version with vectors of norms and errors so that different variables' norms and errors can be returned individually. More... | |
| virtual void | compute_error (FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, double &error, double &norm) |
| Returns the norm of the error and that of the exact solution. More... | |
| virtual void | compute_error (FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, Vector< double > &error, Vector< double > &norm) |
| Returns the norm of the error and that of the exact solution. Version with vectors of norms and errors so that different variables' norms and errors can be returned individually. More... | |
| bool | is_mesh_distributed () const |
| Boolean to indicate if Mesh has been distributed. More... | |
| OomphCommunicator * | communicator_pt () const |
| Read-only access fct to communicator (Null if mesh is not distributed, i.e. if we don't have mpi). More... | |
| void | set_communicator_pt (OomphCommunicator *comm_pt) |
| Function to set communicator (mesh is assumed to be distributed if the communicator pointer is non-null). Only defined if mpi is enabled becaus Comm_pt itself is only defined when mpi is enabled. More... | |
| void | set_keep_all_elements_as_halos () |
| Call this function to keep all the elements as halo elements. More... | |
| void | unset_keep_all_elements_as_halos () |
| Calll this function to unset the flag that keeps all elements in the mesh as halo elements. More... | |
| virtual void | distribute (OomphCommunicator *comm_pt, const Vector< unsigned > &element_domain, Vector< GeneralisedElement * > &deleted_element_pt, DocInfo &doc_info, const bool &report_stats, const bool &overrule_keep_as_halo_element_status) |
| Distribute the problem and doc; make this virtual to allow overloading for particular meshes where further work is required. Add to vector of pointers to deleted elements. More... | |
| void | distribute (OomphCommunicator *comm_pt, const Vector< unsigned > &element_domain, Vector< GeneralisedElement * > &deleted_element_pt, const bool &report_stats=false) |
| Distribute the problem Add to vector of pointers to deleted elements. More... | |
| void | prune_halo_elements_and_nodes (Vector< GeneralisedElement * > &deleted_element_pt, const bool &report_stats=false) |
| (Irreversibly) prune halo(ed) elements and nodes, usually after another round of refinement, to get rid of excessively wide halo layers. Note that the current mesh will be now regarded as the base mesh and no unrefinement relative to it will be possible once this function has been called. More... | |
| void | prune_halo_elements_and_nodes (Vector< GeneralisedElement * > &deleted_element_pt, DocInfo &doc_info, const bool &report_stats) |
| (Irreversibly) prune halo(ed) elements and nodes, usually after another round of refinement, to get rid of excessively wide halo layers. Note that the current mesh will be now regarded as the base mesh and no unrefinement relative to it will be possible once this function has been called. More... | |
| void | get_efficiency_of_mesh_distribution (double &av_efficiency, double &max_efficiency, double &min_efficiency) |
| Get efficiency of mesh distribution: In an ideal distribution without halo overhead, each processor would only hold its own elements. Efficieny per processor = (number of non-halo elements)/ (total number of elements). More... | |
| void | doc_mesh_distribution (DocInfo &doc_info) |
| Doc the mesh distribution, to be processed with tecplot macros. More... | |
| void | check_halo_schemes (DocInfo &doc_info, double &max_permitted_error_for_halo_check) |
| Check halo and shared schemes on the mesh. More... | |
| virtual void | classify_halo_and_haloed_nodes (DocInfo &doc_info, const bool &report_stats) |
| Classify the halo and haloed nodes in the mesh. Virtual so it can be overloaded to perform additional functionality (such as synchronising hanging nodes) in refineable meshes, say. More... | |
| virtual void | classify_halo_and_haloed_nodes (const bool &report_stats=false) |
| Classify the halo and haloed nodes in the mesh. Virtual so it can be overloaded to perform additional functionality (such as synchronising hanging nodes) in refineable meshes, say. More... | |
| void | synchronise_shared_nodes (const bool &report_stats) |
| Synchronise shared node lookup schemes to cater for the the case where: (1) a certain node on the current processor is halo with proc p (i.e. its non-halo counterpart lives on processor p) (2) that node is also exists (also as a halo) on another processor (q, say) where its non-halo counter part is also known to be on processor p. However, without calling this function the current processor does not necessarily know that it shares a node with processor q. This information can be required, e.g. when synchronising hanging node schemes over all processors. More... | |
| void | get_all_halo_data (std::map< unsigned, double * > &map_of_halo_data) |
| Get all the halo data stored in the mesh and add pointers to the data to the map, indexed by global equation number. More... | |
| Vector< GeneralisedElement * > | halo_element_pt (const unsigned &p) |
| Return vector of halo elements in this Mesh whose non-halo counterpart is held on processor p. More... | |
| Vector< GeneralisedElement * > | haloed_element_pt (const unsigned &p) |
| Return vector of haloed elements in this Mesh whose haloing counterpart is held on processor p. More... | |
| unsigned | nnon_halo_element () |
| Total number of non-halo elements in this mesh (Costly call computes result on the fly) More... | |
| unsigned | nroot_halo_element () |
| Total number of root halo elements in this Mesh. More... | |
| unsigned | nroot_halo_element (const unsigned &p) |
| Number of root halo elements in this Mesh whose non-halo counterpart is held on processor p. More... | |
| Vector< GeneralisedElement * > | root_halo_element_pt (const unsigned &p) |
| Vector of pointers to root halo elements in this Mesh whose non-halo counterpart is held on processor p. More... | |
| GeneralisedElement *& | root_halo_element_pt (const unsigned &p, const unsigned &e) |
| Access fct to the e-th root halo element in this Mesh whose non-halo counterpart is held on processor p. More... | |
| void | add_root_halo_element_pt (const unsigned &p, GeneralisedElement *&el_pt) |
| Add root halo element whose non-halo counterpart is held on processor p to this Mesh. More... | |
| unsigned | nhalo_node () |
| Total number of halo nodes in this Mesh. More... | |
| unsigned | nhalo_node (const unsigned &p) |
| Number of halo nodes in this Mesh whose non-halo counterpart is held on processor p. More... | |
| void | add_halo_node_pt (const unsigned &p, Node *&nod_pt) |
| Add halo node whose non-halo counterpart is held on processor p to the storage scheme for halo nodes. More... | |
| Node * | halo_node_pt (const unsigned &p, const unsigned &j) |
| Access fct to the j-th halo node in this Mesh whose non-halo counterpart is held on processor p. More... | |
| unsigned | nroot_haloed_element () |
| Total number of root haloed elements in this Mesh. More... | |
| unsigned | nroot_haloed_element (const unsigned &p) |
| Number of root haloed elements in this Mesh whose non-halo counterpart is held on processor p. More... | |
| Vector< GeneralisedElement * > | root_haloed_element_pt (const unsigned &p) |
| Vector of pointers to root haloed elements in this Mesh whose non-halo counterpart is held on processor p. More... | |
| GeneralisedElement *& | root_haloed_element_pt (const unsigned &p, const unsigned &e) |
| Access fct to the e-th root haloed element in this Mesh whose non-halo counterpart is held on processor p. More... | |
| void | add_root_haloed_element_pt (const unsigned &p, GeneralisedElement *&el_pt) |
| Add root haloed element whose non-halo counterpart is held on processor p to the storage scheme for haloed elements. Note: This does not add the element to the storage scheme for elements as it's understood to naturally live on this processor anyway! More... | |
| unsigned | nhaloed_node () |
| Total number of haloed nodes in this Mesh. More... | |
| unsigned | nhaloed_node (const unsigned &p) |
| Number of haloed nodes in this Mesh whose haloed counterpart is held on processor p. More... | |
| Node * | haloed_node_pt (const unsigned &p, const unsigned &j) |
| Access fct to the j-th haloed node in this Mesh whose halo counterpart is held on processor p. More... | |
| void | add_haloed_node_pt (const unsigned &p, Node *&nod_pt) |
| Add haloed node whose halo counterpart is held on processor p to the storage scheme for haloed nodes. More... | |
| void | disable_resizing_of_halo_nodes () |
| Function to suppress resizing of halo nodes – optmisation but call it at your own risk! More... | |
| void | enable_resizing_of_halo_nodes () |
| Function to (re-)enable resizing of halo nodes – this returns things to the default behaviour. More... | |
| void | disable_output_of_halo_elements () |
| Function to disable halo element output. More... | |
| void | enable_output_of_halo_elements () |
| Function to enable halo element output. More... | |
| unsigned | nshared_node () |
| Total number of shared nodes in this Mesh. More... | |
| void | doc_shared_nodes () |
| Doc shared nodes. More... | |
| unsigned | nshared_node (const unsigned &p) |
| Number of shared nodes in this Mesh who have a counterpart on processor p. More... | |
| Node * | shared_node_pt (const unsigned &p, const unsigned &j) |
| Access fct to the j-th shared node in this Mesh who has a counterpart on processor p. More... | |
| void | get_shared_node_pt (const unsigned &p, Vector< Node * > &shared_node_pt) |
| Get vector of pointers to shared nodes with processor p. Required for faster search in Missing_masters_functions::add_external_haloed_node_helper() and Missing_masters_functions::add_external_haloed_master_node_helper() More... | |
| void | add_shared_node_pt (const unsigned &p, Node *&nod_pt) |
| Add shared node whose counterpart is held on processor p to the storage scheme for shared nodes. (NB: ensure that this routine is called twice, once for each process) More... | |
| void | get_halo_node_stats (double &av_number, unsigned &max_number, unsigned &min_number) |
| Get halo node stats for this distributed mesh: Average/max/min number of halo nodes over all processors. Careful: Involves MPI Broadcasts and must therefore be called on all processors! More... | |
| void | get_haloed_node_stats (double &av_number, unsigned &max_number, unsigned &min_number) |
| Get haloed node stats for this distributed mesh: Average/max/min number of haloed nodes over all processors. Careful: Involves MPI Broadcasts and must therefore be called on all processors! More... | |
| void | output_external_halo_elements (std::ostream &outfile, const unsigned &n_plot=5) |
| Output all external halo elements. More... | |
| void | output_external_halo_elements (const unsigned &p, std::ostream &outfile, const unsigned &n_plot=5) |
| Output all external halo elements with processor p. More... | |
| void | output_external_haloed_elements (std::ostream &outfile, const unsigned &n_plot=5) |
| Output all external haloed elements. More... | |
| void | output_external_haloed_elements (const unsigned &p, std::ostream &outfile, const unsigned &n_plot=5) |
| Output all external haloed elements with processor p. More... | |
| unsigned | nexternal_halo_element () |
| Total number of external halo elements in this Mesh. More... | |
| unsigned | nexternal_halo_element (const unsigned &p) |
| Number of external halo elements in this Mesh whose non-halo counterpart is held on processor p. More... | |
| GeneralisedElement *& | external_halo_element_pt (const unsigned &p, const unsigned &e) |
| Access fct to the e-th external halo element in this Mesh whose non-halo counterpart is held on processor p. More... | |
| void | add_external_halo_element_pt (const unsigned &p, GeneralisedElement *&el_pt) |
| Add external halo element whose non-halo counterpart is held on processor p to this Mesh. More... | |
| unsigned | nexternal_haloed_element () |
| Total number of external haloed elements in this Mesh. More... | |
| unsigned | nexternal_haloed_element (const unsigned &p) |
| Number of external haloed elements in this Mesh whose non-halo counterpart is held on processor p. More... | |
| GeneralisedElement *& | external_haloed_element_pt (const unsigned &p, const unsigned &e) |
| Access fct to the e-th external haloed element in this Mesh whose non-halo counterpart is held on processor p. More... | |
| unsigned | add_external_haloed_element_pt (const unsigned &p, GeneralisedElement *&el_pt) |
| Add external haloed element whose non-halo counterpart is held on processor p to the storage scheme for haloed elements. More... | |
| unsigned | nexternal_halo_node () |
| Total number of external halo nodes in this Mesh. More... | |
| void | get_external_halo_node_pt (Vector< Node * > &external_halo_node_pt) |
| Get vector of pointers to all external halo nodes. More... | |
| unsigned | nexternal_halo_node (const unsigned &p) |
| Number of external halo nodes in this Mesh whose non-halo (external) counterpart is held on processor p. More... | |
| void | add_external_halo_node_pt (const unsigned &p, Node *&nod_pt) |
| Add external halo node whose non-halo (external) counterpart is held on processor p to the storage scheme for halo nodes. More... | |
| Node *& | external_halo_node_pt (const unsigned &p, const unsigned &j) |
| Access fct to the j-th external halo node in this Mesh whose non-halo external counterpart is held on processor p. More... | |
| Vector< Node * > | external_halo_node_pt (const unsigned &p) |
| Access fct to vector of external halo node in this Mesh whose non-halo external counterpart is held on processor p. (read only) More... | |
| void | set_external_halo_node_pt (const unsigned &p, const Vector< Node * > &external_halo_node_pt) |
| Set vector of external halo node in this Mesh whose non-halo external counterpart is held on processor p. More... | |
| void | null_external_halo_node (const unsigned &p, Node *nod_pt) |
| Null out specified external halo node (used when deleting duplicates) More... | |
| void | remove_null_pointers_from_external_halo_node_storage () |
| Consolidate external halo node storage by removing nulled out pointes in external halo and haloed schemes. More... | |
| unsigned | nexternal_haloed_node () |
| Total number of external haloed nodes in this Mesh. More... | |
| unsigned | nexternal_haloed_node (const unsigned &p) |
| Number of external haloed nodes in this Mesh whose halo (external) counterpart is held on processor p. More... | |
| Node *& | external_haloed_node_pt (const unsigned &p, const unsigned &j) |
| Access fct to the j-th external haloed node in this Mesh whose halo external counterpart is held on processor p. More... | |
| unsigned | add_external_haloed_node_pt (const unsigned &p, Node *&nod_pt) |
| Add external haloed node whose halo (external) counterpart is held on processor p to the storage scheme for haloed nodes. More... | |
| Vector< Node * > | external_haloed_node_pt (const unsigned &p) |
| Access fct to vector of external haloed node in this Mesh whose halo external counterpart is held on processor p. (read only) More... | |
| void | set_external_haloed_node_pt (const unsigned &p, const Vector< Node * > &external_haloed_node_pt) |
| Set vector of external haloed node in this Mesh whose halo external counterpart is held on processor p. More... | |
| std::set< int > | external_halo_proc () |
| Return the set of processors that hold external halo nodes. This is required to avoid having to pass a communicator into the node_update functions for Algebraic-based and MacroElement-based Meshes. More... | |
| virtual void | create_shared_boundaries (OomphCommunicator *comm_pt, const Vector< unsigned > &element_domain, const Vector< GeneralisedElement * > &backed_up_el_pt, const Vector< FiniteElement * > &backed_up_f_el_pt, std::map< Data *, std::set< unsigned >> &processors_associated_with_data, const bool &overrule_keep_as_halo_element_status) |
| Creates the shared boundaries, only used in unstructured meshes In this case with the "TriangleMesh" class. More... | |
| virtual unsigned | try_to_add_root_haloed_element_pt (const unsigned &p, GeneralisedElement *&el_pt) |
| virtual unsigned | try_to_add_haloed_node_pt (const unsigned &p, Node *&nod_pt) |
| void | delete_all_external_storage () |
| Wipe the storage for all externally-based elements. More... | |
Static Public Attributes | |
| static double | Tolerance_for_boundary_finding = 1.0e-5 |
| Global static data that specifies the permitted error in the setup of the boundary coordinates. More... | |
| Static Public Attributes inherited from oomph::Mesh | |
| static Steady< 0 > | Default_TimeStepper |
| Default Steady Timestepper, to be used in default arguments to Mesh constructors. More... | |
| static bool | Suppress_warning_about_empty_mesh_level_time_stepper_function |
| Boolean used to control warning about empty mesh level timestepper function. More... | |
Protected Attributes | |
| Vector< Vector< FiniteElement * > > | Region_element_pt |
| Vectors of vectors of elements in each region (note: this just stores them; the region IDs are contained in Region_attribute!) More... | |
| Vector< double > | Region_attribute |
| Vector of attributes associated with the elements in each region NOTE: double is enforced on us by tetgen. We use it as an unsigned to indicate the actual (zero-based) region ID. More... | |
| Vector< std::map< unsigned, Vector< FiniteElement * > > > | Boundary_region_element_pt |
| Storage for elements adjacent to a boundary in a particular region. More... | |
| Vector< std::map< unsigned, Vector< int > > > | Face_index_region_at_boundary |
| Storage for the face index adjacent to a boundary in a particular region. More... | |
| TetMeshFacetedClosedSurface * | Outer_boundary_pt |
| Faceted surface that defines outer boundaries. More... | |
| Vector< TetMeshFacetedSurface * > | Internal_surface_pt |
| Vector to faceted surfaces that define internal boundaries. More... | |
| std::map< unsigned, TetMeshFacetedSurface * > | Tet_mesh_faceted_surface_pt |
| Reverse lookup scheme: Pointer to faceted surface (if any!) associated with boundary b. More... | |
| std::map< unsigned, TetMeshFacet * > | Tet_mesh_facet_pt |
| Reverse lookup scheme: Pointer to facet (if any!) associated with boundary b. More... | |
| std::map< unsigned, Vector< Vector< double > > > | Triangular_facet_vertex_boundary_coordinate |
| Boundary coordinates of vertices in triangular facets associated with given boundary. Is only set up for triangular facets! More... | |
| TimeStepper * | Time_stepper_pt |
| Timestepper used to build nodes. More... | |
| Protected Attributes inherited from oomph::Mesh | |
| Vector< Vector< Node * > > | Boundary_node_pt |
| Vector of Vector of pointers to nodes on the boundaries: Boundary_node_pt(b,n). Note that this is private to force the use of the add_boundary_node() function, which ensures that the reverse look-up schemes for the nodes are set up. More... | |
| bool | Lookup_for_elements_next_boundary_is_setup |
| Flag to indicate that the lookup schemes for elements that are adjacent to the boundaries has been set up. More... | |
| Vector< Vector< FiniteElement * > > | Boundary_element_pt |
| Vector of Vector of pointers to elements on the boundaries: Boundary_element_pt(b,e) More... | |
| Vector< Vector< int > > | Face_index_at_boundary |
| For the e-th finite element on boundary b, this is the index of the face that lies along that boundary. More... | |
| std::map< unsigned, Vector< GeneralisedElement * > > | Root_halo_element_pt |
| Map of vectors holding the pointers to the root halo elements. More... | |
| std::map< unsigned, Vector< GeneralisedElement * > > | Root_haloed_element_pt |
| Map of vectors holding the pointers to the root haloed elements. More... | |
| std::map< unsigned, Vector< Node * > > | Halo_node_pt |
| Map of vectors holding the pointers to the halo nodes. More... | |
| std::map< unsigned, Vector< Node * > > | Haloed_node_pt |
| Map of vectors holding the pointers to the haloed nodes. More... | |
| std::map< unsigned, Vector< Node * > > | Shared_node_pt |
| Map of vectors holding the pointers to the shared nodes. These are all the nodes that are on two "neighbouring" processes (the halo(ed) lookup scheme depends upon which processor is in charge. More... | |
| OomphCommunicator * | Comm_pt |
| Pointer to communicator – set to NULL if mesh is not distributed. More... | |
| std::map< unsigned, Vector< GeneralisedElement * > > | External_halo_element_pt |
| External halo(ed) elements are created as and when they are needed to act as source elements for the particular process's mesh. The storage is wiped and rebuilt every time the mesh is refined. More... | |
| std::map< unsigned, Vector< GeneralisedElement * > > | External_haloed_element_pt |
| Map of vectors holding the pointers to the external haloed elements. More... | |
| std::map< unsigned, Vector< Node * > > | External_halo_node_pt |
| Map of vectors holding the pointers to the external halo nodes. More... | |
| std::map< unsigned, Vector< Node * > > | External_haloed_node_pt |
| Map of vectors holding the pointers to the external haloed nodes. More... | |
| bool | Keep_all_elements_as_halos |
| bool to indicate whether to keep all elements in a mesh as halos or not More... | |
| bool | Resize_halo_nodes_not_required |
| Set this to true to suppress resizing of halo nodes (at your own risk!) More... | |
| Vector< Node * > | Node_pt |
| Vector of pointers to nodes. More... | |
| Vector< GeneralisedElement * > | Element_pt |
| Vector of pointers to generalised elements. More... | |
| std::vector< bool > | Boundary_coordinate_exists |
| Vector of boolean data that indicates whether the boundary coordinates have been set for the boundary. More... | |
Additional Inherited Members | |
| Public Types inherited from oomph::Mesh | |
| typedef void(FiniteElement::* | SteadyExactSolutionFctPt) (const Vector< double > &x, Vector< double > &soln) |
| Typedef for function pointer to function that computes steady exact solution. More... | |
| typedef void(FiniteElement::* | UnsteadyExactSolutionFctPt) (const double &time, const Vector< double > &x, Vector< double > &soln) |
| Typedef for function pointer to function that computes unsteady exact solution. More... | |
| Public Attributes inherited from oomph::Mesh | |
| bool | Output_halo_elements |
| Bool for output of halo elements. More... | |
| Protected Member Functions inherited from oomph::Mesh | |
| void | setup_shared_node_scheme () |
| Setup shared node scheme. More... | |
| unsigned long | assign_global_eqn_numbers (Vector< double * > &Dof_pt) |
| Assign the global equation numbers in the Data stored at the nodes and also internal element Data. Also, build (via push_back) the Vector of pointers to the dofs (variables). More... | |
| void | describe_dofs (std::ostream &out, const std::string ¤t_string) const |
| Function to describe the dofs of the Mesh. The ostream specifies the output stream to which the description is written; the string stores the currently assembled output that is ultimately written to the output stream by Data::describe_dofs(...); it is typically built up incrementally as we descend through the call hierarchy of this function when called from Problem::describe_dofs(...) More... | |
| void | describe_local_dofs (std::ostream &out, const std::string ¤t_string) const |
| Function to describe the local dofs of the elements. The ostream specifies the output stream to which the description is written; the string stores the currently assembled output that is ultimately written to the output stream by Data::describe_dofs(...); it is typically built up incrementally as we descend through the call hierarchy of this function when called from Problem::describe_dofs(...) More... | |
| void | assign_local_eqn_numbers (const bool &store_local_dof_pt) |
| Assign the local equation numbers in all elements If the boolean argument is true then also store pointers to dofs. More... | |
| void | convert_to_boundary_node (Node *&node_pt, const Vector< FiniteElement * > &finite_element_pt) |
| A function that upgrades an ordinary node to a boundary node We shouldn't ever really use this, but it does make life that bit easier for the lazy mesh writer. The pointer to the node is replaced by a pointer to the new boundary node in all element look-up schemes and in the mesh's Node_pt vector. The new node is also addressed by node_pt on return from the function. More... | |
| void | convert_to_boundary_node (Node *&node_pt) |
| A function that upgrades an ordinary node to a boundary node. All pointers to the node from the mesh's elements are found. and replaced by pointers to the new boundary node. If the node is present in the mesh's list of nodes, that pointer is also replaced. Finally, the pointer argument node_pt addresses the new node on return from the function. We shouldn't ever really use this, but it does make life that bit easier for the lazy mesh writer. More... | |
Detailed Description
//////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////// Base class for tet meshes (meshes made of 3D tet elements).
Definition at line 660 of file tet_mesh.h.
Constructor & Destructor Documentation
◆ TetMeshBase() [1/2]
|
inline |
Constructor.
Definition at line 664 of file tet_mesh.h.
◆ TetMeshBase() [2/2]
|
delete |
Broken copy constructor.
◆ ~TetMeshBase()
|
inlinevirtual |
Destructor (empty)
Definition at line 673 of file tet_mesh.h.
Member Function Documentation
◆ assess_mesh_quality()
| void oomph::TetMeshBase::assess_mesh_quality | ( | std::ofstream & | some_file | ) |
Assess mesh quality: Ratio of max. edge length to min. height, so if it's very large it's BAAAAAD.
Definition at line 373 of file tet_mesh.cc.
References e, oomph::Mesh::finite_element_pt(), i, oomph::Mesh::nelement(), oomph::FiniteElement::node_pt(), oomph::oomph_info, and oomph::Node::x().
◆ boundary_element_in_region_pt()
|
inline |
Return pointer to the e-th element adjacent to boundary b in region r.
Definition at line 816 of file tet_mesh.h.
References Boundary_region_element_pt, and e.
Referenced by oomph::RefineableGmshTetMesh< ELEMENT >::adapt(), and oomph::RefineableTetgenMesh< ELEMENT >::adapt().
◆ face_index_at_boundary_in_region()
|
inline |
Return face index of the e-th element adjacent to boundary b in region r.
Definition at line 834 of file tet_mesh.h.
References e, and Face_index_region_at_boundary.
Referenced by oomph::RefineableGmshTetMesh< ELEMENT >::adapt(), and oomph::RefineableTetgenMesh< ELEMENT >::adapt().
◆ nboundary_element_in_region()
|
inline |
Return the number of elements adjacent to boundary b in region r.
Definition at line 797 of file tet_mesh.h.
References Boundary_region_element_pt.
Referenced by oomph::RefineableGmshTetMesh< ELEMENT >::adapt(), and oomph::RefineableTetgenMesh< ELEMENT >::adapt().
◆ nregion()
|
inline |
Return the number of regions specified by attributes.
Definition at line 860 of file tet_mesh.h.
References Region_element_pt.
Referenced by oomph::RefineableGmshTetMesh< ELEMENT >::adapt(), and oomph::RefineableTetgenMesh< ELEMENT >::adapt().
◆ nregion_element()
|
inline |
Return the number of elements in region r.
Definition at line 866 of file tet_mesh.h.
References i, Region_attribute, and Region_element_pt.
Referenced by oomph::RefineableGmshTetMesh< ELEMENT >::adapt(), and oomph::RefineableTetgenMesh< ELEMENT >::adapt().
◆ operator=()
|
delete |
Broken assignment operator.
◆ region_attribute()
|
inline |
Return the i-th region attribute (here only used as the (assumed to be unsigned) region id.
Definition at line 906 of file tet_mesh.h.
References i, and Region_attribute.
Referenced by oomph::RefineableGmshTetMesh< ELEMENT >::adapt(), and oomph::RefineableTetgenMesh< ELEMENT >::adapt().
◆ region_element_pt()
|
inline |
Return the e-th element in the r-th region.
Definition at line 912 of file tet_mesh.h.
References e, i, Region_attribute, and Region_element_pt.
Referenced by oomph::RefineableGmshTetMesh< ELEMENT >::adapt(), and oomph::RefineableTetgenMesh< ELEMENT >::adapt().
◆ setup_boundary_coordinates() [1/4]
|
inline |
Setup boundary coordinate on boundary b which is assumed to be planar. Boundary coordinates are the x-y coordinates in the plane of that boundary, with the x-axis along the line from the (lexicographically) "lower left" to the "upper right" node. The y axis is obtained by taking the cross-product of the positive x direction with the outer unit normal computed by the face elements (or its negative if switch_normal is set to true). Doc faces in output file (if it's open).
Note 1: Setup of boundary coordinates is not done if the boundary in question turns out to be nonplanar.
Note 2: If a triangular TetMeshFacet is associated with a boundary we also store the boundary coordinates of its vertices. They are needed to interpolated intrinsic coordinates of an associated GeomObject (if any) into the interior.
Definition at line 702 of file tet_mesh.h.
◆ setup_boundary_coordinates() [2/4]
|
inline |
Setup boundary coordinate on boundary b which is assumed to be planar. Boundary coordinates are the x-y coordinates in the plane of that boundary, with the x-axis along the line from the (lexicographically) "lower left" to the "upper right" node. The y axis is obtained by taking the cross-product of the positive x direction with the outer unit normal computed by the face elements (or its negative if switch_normal is set to true). Doc faces in output file (if it's open).
Note 1: Setup of boundary coordinates is not done if the boundary in question turns out to be nonplanar.
Note 2: If a triangular TetMeshFacet is associated with a boundary we also store the boundary coordinates of its vertices. They are needed to interpolated intrinsic coordinates of an associated GeomObject (if any) into the interior. Final boolean argument allows switching of the direction of the outer unit normal.
Definition at line 733 of file tet_mesh.h.
◆ setup_boundary_coordinates() [3/4]
| void oomph::TetMeshBase::setup_boundary_coordinates | ( | const unsigned & | b, |
| const bool & | switch_normal, | ||
| std::ofstream & | outfile | ||
| ) |
Setup boundary coordinate on boundary b which is assumed to be planar. Boundary coordinates are the x-y coordinates in the plane of that boundary, with the x-axis along the line from the (lexicographically) "lower left" to the "upper right" node. The y axis is obtained by taking the cross-product of the positive x direction with the outer unit normal computed by the face elements (or its negative if switch_normal is set to true). Doc faces in output file (if it's open).
/////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////
Note 1: Setup of boundary coordinates is not done if the boundary in question turns out to be nonplanar.
Note 2: If a triangular TetMeshFacet is associated with a boundary we also store the boundary coordinates of its vertices. They are needed to interpolated intrinsic coordinates of an associated GeomObject (if any) into the interior. Boolean argument allows switching of the direction of the outer unit normal. Output file for doc.
Setup boundary coordinate on boundary b which is assumed to be planar. Boundary coordinates are the x-y coordinates in the plane of that boundary, with the x-axis along the line from the (lexicographically) "lower left" to the "upper right" node. The y axis is obtained by taking the cross-product of the positive x direction with the outer unit normal computed by the face elements (or its negative if switch_normal is set to true). Doc faces in output file (if it's open).
Note 1: Setup of boundary coordinates is not done if the boundary in question turns out to be nonplanar.
Note 2: If a triangular TetMeshFacet is associated with a boundary we also store the boundary coordinates of its vertices. They are needed to interpolated intrinsic coordinates of an associated GeomObject (if any) into the interior.
Definition at line 1092 of file tet_mesh.h.
References oomph::Mesh::Boundary_coordinate_exists, oomph::Mesh::boundary_element_pt(), oomph::Mesh::boundary_node_pt(), e, oomph::Mesh::face_index_at_boundary(), oomph::Mesh::nboundary_element(), oomph::Mesh::nboundary_node(), oomph::TetMeshFacet::nvertex(), s, oomph::Node::set_coordinates_on_boundary(), Tet_mesh_facet_pt, Tolerance_for_boundary_finding, Triangular_facet_vertex_boundary_coordinate, oomph::TetMeshFacet::vertex_pt(), oomph::Node::x(), and oomph::TetMeshVertex::x().
◆ setup_boundary_coordinates() [4/4]
|
inline |
Setup boundary coordinate on boundary b which is assumed to be planar. Boundary coordinates are the x-y coordinates in the plane of that boundary, with the x-axis along the line from the (lexicographically) "lower left" to the "upper right" node. The y axis is obtained by taking the cross-product of the positive x direction with the outer unit normal computed by the face elements (or its negative if switch_normal is set to true). Doc faces in output file (if it's open).
Note 1: Setup of boundary coordinates is not done if the boundary in question turns out to be nonplanar.
Note 2: If a triangular TetMeshFacet is associated with a boundary we also store the boundary coordinates of its vertices. They are needed to interpolated intrinsic coordinates of an associated GeomObject (if any) into the interior. Output file for doc.
Definition at line 788 of file tet_mesh.h.
◆ setup_boundary_element_info() [1/2]
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inlinevirtual |
Setup lookup schemes which establish which elements are located next to mesh's boundaries (wrapper to suppress doc).
Reimplemented from oomph::Mesh.
Definition at line 1007 of file tet_mesh.h.
Referenced by split_elements_in_corners().
◆ setup_boundary_element_info() [2/2]
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virtual |
Setup lookup schemes which establish which elements are located next to mesh's boundaries. Doc in outfile (if it's open).
Setup lookup schemes which establish which elements are located next to which boundaries (Doc to outfile if it's open).
Reimplemented from oomph::Mesh.
Definition at line 100 of file tet_mesh.cc.
References oomph::Mesh::Boundary_element_pt, oomph::FiniteElement::dim(), oomph::LeakCheckNames::doc(), e, oomph::Mesh::Face_index_at_boundary, oomph::Mesh::finite_element_pt(), oomph::Node::get_boundaries_pt(), i, oomph::Mesh::Lookup_for_elements_next_boundary_is_setup, oomph::Mesh::nboundary(), oomph::Mesh::nelement(), oomph::FiniteElement::node_pt(), and oomph::FiniteElement::output().
◆ snap_nodes_onto_geometric_objects()
| void oomph::TetMeshBase::snap_nodes_onto_geometric_objects | ( | ) |
Move the nodes on boundaries with associated GeomObjects so that they exactly coincide with the geometric object. This requires that the boundary coordinates are set up consistently.
Move the nodes on boundaries with associated Geometric Objects (if any) so that they exactly coincide with the geometric object. This requires that the boundary coordinates are set up consistently.
Definition at line 483 of file tet_mesh.cc.
References oomph::Mesh::Boundary_coordinate_exists, oomph::Mesh::boundary_node_pt(), oomph::TetMeshFacetedSurface::boundary_zeta01(), oomph::TetMeshFacetedSurface::boundary_zeta12(), oomph::TetMeshFacetedSurface::boundary_zeta20(), oomph::FiniteElement::check_J_eulerian_at_knots(), e, oomph::TetMeshFacetedSurface::facet_pt(), oomph::Mesh::finite_element_pt(), oomph::TetMeshFacetedSurface::geom_object_with_boundaries_pt(), oomph::Node::get_coordinates_on_boundary(), i, oomph::Mesh::nboundary(), oomph::Mesh::nboundary_node(), oomph::Mesh::nelement(), oomph::TetMeshFacetedSurface::nfacet(), oomph::FiniteElement::nnode(), oomph::Mesh::nnode(), oomph::FiniteElement::nnode_1d(), oomph::FiniteElement::node_pt(), oomph::Mesh::node_pt(), oomph::TimeStepper::nprev_values(), oomph::TetMeshFacet::nvertex(), oomph::TetMeshFacetedSurface::one_based_facet_boundary_id(), oomph::oomph_info, oomph::FiniteElement::output(), oomph::GeomObject::position(), oomph::Node::position(), oomph::Node::position_time_stepper_pt(), t, Tet_mesh_faceted_surface_pt, Triangular_facet_vertex_boundary_coordinate, oomph::TetMeshFacet::vertex_pt(), oomph::Node::x(), and oomph::TetMeshVertex::zeta_in_geom_object().
Referenced by oomph::GmshTetMesh< ELEMENT >::build_it(), oomph::RefineableTetgenMesh< ELEMENT >::RefineableTetgenMesh(), and oomph::TetgenMesh< ELEMENT >::TetgenMesh().
◆ snap_to_quadratic_surface() [1/2]
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inline |
Snap boundaries specified by the IDs listed in boundary_id to a quadratric surface, specified in the file quadratic_surface_file_name. This is usually used with vmtk-based meshes for which oomph-lib's xda to poly conversion code produces the files "quadratic_fsi_boundary.dat" and "quadratic_outer_solid_boundary.dat" which specify the quadratic FSI boundary (for the fluid and the solid) and the quadratic representation of the outer boundary of the solid. When used with these files, the flag switch_normal should be set to true when calling the function for the outer boundary of the solid.
Definition at line 979 of file tet_mesh.h.
References oomph::DocInfo::disable_doc().
◆ snap_to_quadratic_surface() [2/2]
| void oomph::TetMeshBase::snap_to_quadratic_surface | ( | const Vector< unsigned > & | boundary_id, |
| const std::string & | quadratic_surface_file_name, | ||
| const bool & | switch_normal, | ||
| DocInfo & | doc_info | ||
| ) |
Snap boundaries specified by the IDs listed in boundary_id to a quadratric surface, specified in the file quadratic_surface_file_name. This is usually used with vmtk-based meshes for which oomph-lib's xda to poly conversion code produces the files "quadratic_fsi_boundary.dat" and "quadratic_outer_solid_boundary.dat" which specify the quadratic FSI boundary (for the fluid and the solid) and the quadratic representation of the outer boundary of the solid. When used with these files, the flag switch_normal should be set to true when calling the function for the outer boundary of the solid. The DocInfo object can be used to label optional output files. (Uses directory and label).
Definition at line 1459 of file tet_mesh.h.
References oomph::Mesh::boundary_element_pt(), oomph::DocInfo::directory(), e, oomph::Node::get_coordinates_on_boundary(), i, oomph::DocInfo::is_doc_enabled(), oomph::Node::is_on_boundary(), oomph::DocInfo::label(), oomph::Mesh::nboundary_element(), oomph::FiniteElement::nnode(), oomph::FiniteElement::node_pt(), oomph::GeomObject::position(), s, oomph::Node::set_coordinates_on_boundary(), oomph::Global_string_for_annotation::string(), Tolerance_for_boundary_finding, and oomph::Node::x().
◆ split_elements_in_corners()
| void oomph::TetMeshBase::split_elements_in_corners | ( | TimeStepper * | time_stepper_pt = &Mesh::Default_TimeStepper | ) |
Non-Delaunay split elements that have three faces on a boundary into sons. Timestepper species timestepper for new nodes; defaults to to steady timestepper.
Non-delaunay split elements that have three faces on a boundary into sons.
Definition at line 1950 of file tet_mesh.h.
References oomph::Mesh::add_node_pt(), oomph::Mesh::boundary_element_pt(), Boundary_region_element_pt, oomph::FiniteElement::construct_boundary_node(), oomph::FiniteElement::construct_node(), e, oomph::Mesh::Element_pt, oomph::Mesh::face_index_at_boundary(), Face_index_region_at_boundary, oomph::Mesh::finite_element_pt(), i, oomph::Mesh::Lookup_for_elements_next_boundary_is_setup, oomph::Mesh::nboundary(), oomph::Mesh::nboundary_element(), oomph::Mesh::nelement(), oomph::FiniteElement::nnode(), oomph::Mesh::nnode(), oomph::FiniteElement::nnode_1d(), oomph::FiniteElement::node_pt(), oomph::oomph_info, Region_attribute, Region_element_pt, setup_boundary_element_info(), and oomph::Node::x().
Member Data Documentation
◆ Boundary_region_element_pt
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protected |
Storage for elements adjacent to a boundary in a particular region.
Definition at line 1031 of file tet_mesh.h.
Referenced by boundary_element_in_region_pt(), oomph::GmshTetMesh< ELEMENT >::build_from_scaffold(), nboundary_element_in_region(), and split_elements_in_corners().
◆ Face_index_region_at_boundary
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protected |
Storage for the face index adjacent to a boundary in a particular region.
Definition at line 1035 of file tet_mesh.h.
Referenced by oomph::GmshTetMesh< ELEMENT >::build_from_scaffold(), face_index_at_boundary_in_region(), and split_elements_in_corners().
◆ Internal_surface_pt
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protected |
Vector to faceted surfaces that define internal boundaries.
Definition at line 1041 of file tet_mesh.h.
Referenced by oomph::GmshTetMesh< ELEMENT >::build_it(), oomph::RefineableTetgenMesh< ELEMENT >::RefineableTetgenMesh(), and oomph::TetgenMesh< ELEMENT >::TetgenMesh().
◆ Outer_boundary_pt
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protected |
Faceted surface that defines outer boundaries.
Definition at line 1038 of file tet_mesh.h.
Referenced by oomph::GmshTetMesh< ELEMENT >::build_it(), oomph::RefineableTetgenMesh< ELEMENT >::RefineableTetgenMesh(), and oomph::TetgenMesh< ELEMENT >::TetgenMesh().
◆ Region_attribute
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protected |
Vector of attributes associated with the elements in each region NOTE: double is enforced on us by tetgen. We use it as an unsigned to indicate the actual (zero-based) region ID.
Definition at line 1027 of file tet_mesh.h.
Referenced by oomph::GmshTetMesh< ELEMENT >::build_from_scaffold(), oomph::GmshTetScaffoldMesh::create_mesh_from_msh_file(), nregion_element(), region_attribute(), region_element_pt(), and split_elements_in_corners().
◆ Region_element_pt
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protected |
Vectors of vectors of elements in each region (note: this just stores them; the region IDs are contained in Region_attribute!)
Definition at line 1022 of file tet_mesh.h.
Referenced by oomph::GmshTetMesh< ELEMENT >::build_from_scaffold(), oomph::GmshTetScaffoldMesh::create_mesh_from_msh_file(), nregion(), nregion_element(), region_element_pt(), and split_elements_in_corners().
◆ Tet_mesh_facet_pt
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protected |
Reverse lookup scheme: Pointer to facet (if any!) associated with boundary b.
Definition at line 1049 of file tet_mesh.h.
Referenced by oomph::GmshTetMesh< ELEMENT >::build_it(), and setup_boundary_coordinates().
◆ Tet_mesh_faceted_surface_pt
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protected |
Reverse lookup scheme: Pointer to faceted surface (if any!) associated with boundary b.
Definition at line 1045 of file tet_mesh.h.
Referenced by oomph::GmshTetMesh< ELEMENT >::build_it(), and snap_nodes_onto_geometric_objects().
◆ Time_stepper_pt
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protected |
Timestepper used to build nodes.
Definition at line 1057 of file tet_mesh.h.
Referenced by oomph::GmshTetMesh< ELEMENT >::build_it(), oomph::RefineableTetgenMesh< ELEMENT >::RefineableTetgenMesh(), oomph::TetgenMesh< ELEMENT >::set_mesh_level_time_stepper(), and oomph::TetgenMesh< ELEMENT >::TetgenMesh().
◆ Tolerance_for_boundary_finding
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static |
Global static data that specifies the permitted error in the setup of the boundary coordinates.
Definition at line 677 of file tet_mesh.h.
Referenced by setup_boundary_coordinates(), and snap_to_quadratic_surface().
◆ Triangular_facet_vertex_boundary_coordinate
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protected |
Boundary coordinates of vertices in triangular facets associated with given boundary. Is only set up for triangular facets!
Definition at line 1054 of file tet_mesh.h.
Referenced by setup_boundary_coordinates(), and snap_nodes_onto_geometric_objects().
The documentation for this class was generated from the following files: