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openCARP
Doxygen code documentation for the open cardiac electrophysiology simulator openCARP
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Namespaces | |
| detail | |
Classes | |
| class | dmat |
| Dense matrix class. More... | |
| struct | abstract_linear_solver |
| class | abstract_matrix |
| class | abstract_vector |
| class | scattering |
| Container for a PETSc VecScatter. More... | |
| class | scatter_registry |
| The scatterer registry class. More... | |
| struct | Point |
| Point and vector struct. More... | |
| class | overlapping_layout |
| The overlapping_layout class contains the algorithms related to managing overlapping parallel index sets, such as the indexing of the nodes, faces or edges of a distributed mesh. More... | |
| class | non_overlapping_layout |
| The parallel layout of non overlapping indices. More... | |
| class | index_mapping |
| Index mapping class. This is a bijective mapping. More... | |
| class | meshdata |
| The mesh storage class. It contains both element and vertex data. More... | |
| class | commgraph |
| The class holds the communication graph for a MPI_Exchange() call. More... | |
| struct | tuple |
| struct | mixed_tuple |
| struct | triple |
| struct | mixed_triple |
| struct | quadruple |
| class | element_view |
| Comfort class. Provides getter functions to access the mesh member variables more comfortably. More... | |
| class | matrix_integrator |
| Abstract matrix integration base class. More... | |
| class | vector_integrator |
| Abstract vector integration base class. More... | |
| class | sparse_multiply_transpose |
| Functor for the sparse matrix multiply-transpose operation. More... | |
| class | numbering |
| The abstract numbering class. More... | |
| class | submesh_numbering |
| Functor class applying a submesh renumbering. More... | |
| class | petsc_numbering |
| Functor class generating a numbering optimized for PETSc. More... | |
| class | parallel_layout |
| The base class for parallel layouts. More... | |
| class | abstract_partitioner |
| Abstract base class for a mesh partitioner. More... | |
| class | kdtree_partitioner |
| class | vector |
| A vector storing arbitrary data. More... | |
Enumerations | |
| enum | elem_t { Tetra = 0 , Hexa , Octa , Pyramid , Prism , Quad , Tri , Line } |
| element type enum More... | |
| enum | SF_nbr { NBR_REF , NBR_SUBMESH , NBR_PETSC , NBR_ELEM_REF , NBR_ELEM_SUBMESH } |
| Enumeration encoding the different supported numberings. More... | |
Functions | |
| template<class S > | |
| dmat< S > | operator* (const dmat< S > &a, const dmat< S > &b) |
| template<class S > | |
| S * | operator* (const dmat< S > &a, const S *v) |
| template<class S > | |
| dmat< S > | operator* (const dmat< S > &a, const S v) |
| template<class S > | |
| dmat< S > | operator* (const S v, const dmat< S > &a) |
| template<class S > | |
| dmat< S > | operator/ (const dmat< S > &a, const S v) |
| template<class S > | |
| dmat< S > | operator+ (const dmat< S > &a, const dmat< S > &b) |
| template<class S > | |
| dmat< S > | operator- (const dmat< S > &a, const dmat< S > &b) |
| template<class S > | |
| dmat< S > | transpose (const dmat< S > &a) |
| template<class S > | |
| double | double_cont (const dmat< S > &A, const dmat< S > &B) |
| mat-mat double contraction A:B More... | |
| template<class S > | |
| void | invert_3x3 (S *ele, S &det) |
| template<class S > | |
| void | invert_3x3 (dmat< S > &m, S &det) |
| template<class S > | |
| dmat< S > | invert_3x3 (const dmat< S > &m) |
| template<class S > | |
| S | det_3x3 (const dmat< S > &m) |
| template<class S > | |
| dmat< S > | invert_2x2 (const dmat< S > &m) |
| template<class S > | |
| void | invert_2x2 (S *ele, S &det) |
| template<class S > | |
| void | invert_2x2 (dmat< S > &m, S &det) |
| template<class S , class V > | |
| void | array_to_tensors (const vector< S > &arr, vector< dmat< V > > &m) |
| template<class S , class V > | |
| void | tensors_to_array (const vector< dmat< S > > &m, vector< V > &arr) |
| template<class T , class S > | |
| bool | is_init (const abstract_vector< T, S > *v) |
| template<typename V , typename W > | |
| V | clamp (const V val, const W start, const W end) |
| Clamp a value into an interval [start, end]. More... | |
| template<class V > | |
| Point | arr_to_point (V *arr) |
| template<class V > | |
| void | point_to_arr (Point &p, V *arr) |
| Point | cross (const Point &a, const Point &b) |
| cross product More... | |
| double | inner_prod (const Point &a, const Point &b) |
| void | outer_prod (const Point &a, const Point &b, const double s, double *buff, const bool add=false) |
| void | outer_prod (const Point &a, const Point &b, double *buff) |
| double | mag (const Point &vect) |
| vector magnitude More... | |
| Point | normalize (const Point &vect) |
| Point | operator- (const Point &a, const Point &b) |
| Point | operator+ (const Point &a, const Point &b) |
| Point | operator* (const Point &a, const double &s) |
| Point | operator* (const double &s, const Point &a) |
| Point | operator* (const dmat< double > &A, const Point &b) |
| Point | project (const Point &a, const Point &b) |
| project b onto a More... | |
| Point | orthogonalize (const Point &a, const Point &b) |
| double | distance (const Point &a, const Point &b) |
| elem_t | getElemTypeID (char *eletype) |
| Generate element type enum from string. More... | |
| template<class S , class POINT > | |
| void | array_to_points (const vector< S > &arr, vector< POINT > &pts) |
| template<class T , class S > | |
| void | nodal_connectivity_graph (const meshdata< T, S > &mesh, vector< T > &n2n_cnt, vector< T > &n2n_con) |
| Compute the node-to-node connectivity. More... | |
| template<class T , class S > | |
| int | max_nodal_edgecount (const meshdata< T, S > &mesh) |
| Compute the maximum number of node-to-node edges for a mesh. More... | |
| template<class T , class S > | |
| void | get_alg_mask (const meshdata< T, S > &mesh, vector< bool > &alg_mask) |
| template<class T > | |
| bool | operator< (const struct tuple< T > &lhs, const struct tuple< T > &rhs) |
| template<class T , class S > | |
| bool | operator< (const struct mixed_tuple< T, S > &lhs, const struct mixed_tuple< T, S > &rhs) |
| template<class T > | |
| bool | operator< (const struct triple< T > &lhs, const struct triple< T > &rhs) |
| template<class T > | |
| bool | operator< (const struct quadruple< T > &lhs, const struct quadruple< T > &rhs) |
| short | num_dof (elem_t type, short order) |
| Get number of d.o.f. for an element type and an Ansatz function order. More... | |
| void | general_integration_points (const elem_t type, const short order, Point *ip, double *w, int &nint) |
| Compute the integration point locations and weights. More... | |
| void | reference_shape (const elem_t type, const Point ip, dmat< double > &rshape) |
| Compute shape function and its derivatives on a reference element. More... | |
| void | jacobian_matrix (const dmat< double > &rshape, const int npts, const Point *pts, double *J) |
| Compute Jacobian matrix from the real element to the reference element. More... | |
| void | invert_jacobian_matrix (const elem_t type, double *J, double &detJ) |
| void | shape_deriv (const double *iJ, const dmat< double > &rshape, const int ndof, dmat< double > &shape) |
| Compute shape derivatives for an element, based on the shape derivatives of the associated reference element. More... | |
| template<typename T , typename V > | |
| void | canonic_indices (const T *nidx, const T *nbr, const T esize, const short dpn, V *cidx) |
| Compute canonical indices from nodal indices and dpn. More... | |
| template<class T , class S > | |
| void | assemble_matrix (abstract_matrix< T, S > &mat, meshdata< mesh_int_t, mesh_real_t > &domain, matrix_integrator< mesh_int_t, mesh_real_t > &integrator) |
| Generalized matrix assembly. More... | |
| template<class T , class S > | |
| void | assemble_lumped_matrix (abstract_matrix< T, S > &mat, meshdata< mesh_int_t, mesh_real_t > &domain, matrix_integrator< mesh_int_t, mesh_real_t > &integrator) |
| template<class T , class S > | |
| void | assemble_vector (abstract_vector< T, S > &vec, meshdata< mesh_int_t, mesh_real_t > &domain, vector_integrator< mesh_int_t, mesh_real_t > &integrator) |
| Generalized vector assembly. More... | |
| template<class T , class S > | |
| void | extract_element_data (const element_view< mesh_int_t, mesh_real_t > &view, abstract_vector< T, S > &vec, SF_real *buffer) |
| template<class T , class S > | |
| void | set_element_data (const element_view< mesh_int_t, mesh_real_t > &view, SF_real *buffer, abstract_vector< T, S > &vec) |
| template<class T , class S > | |
| void | get_transformed_pts (const element_view< T, S > &view, Point *loc_pts, Point &trsf_fibre, bool orthogonal=true) |
| template<typename T > | |
| T | byte_swap (T in) |
| swap the bytes of int, float, doubles, etc.. More... | |
| bool | fileExists (std::string filename) |
| Function which checks if a given file exists. More... | |
| size_t | file_size (FILE *fd) |
| return file size from a file descriptor More... | |
| void | treat_file_open_error (const char *file, const char *caller, const int errnum, const bool do_exit, int rank) |
| treat a file open error by displaying the errnum string interpretation and the caller More... | |
| template<class T > | |
| void | multiply_connectivities (const vector< T > &a_cnt, const vector< T > &a_con, const vector< T > &b_cnt, const vector< T > &b_con, vector< T > &c_cnt, vector< T > &c_con) |
| template<class T > | |
| void | transpose_connectivity (const vector< T > &a_cnt, const vector< T > &a_con, vector< T > &b_cnt, vector< T > &b_con) |
| Transpose CRS matrix graph A into B. More... | |
| size_t | read_num_pts (std::string basename) |
| Function returns the number of points in a CARP points file. More... | |
| void | read_headers (FILE *ele_fd, FILE *fib_fd, bool read_binary, size_t &numelem, int &nFib) |
| Read the header from the element and fiber files. More... | |
| void | write_elem_headers (FILE *&ele_fd, FILE *&fib_fd, bool binary, size_t numelem, int nFib) |
| Write the header of the element and fiber files. More... | |
| void | write_pts_header (FILE *&pts_fd, bool binary, size_t numpts) |
| Write the header of the points file. More... | |
| template<class T , class S > | |
| void | read_elem_block (FILE *&fd, bool read_binary, size_t bstart, size_t bsize, meshdata< T, S > &mesh) |
| Read a block of size bsize from an CARP element file. More... | |
| template<class T , class S > | |
| void | write_elem_block (FILE *fd, bool write_binary, const meshdata< T, S > &mesh) |
| Write the local element block to a file. More... | |
| template<class T , class S > | |
| void | read_fib_block (FILE *&fd, bool read_binary, int nFib, size_t bsize, meshdata< T, S > &mesh) |
| Read a chunk of fibers from a file descriptor. More... | |
| template<class T , class S > | |
| void | write_fib_block (FILE *&fd, bool write_binary, const meshdata< T, S > &mesh) |
| Write the local chunk of fibers to a file. More... | |
| template<class T , class S > | |
| void | read_element_tags (meshdata< T, S > &mesh, std::string filename) |
| Override element tags from an ASCII file (one int per element, global element order). More... | |
| template<class T , class S > | |
| void | read_elements (meshdata< T, S > &mesh, std::string basename, bool require_fibers=true) |
| Read the element data (elements and fibers) of a CARP mesh. More... | |
| template<class T , class S > | |
| void | write_elements (const meshdata< T, S > &mesh, bool binary, std::string basename) |
| Read the element data (elements and fibers) of a CARP mesh. More... | |
| template<class T , class S > | |
| void | write_surface (const meshdata< T, S > &surfmesh, std::string surffile) |
| template<class S > | |
| void | read_pts_block (FILE *&fd, bool read_binary, size_t bsize, vector< S > &xyz) |
| Read a chunk of points from a file descriptor. More... | |
| template<class S > | |
| void | write_pts_block (FILE *&fd, bool write_binary, const vector< S > &xyz) |
| Write a chunk of points to a file. More... | |
| template<class T , class S > | |
| void | read_points (const std::string basename, const MPI_Comm comm, vector< S > &pts, vector< T > &ptsidx) |
| Read the points and insert them into a list of meshes. More... | |
| template<class T , class S > | |
| void | insert_points (const vector< S > &pts, const vector< T > &ptsidx, std::list< meshdata< T, S > * > &meshlist) |
| Insert the points from the read-in buffers into a list of distributed meshes. More... | |
| template<class T , class S > | |
| void | writeVTKmesh_binary (const meshdata< T, S > &mesh, std::string file) |
| Write a mesh in binary vtk format. More... | |
| template<class T , class S > | |
| void | permute_mesh (const meshdata< T, S > &inmesh, meshdata< T, S > &outmesh, const vector< T > &perm) |
| Permute the element data of a mesh based on a given permutation. More... | |
| template<class T , class S > | |
| void | redistribute_elements (meshdata< T, S > &mesh, meshdata< T, S > &sendbuff, vector< T > &part) |
| Redistribute the element data of a parallel mesh among the ranks based on a partitioning. More... | |
| template<class T , class S > | |
| void | redistribute_elements (meshdata< T, S > &mesh, vector< T > &part) |
| Redistribute the element data of a parallel mesh among the ranks based on a partitioning. More... | |
| template<class T , class S > | |
| void | redistribute_mesh (meshdata< T, S > &mesh, vector< T > &part) |
| Redistribute both element and vertex data of a mesh. More... | |
| template<class T , class S > | |
| void | write_mesh_parallel (const meshdata< T, S > &mesh, bool binary, std::string basename) |
| Write a parallel mesh to harddisk without gathering it on one rank. More... | |
| template<class T , class S > | |
| void | gather_mesh (const meshdata< T, S > &locmesh, meshdata< T, S > &globmesh) |
| Gather a mesh on rank 0. More... | |
| template<class T , class S > | |
| void | print_DD_info (const meshdata< T, S > &mesh) |
| Print some basic information on the domain decomposition of a mesh. More... | |
| template<class T , class S > | |
| void | extract_mesh (const vector< bool > &keep, const meshdata< T, S > &mesh, meshdata< T, S > &submesh) |
| Extract a submesh from a given mesh. More... | |
| template<class T , class S > | |
| void | rebalance_mesh (meshdata< T, S > &mesh) |
| Rebalance the parallel distribution of a mesh, if a local size is 0. More... | |
| template<class T , class S > | |
| void | extract_myocardium (const meshdata< T, S > &mesh, meshdata< T, S > &submesh, bool require_fibers=true) |
| Extract the myocardium submesh. More... | |
| template<class T , class S > | |
| void | extract_tagbased (const meshdata< T, S > &mesh, meshdata< T, S > &submesh) |
| Extract a submesh based on element tags. More... | |
| template<class T , class S > | |
| void | print_mesh_graph (meshdata< T, S > &mesh) |
| One-by-one each process prints the graph of a given mesh. More... | |
| template<class T , class S > | |
| void | inter_domain_mapping (const meshdata< T, S > &mesh_a, const meshdata< T, S > &mesh_b, const SF_nbr snbr, index_mapping< T > &a_to_b) |
| Submesh index mapping between different domains/meshes. More... | |
| template<class T > | |
| void | insert_surf_tri (T n1, T n2, T n3, size_t eidx, triple< T > &surf, tri_sele< T > &sele, hashmap::unordered_map< triple< T >, tri_sele< T > > &surfmap) |
| template<class T > | |
| void | insert_surf_quad (T n1, T n2, T n3, T n4, size_t eidx, vector< T > &buff, quadruple< T > &surf, quad_sele< T > &sele, hashmap::unordered_map< quadruple< T >, quad_sele< T > > &surfmap) |
| template<class T > | |
| void | insert_surf_tet (const T *nod, const size_t eidx, hashmap::unordered_map< triple< T >, tri_sele< T > > &surfmap) |
| template<class T > | |
| void | insert_surf_pyr (const T *nod, const size_t eidx, vector< T > &buff, hashmap::unordered_map< triple< T >, tri_sele< T > > &surfmap, hashmap::unordered_map< quadruple< T >, quad_sele< T > > &qsurfmap) |
| template<class T > | |
| void | insert_surf_pri (const T *nod, const size_t eidx, vector< T > &buff, hashmap::unordered_map< triple< T >, tri_sele< T > > &surfmap, hashmap::unordered_map< quadruple< T >, quad_sele< T > > &qsurfmap) |
| template<class T > | |
| void | insert_surf_hex (const T *nod, const size_t eidx, vector< T > &buff, hashmap::unordered_map< quadruple< T >, quad_sele< T > > &surfmap) |
| template<class T , class S > | |
| void | search_for_surface (const meshdata< T, S > &mesh, const SF_nbr numbering, const hashmap::unordered_map< triple< T >, tri_sele< T > > &search_tri, const hashmap::unordered_map< quadruple< T >, quad_sele< T > > &search_quad, hashmap::unordered_map< triple< T >, tri_sele< T > > &found_tri, hashmap::unordered_map< quadruple< T >, quad_sele< T > > &found_quad) |
| template<class T , class S > | |
| void | compute_surface (const meshdata< T, S > &mesh, const SF_nbr numbering, const hashmap::unordered_set< T > &tags, hashmap::unordered_map< triple< T >, tri_sele< T > > &tri_surf, hashmap::unordered_map< quadruple< T >, quad_sele< T > > &quad_surf) |
| template<class T , class S > | |
| void | compute_surface (const meshdata< T, S > &mesh, const SF_nbr numbering, hashmap::unordered_map< triple< T >, tri_sele< T > > &tri_surf, hashmap::unordered_map< quadruple< T >, quad_sele< T > > &quad_surf) |
| template<class V > | |
| void | get_hashmap_duplicates (const vector< V > &data, const MPI_Comm comm, vector< bool > &is_dup) |
| template<class K , class V > | |
| void | remove_duplicates (hashmap::unordered_map< K, V > &map, const MPI_Comm comm) |
| remove parallel duplicates from a hashmap::unordered_map More... | |
| template<class K > | |
| void | remove_duplicates (hashmap::unordered_set< K > &set, const MPI_Comm comm) |
| remove parallel duplicates from a hashmap::unordered_set More... | |
| template<class T > | |
| void | remove_parallel_duplicates (hashmap::unordered_map< triple< T >, tri_sele< T >> &tri_surf, hashmap::unordered_map< quadruple< T >, quad_sele< T > > &quad_surf, MPI_Comm comm) |
| template<class T , class S > | |
| void | convert_surface_mesh (hashmap::unordered_map< triple< T >, tri_sele< T >> &tri_surf, hashmap::unordered_map< quadruple< T >, quad_sele< T > > &quad_surf, meshdata< T, S > &surfmesh, vector< T > &elem_orig) |
| template<class T , class S > | |
| void | convert_mesh_surface (const meshdata< T, S > &surfmesh, hashmap::unordered_map< triple< T >, tri_sele< T >> &tri_surf, hashmap::unordered_map< quadruple< T >, quad_sele< T >> &quad_surf) |
| template<class T , class S > | |
| void | compute_surface_mesh (const meshdata< T, S > &mesh, const SF_nbr numbering, const hashmap::unordered_set< T > &tags, meshdata< T, S > &surfmesh) |
| Compute the surface of a given mesh. More... | |
| template<class T , class S > | |
| void | compute_surface_mesh (const meshdata< T, S > &mesh, const SF_nbr numbering, meshdata< T, S > &surfmesh) |
| Compute the surface of a given mesh. More... | |
| template<class T , class S > | |
| void | read_surface_mesh (const meshdata< T, S > &mesh, meshdata< T, S > &surface, std::string filename) |
| template<class T > | |
| void | restrict_to_set (vector< T > &v, const hashmap::unordered_set< T > &set) |
| template<class T > | |
| void | restrict_to_set (vector< T > &v, const vector< T > &vset) |
| template<class T , class S > | |
| void | MPI_Exchange (commgraph< T > &grph, vector< S > &send, vector< S > &recv, MPI_Comm comm) |
| Exchange data in parallel over MPI. More... | |
| template<class T > | |
| T | parallel_fallback_value (const vector< T > &vec, MPI_Comm comm) |
| Get a fallback value for operations on parallel vectors if the local vector is of 0 size. More... | |
| template<class T > | |
| T | global_min (const vector< T > &vec, MPI_Comm comm) |
| Compute the global minimum of a distributed vector. More... | |
| template<class T > | |
| T | global_max (const vector< T > &vec, MPI_Comm comm) |
| Compute the global maximum of a distributed vector. More... | |
| template<class T > | |
| T | global_max (const T val, MPI_Comm comm) |
| Compute the global maximum of a distributed vector. More... | |
| template<class T > | |
| void | layout_from_count (const T count, vector< T > &layout, MPI_Comm comm) |
| template<class T > | |
| T | index_in_layout (const T idx, const vector< T > &layout) |
| template<class T > | |
| void | make_global (const vector< T > &vec, vector< T > &out, MPI_Comm comm) |
| make a parallel vector global More... | |
| template<class T > | |
| void | make_global (vector< T > &vec, MPI_Comm comm) |
| template<class T > | |
| void | reindex_cuthill_mckee (const vector< T > &n2n_cnt, const vector< T > &n2n_dsp, const vector< T > &n2n_con, const bool reverse, hashmap::unordered_map< T, T > &old2new) |
| template<class T > | |
| void | parallel_distribution (const vector< T > >arget, const vector< T > &cnt, const vector< T > &dsp, const vector< T > &ranks, const int myrank, vector< T > &owner, vector< T > &counts) |
| The distribution distributes entities between all ranks. More... | |
| template<class T > | |
| void | refine_distribution (const vector< T > >arget, const vector< T > &cnt, const vector< T > &dsp, const vector< T > &ranks, const int myrank, vector< T > &owner, vector< T > &counts) |
| Further refine a distribution generated by parallel_distribution(). More... | |
| template<class T > | |
| void | parallel_distribution_minrank (const vector< T > >arget, const vector< T > &cnt, const vector< T > &dsp, const vector< T > &ranks, vector< T > &owner, vector< T > &counts) |
| template<class T , class S > | |
| T | local_nodal_to_local_petsc (const meshdata< T, S > &mesh, int rank, T local_nodal) |
| template<class T , class S > | |
| T | local_petsc_to_local_nodal (const meshdata< T, S > &mesh, int rank, T local_petsc) |
| template<class T , class S > | |
| void | local_petsc_to_nodal_mapping (const meshdata< T, S > &mesh, index_mapping< T > &petsc_to_nodal) |
| template<class T > | |
| void | sort_parallel (MPI_Comm comm, const vector< T > &idx, vector< T > &out_idx) |
| Sort index values parallel ascending across the ranks. More... | |
| template<class T , class V > | |
| void | sort_parallel (MPI_Comm comm, const vector< T > &idx, const vector< V > &val, vector< T > &out_idx, vector< V > &out_val) |
| Sort index-value tuples parallel ascending across the ranks. More... | |
| template<class T , class V > | |
| void | sort_parallel (MPI_Comm comm, const vector< T > &idx, const vector< T > &cnt, const vector< V > &val, vector< T > &out_idx, vector< T > &out_cnt, vector< V > &out_val) |
| template<class V > | |
| size_t | root_write (FILE *fd, const vector< V > &vec, MPI_Comm comm) |
| Write vector data binary to disk. More... | |
| template<class V > | |
| size_t | root_write (FILE *fd, V *vec, const size_t vec_size, MPI_Comm comm) |
| root_write wrapper that takes array pointers instead of vectors. More... | |
| template<class V > | |
| size_t | root_read (FILE *fd, vector< V > &vec, MPI_Comm comm) |
| Read binary data into a vector. More... | |
| template<class V > | |
| size_t | root_read_ascii (FILE *fd, vector< V > &vec, MPI_Comm comm, bool int_data) |
| Read binary data into a vector. More... | |
| size_t | root_count_ascii_lines (std::string file, MPI_Comm comm) |
| count the lines in a ascii file More... | |
| template<class V > | |
| size_t | root_read (FILE *fd, V *vec, const size_t vec_size, MPI_Comm comm) |
| root_read wrapper that takes array pointers instead of vectors. More... | |
| template<class V > | |
| size_t | root_read_ascii (FILE *fd, V *vec, const size_t vec_size, MPI_Comm comm, bool int_type) |
| root_read_ascii wrapper that takes array pointers instead of vectors. More... | |
| template<class T , class V > | |
| size_t | root_write_ordered (FILE *fd, const vector< T > &idx, const vector< V > &vec, MPI_Comm comm) |
| Write index value pairs to disk in ordered permutation. More... | |
| template<class T , class V > | |
| size_t | root_write_ordered (FILE *fd, const vector< T > &idx, const vector< T > &cnt, const vector< V > &vec, MPI_Comm comm) |
| Write index value pairs to disk in ordered permutation. More... | |
| template<class T , class V > | |
| size_t | root_write_ordered (FILE *fd, T *idx, V *vec, const size_t vec_size, MPI_Comm comm) |
| root_write_ordered wrapper that takes array pointers instead of vectors. More... | |
| template<class T , class V > | |
| size_t | root_write_ordered (FILE *fd, T *idx, T *cnt, V *vec, const size_t idx_size, const size_t vec_size, MPI_Comm comm) |
| root_write_ordered wrapper that takes array pointers instead of vectors. More... | |
| template<class T > | |
| void | print_vector (MPI_Comm comm, const vector< T > &vec, const short dpn, FILE *fd) |
| template<class T , class S > | |
| void | write_data_ascii (const MPI_Comm comm, const vector< T > &idx, const vector< S > &data, std::string file, short dpn=1) |
| template<class T > | |
| void | _binary_sort (T *_P, T *_Q, T s) |
| template<class T , class S > | |
| void | _binary_sort_copy (T *_P, T *_Q, S *_U, S *_V, T s) |
| template<class T , class S , class R > | |
| void | _binary_sort_copy_copy (T *_P, T *_Q, S *_A, S *_B, R *_U, R *_V, T s) |
| template<class T > | |
| void | _binary_sort_sort (T *_P, T *_Q, T *_A, T *_B, T s, T t) |
| template<class T , class S > | |
| void | _binary_sort_sort_copy (T *_P, T *_Q, T *_A, T *_B, S *_U, S *_V, T s, T t) |
| template<class T > | |
| T | _binary_log (const T *P, const T *Q) |
| template<class T > | |
| void | binary_sort (vector< T > &_V) |
| template<class T , class S > | |
| void | binary_sort_copy (vector< T > &_V, vector< S > &_W) |
| template<class T , class S , class R > | |
| void | binary_sort_copy_copy (vector< T > &_V, vector< S > &_W, vector< R > &_A) |
| template<class T > | |
| void | binary_sort_sort (vector< T > &_V, vector< T > &_W) |
| template<class T , class S > | |
| void | binary_sort_sort_copy (vector< T > &_V, vector< T > &_W, vector< S > &_A) |
| template<class T > | |
| void | unique_resize (vector< T > &_P) |
| template<class T > | |
| void | unique_resize (vector< T > &_P, vector< T > &_U) |
| template<class T , class S > | |
| void | unique_accumulate (vector< T > &_P, vector< S > &_A) |
| template<class T , class S > | |
| void | unique_accumulate (vector< T > &_P, vector< T > &_U, vector< S > &_A) |
| template<class T > | |
| void | global_to_local_sorted (const vector< T > &glob, vector< T > &data, bool sortedData, bool doWarn) |
| template<class T > | |
| void | global_to_local (const vector< T > &glob, vector< T > &data, bool sortedData, bool doWarn) |
| template<class T > | |
| void | global_to_local (const hashmap::unordered_map< T, T > &g2l, vector< T > &data, bool doWarn) |
| template<class T > | |
| void | dsp_from_cnt (const vector< T > &cnt, vector< T > &dsp) |
| Compute displacements from counts. More... | |
| template<class T > | |
| void | cnt_from_dsp (const vector< T > &dsp, vector< T > &cnt) |
| Compute counts from displacements. More... | |
| template<class T , class S > | |
| void | count (const vector< T > &data, vector< S > &cnt) |
| Count number of occurrences of indices. More... | |
| template<class T > | |
| T | sum (const vector< T > &vec) |
| Compute sum of a vector's entries. More... | |
| template<class T > | |
| void | interval (vector< T > &vec, size_t start, size_t end) |
| Create an integer interval between start and end. More... | |
| template<class T > | |
| void | divide (const size_t gsize, const size_t num_parts, vector< T > &loc_sizes) |
| divide gsize into num_parts local parts with even distribution of the remainder More... | |
| template<class S , class V > | |
| void | vec_assign (S *lhs, const V *rhs, size_t size) |
| Assign the values in rhs to lhs. The data-type of rhs is cast to the type of lhs. More... | |
| template<class T > | |
| bool | isEmpty (vector< T > &v) |
| Return whether an vector is empty (all values are 0). More... | |
| template<class T , class S > | |
| void | init_vector (SF::abstract_vector< T, S > **vec) |
| template<class T , class S > | |
| void | init_vector (SF::abstract_vector< T, S > **vec, int igsize, int ilsize, int idpn=1, typename abstract_vector< T, S >::ltype ilayout=abstract_vector< T, S >::unset) |
| template<class T , class S > | |
| void | init_vector (SF::abstract_vector< T, S > **vec, const SF::meshdata< mesh_int_t, mesh_real_t > &mesh, int i, typename SF::abstract_vector< T, S >::ltype ltype) |
| template<class T , class S > | |
| void | init_vector (SF::abstract_vector< T, S > **vec, SF::abstract_vector< T, S > *in) |
| template<class T , class S > | |
| void | init_matrix (SF::abstract_matrix< T, S > **mat) |
| template<class T , class S > | |
| void | init_solver (SF::abstract_linear_solver< T, S > **sol) |
| enum SF::elem_t |
element type enum
| Enumerator | |
|---|---|
| Tetra | |
| Hexa | |
| Octa | |
| Pyramid | |
| Prism | |
| Quad | |
| Tri | |
| Line | |
Definition at line 52 of file SF_container.h.
| enum SF::SF_nbr |
Enumeration encoding the different supported numberings.
Definition at line 200 of file SF_container.h.
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Definition at line 72 of file SF_container.h.
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Definition at line 192 of file SF_container.h.
| void SF::array_to_tensors | ( | const vector< S > & | arr, |
| vector< dmat< V > > & | m | ||
| ) |
Definition at line 547 of file dense_mat.hpp.
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Generalized matrix assembly.
All the assembly details – both the computation as well as the parameters handling – are encapsulated in the used integrator.
| mat | matrix to add values into |
| domain | The domain we compute the integral on |
| integrator | The integral computation functor |
Definition at line 1010 of file SF_fem_utils.h.
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Generalized vector assembly.
All the assembly details – both the computation as well as the parameters handling – are encapsulated in the used integrator.
| vec | vector to add values into |
| domain | The domain we compute the integral on |
| integrator | The integral computation functor |
| prg | Progress display class |
Definition at line 1119 of file SF_fem_utils.h.
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The binary_sort_copy procedure partially sorts pairs in place in ascending order only looking at the first argument.
| _V | Input: Vector of nonnegative integers to sort, first argument. Output: Partially sorted vector in ascending order, first argument. |
| _W | Input: Vector of arbitrary type to sort, second argument. Output: Partially sorted vector in ascending order, second argument. |
Definition at line 296 of file SF_sort.h.
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The binary_sort_copy_copy procedure partially sorts triples in place in ascending order only looking at the first argument.
| _V | Input: Vector of nonnegative integers to sort, first argument. Output: Partially sorted vector in ascending order, first argument. |
| _W | Input: Vector of arbitrary type to sort, second argument. Output: Partially sorted vector in ascending order, second argument. |
| _A | Input: Vector of arbitrary type to sort, third argument. Output: Partially sorted vector in ascending order, second argument. |
The binary_sort_sort procedure sorts pairs of nonnegative integers in place in lexicographic order looking at both arguments.
| _V | Input: Vector of nonnegative integers to sort, first argument. Output: Sorted vector in ascending order, first argument. |
| _W | Input: Vector of nonnegative integers to sort, second argument. Output: Sorted vector in ascending order, second argument. |
Definition at line 321 of file SF_sort.h.
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The binary_sort_sort_copy procedure partially sorts triples in place in lexicographic order only looking at the first and second argument.
| _V | Input: Vector of nonnegative integers to sort, first argument. Output: Partially sorted vector in ascending order, first argument. |
| _W | Input: Vector of nonnegative integers to sort, second argument. Output: Partially sorted vector in ascending order, second argument. |
| _A | Input: Vector of arbitrary type to sort, third argument. Output: Partially sorted vector in ascending order, third argument. |
| T SF::byte_swap | ( | T | in | ) |
swap the bytes of int, float, doubles, etc..
Definition at line 22 of file SF_io_base.h.
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Compute canonical indices from nodal indices and dpn.
| nidx | Nodal indices in local indexing. |
| nbr | Numbering to use. |
| esize | Element size. |
| dpn | Degrees of freedom per node. |
| cidx | Canonical indices. |
Definition at line 988 of file SF_fem_utils.h.
| V SF::clamp | ( | const V | val, |
| const W | start, | ||
| const W | end | ||
| ) |
Compute counts from displacements.
Definition at line 319 of file SF_vector.h.
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Definition at line 1191 of file SF_mesh_utils.h.
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Compute the surface of a given mesh.
| T | Integer type. |
| S | Floating point type. |
| mesh | Input mesh. |
| numbering | Input global numbering. |
| tags | Surface is computed for region defined by these tags. |
| surfmesh | Output surface. |
Definition at line 1397 of file SF_mesh_utils.h.
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Compute the surface of a given mesh.
| T | Integer type. |
| S | Floating point type. |
| mesh | Input mesh. |
| numbering | Input global numbering. |
| surfmesh | Output surface. |
Definition at line 1443 of file SF_mesh_utils.h.
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this is somewhat similar to extract_surface(), but we dont try to be smart and just assume the surface con is already in correct indexing and we have a surface mesh and we dont care about the element indices. Maybe we can use compute_surface() but I dont have time to make it work nicely .. Aurel, 20.06.2023
Definition at line 1365 of file SF_mesh_utils.h.
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Count number of occurrences of indices.
| data | Vector of index data. |
| cnt | cnt[i] is the number of occurrences of index i. |
Definition at line 332 of file SF_vector.h.
cross product
Definition at line 84 of file SF_container.h.
| S SF::det_3x3 | ( | const dmat< S > & | m | ) |
Definition at line 497 of file dense_mat.hpp.
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divide gsize into num_parts local parts with even distribution of the remainder
Definition at line 358 of file SF_vector.h.
mat-mat double contraction A:B
Definition at line 438 of file dense_mat.hpp.
Compute displacements from counts.
Definition at line 310 of file SF_vector.h.
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Definition at line 1160 of file SF_fem_utils.h.
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Extract a submesh from a given mesh.
| [in] | keep | keep[i] tell whether element i is extracted into the submesh. |
| [in] | mesh | The mesh to extract from. |
| [out] | submesh | The submesh extracted into. |
Definition at line 538 of file SF_mesh_utils.h.
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Extract the myocardium submesh.
The myocardium is currently identified by empty fiber definitions.
| [in] | mesh | The mesh to extract from. |
| [out] | submesh | The submesh extracted into. |
Definition at line 665 of file SF_mesh_utils.h.
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Extract a submesh based on element tags.
Note: The tag set the extraction is based on is expected to be in the submesh!
| [in] | mesh | The mesh. |
| [out] | submesh | The extracted submesh. |
Definition at line 711 of file SF_mesh_utils.h.
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return file size from a file descriptor
Definition at line 72 of file SF_io_base.h.
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Function which checks if a given file exists.
| [in] | filename | Name of the file. |
Definition at line 66 of file SF_io_base.h.
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Gather a mesh on rank 0.
| [in] | locmesh | The local mesh. |
| [out] | globmesh | The gathered global mesh. |
Definition at line 470 of file SF_mesh_utils.h.
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Compute the integration point locations and weights.
| type | Element type. |
| order | Integration order. |
| ip | Integration point locations. |
| w | Integration weights. |
| nint | Number of integration points. |
Definition at line 121 of file SF_fem_utils.h.
| void SF::get_alg_mask | ( | const meshdata< T, S > & | mesh, |
| vector< bool > & | alg_mask | ||
| ) |
Definition at line 623 of file SF_container.h.
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Generate element type enum from string.
Definition at line 167 of file SF_container.h.
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Compute the global maximum of a distributed vector.
| [in] | vec | |
| [in] | comm |
Definition at line 186 of file SF_network.h.
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Compute the global maximum of a distributed vector.
| [in] | vec | |
| [in] | comm |
Definition at line 156 of file SF_network.h.
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Compute the global minimum of a distributed vector.
| [in] | vec | |
| [in] | comm |
Definition at line 126 of file SF_network.h.
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Map data, which consists of indices defined by glob, with glob.size() == N, to the range [0, ..., N-1]. glob can be unsorted.
| glob | The global index set. |
| data | The data to map. |
| sortedData | Whether the data is sorted or not. |
| doWarn | Whether to issue a warning if an index cannot be mapped. |
Definition at line 540 of file SF_sort.h.
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Map data, which consists of indices in the range [glob[0], ..., glob[N-1]] to the range [0, ..., N-1]. glob needs to be sorted in ascending order.
| glob | The global index set. |
| data | The data to map. |
| sortedData | Whether the data is sorted or not. |
| doWarn | Whether to issue a warning if an index cannot be mapped. |
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Definition at line 212 of file SF_network.h.
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Initialize a default SF::abstract_matrix based on the param_globals::flavor setting.
| mat | The matrix to initialize |
| T | Integer type (indices). |
| S | Floating point type (values). |
| std::error | if the user requests an uncompiled flavor |
Definition at line 199 of file SF_init.h.
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Initialize a default SF::abstract_linear_solver based on the param_globals::flavor setting.
| sol | The solver to initialize |
| T | Integer type (indices). |
| S | Floating point type (values). |
| std::error | if the user requests an uncompiled flavor |
Definition at line 220 of file SF_init.h.
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Initialize a default SF::abstract_vector based on the param_globals::flavor setting.
| vec | The vector to initialize.j |
| T | Integer type (indices). |
| S | Floating point type (values). |
| std::error | if the user requests an uncompiled flavor |
Definition at line 99 of file SF_init.h.
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Initialize an SF::abstract_vector from a mesh based on the param_globals::flavor setting.
| vec | The vector to initialize |
| mesh | The mesh defining the parallel layout of the vector. |
| i | The number of d.o.f. per mesh vertex. |
| ltype | The vector layout. |
| T | Integer type (indices). |
| S | Floating point type (values). |
| std::error | if the user requests an uncompiled flavor |
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Initialize an SF::abstract_vector with specified sizes based on the param_globals::flavor setting.
| vec | The vector to initialize |
| igsize | Global size |
| ilsize | Local size |
| idpn | Number of d.o.f. used per mesh node |
| ilayout | Vector layout w.r.t. used mesh. |
| T | Integer type (indices). |
| S | Floating point type (values). |
| std::error | if the user requests an uncompiled flavor |
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Initialize an SF::abstract_vector from another vector based on the param_globals::flavor setting.
| vec | The vector to initialize |
| in | The vector to initialize from |
| T | Integer type (indices). |
| S | Floating point type (values). |
| std::error | if the user requests an uncompiled flavor |
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Insert the points from the read-in buffers into a list of distributed meshes.
| meshlist | A list of meshes. | |
| [in] | The | basename of the points file. |
Definition at line 987 of file SF_mesh_io.h.
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Submesh index mapping between different domains/meshes.
Since the parallel distribution is not the same for different meshes, we need MPI communication to generate the mapping information.
| T | Integer type. |
| S | Floating point type. |
| [in] | mesh_a | Mesh A. |
| [in] | mesh_b | Mesh B. |
| [in] | snbr | The type of submesh indexing (NBR_SUBMESH or NBR_PETSC). |
| [out] | a_to_b | The index mapping. |
Definition at line 787 of file SF_mesh_utils.h.
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Create an integer interval between start and end.
Definition at line 350 of file SF_vector.h.
| void SF::invert_2x2 | ( | dmat< S > & | m, |
| S & | det | ||
| ) |
Definition at line 537 of file dense_mat.hpp.
| void SF::invert_2x2 | ( | S * | ele, |
| S & | det | ||
| ) |
Definition at line 521 of file dense_mat.hpp.
Definition at line 483 of file dense_mat.hpp.
| void SF::invert_3x3 | ( | dmat< S > & | m, |
| S & | det | ||
| ) |
Definition at line 474 of file dense_mat.hpp.
| void SF::invert_3x3 | ( | S * | ele, |
| S & | det | ||
| ) |
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check is v is initialized. since we have abstract vector pointers in the simulator we need to first check for nullptr, then for v->is_init().
Definition at line 675 of file SF_abstract_vector.h.
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Return whether an vector is empty (all values are 0).
Definition at line 378 of file SF_vector.h.
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Compute Jacobian matrix from the real element to the reference element.
| rshape | Reference element shape derivatives. |
| npts | Number of points. |
| pts | Points array. |
| J | Jacobian matrix. |
Definition at line 610 of file SF_fem_utils.h.
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compute a vector holding the parallel partitioning displacements (i.e. the layout) from a data count input
Definition at line 201 of file SF_network.h.
| T SF::local_nodal_to_local_petsc | ( | const meshdata< T, S > & | mesh, |
| int | rank, | ||
| T | local_nodal | ||
| ) |
A helper function to convert from a local node index in the DD data to the local index of a local PETSc vector chunk. This function expects local_nodal to be in the set mesh.pl.algebraic_nodes().
Definition at line 912 of file SF_parallel_layout.h.
| T SF::local_petsc_to_local_nodal | ( | const meshdata< T, S > & | mesh, |
| int | rank, | ||
| T | local_petsc | ||
| ) |
A helper function to convert from the index in a local PETSc vector chunk to a local node index in the DD data. For many calls use a SF::mapping instead!
Definition at line 925 of file SF_parallel_layout.h.
| void SF::local_petsc_to_nodal_mapping | ( | const meshdata< T, S > & | mesh, |
| index_mapping< T > & | petsc_to_nodal | ||
| ) |
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vector magnitude
Definition at line 111 of file SF_container.h.
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make a parallel vector global
Definition at line 225 of file SF_network.h.
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Definition at line 237 of file SF_network.h.
| int SF::max_nodal_edgecount | ( | const meshdata< T, S > & | mesh | ) |
Compute the maximum number of node-to-node edges for a mesh.
| T | Integer type. |
| S | Floating point type. |
| mesh | The mesh. |
Definition at line 608 of file SF_container.h.
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Exchange data in parallel over MPI.
| [in] | grph | The communications graph. |
| [in] | send | The send buffer. |
| [out] | revc | The receive buffer. |
Definition at line 47 of file SF_network.h.
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Matrix graph (aka connectivity) multiplication function.
We compute the matrix multiplications C := (A * B)'. Only the matrix graphs are exposed to the outside.
| T | Integer type |
| a_cnt | [in] A matrix counts |
| a_con | [in] A matrix column indices |
| b_cnt | [in] B matrix counts |
| b_con | [in] B matrix column indices |
| b_cnt | [out] C matrix counts |
| b_con | [out] C matrix column indices |
Definition at line 159 of file SF_linalg_utils.h.
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Compute the node-to-node connectivity.
| mesh | The mesh. |
| n2n_cnt | Counts of the connectivity matrix rows. |
| n2n_con | Column indices of the connectivity matrix. |
Definition at line 583 of file SF_container.h.
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Get number of d.o.f. for an element type and an Ansatz function order.
| type | Element type. |
| order | Ansatz function order |
Definition at line 58 of file SF_fem_utils.h.
Definition at line 142 of file SF_container.h.
Definition at line 373 of file dense_mat.hpp.
| S* SF::operator* | ( | const dmat< S > & | a, |
| const S * | v | ||
| ) |
Definition at line 381 of file dense_mat.hpp.
Definition at line 389 of file dense_mat.hpp.
Definition at line 137 of file SF_container.h.
Definition at line 132 of file SF_container.h.
Definition at line 397 of file dense_mat.hpp.
Definition at line 413 of file dense_mat.hpp.
Definition at line 127 of file SF_container.h.
Definition at line 421 of file dense_mat.hpp.
Definition at line 122 of file SF_container.h.
Definition at line 405 of file dense_mat.hpp.
| bool SF::operator< | ( | const struct mixed_tuple< T, S > & | lhs, |
| const struct mixed_tuple< T, S > & | rhs | ||
| ) |
Definition at line 781 of file SF_container.h.
| bool SF::operator< | ( | const struct quadruple< T > & | lhs, |
| const struct quadruple< T > & | rhs | ||
| ) |
Definition at line 801 of file SF_container.h.
| bool SF::operator< | ( | const struct triple< T > & | lhs, |
| const struct triple< T > & | rhs | ||
| ) |
Definition at line 790 of file SF_container.h.
| bool SF::operator< | ( | const struct tuple< T > & | lhs, |
| const struct tuple< T > & | rhs | ||
| ) |
Definition at line 773 of file SF_container.h.
Definition at line 155 of file SF_container.h.
Definition at line 105 of file SF_container.h.
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The distribution distributes entities between all ranks.
The graph (cnt, dsp, ranks) holds the redistribution candidates. For each entity index i, cnt[i] is the number of ranks that i can be assigned to and the rank indices are ranks[dsp[i]] to ranks[dsp[i+1]].
| [in] | gtarget | Global number of entities that need to be assigned to each rank. |
| [in] | cnt | Counts w.r.t. the ranks vector. |
| [in] | dsp | Displacements w.r.t. the ranks vector. |
| [in] | ranks | The ranks which can be assigned to each individual entity. |
| [in] | myrank | The rank of the calling process. |
| [out] | owner | The process index of the owner of each entity. |
| [out] | counts | The number of entities that has been assigned to each process. |
Definition at line 57 of file SF_parallel_layout.h.
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Definition at line 201 of file SF_parallel_layout.h.
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Get a fallback value for operations on parallel vectors if the local vector is of 0 size.
The fallback value is the first value of the first rank with a nonzero local size.
| T | Vector data type |
| vec | the vector. |
| comm | MPI communicator used. |
Definition at line 92 of file SF_network.h.
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Permute the element data of a mesh based on a given permutation.
| [in] | inmesh | The input mesh. |
| [out] | outmesh | The output mesh. |
| [in] | perm | The permutation as in: outmesh[i] = inmesh[perm[i]] |
Definition at line 56 of file SF_mesh_utils.h.
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Definition at line 78 of file SF_container.h.
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Print some basic information on the domain decomposition of a mesh.
Definition at line 487 of file SF_mesh_utils.h.
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One-by-one each process prints the graph of a given mesh.
| mesh | The mesh to print the graph of. |
Definition at line 754 of file SF_mesh_utils.h.
| void SF::print_vector | ( | MPI_Comm | comm, |
| const vector< T > & | vec, | ||
| const short | dpn, | ||
| FILE * | fd | ||
| ) |
project b onto a
Definition at line 150 of file SF_container.h.
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Read a block of size bsize from an CARP element file.
| [in] | fd | File descriptor of the element file. |
| [in] | read_binary | Boolean telling if the file is in binary format. |
| [in] | bstart | Starting index of elements. |
| [in] | bsize | Number of elements to read. |
| [out] | mesh | Mesh structure. |
Definition at line 209 of file SF_mesh_io.h.
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Override element tags from an ASCII file (one int per element, global element order).
File format: header line with number of elements, then one tag per line. Must be called after read_elements() so that mesh.g_numelem and mesh.tag are already initialized. Tags are distributed linearly across ranks to match the element distribution. Aborts if the file cannot be opened or if the element count does not match.
| [in,out] | mesh | The mesh whose tag vector is overwritten. |
| [in] | filename | Path to the ASCII tag file. |
Definition at line 520 of file SF_mesh_io.h.
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Read the element data (elements and fibers) of a CARP mesh.
The elements are distributed linearly across the process range.
| [out] | mesh | The mesh. |
| [in] | basename | Base of the element file (without file extension). |
Definition at line 611 of file SF_mesh_io.h.
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Read a chunk of fibers from a file descriptor.
| [in] | fd | The file descriptor. |
| [in] | read_binary | Whether the file is in binary format. |
| [in] | nFib | Number of fiber orientations provided. |
| [in] | bsize | The chunk size to read. |
| [out] | mesh | The mesh. |
Definition at line 395 of file SF_mesh_io.h.
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Read the header from the element and fiber files.
The files can be in either text or binary format.
| [in] | ele_fd | File descriptor of the element file. |
| [in] | fib_fd | File descriptor of the fibers file. |
| [in] | read_binary | Boolean telling if the file is in binary format. |
| [out] | numelem | The number of elements. |
| [out] | nFib | Number of fiber directions used. |
Definition at line 90 of file SF_mesh_io.h.
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Function returns the number of points in a CARP points file.
| [in] | filename | Name of the file. |
Definition at line 55 of file SF_mesh_io.h.
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Read the points and insert them into a list of meshes.
| meshlist | A list of meshes. | |
| [in] | The | basename of the points file. |
Definition at line 917 of file SF_mesh_io.h.
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Read a chunk of points from a file descriptor.
| [in] | fd | The file descriptor. |
| [in] | read_binary | Whether the file is in binary format. |
| [in] | bsize | The chunk size to read. |
| [out] | xyz | The buffer where the coordinates are read. |
Definition at line 853 of file SF_mesh_io.h.
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Definition at line 1451 of file SF_mesh_utils.h.
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Rebalance the parallel distribution of a mesh, if a local size is 0.
| mesh | The mesh to rebalance. |
Definition at line 627 of file SF_mesh_utils.h.
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Redistribute the element data of a parallel mesh among the ranks based on a partitioning.
| [in,out] | mesh | The mesh before and after redistribution. |
| [out] | sendbuff | An auxiliary mesh used for communication. |
| [in] | part | The partitioning. One process rank per element. |
Definition at line 133 of file SF_mesh_utils.h.
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Redistribute the element data of a parallel mesh among the ranks based on a partitioning.
| [in,out] | mesh | The mesh. |
| [in] | part | The partitioning. One process rank per element. |
Definition at line 220 of file SF_mesh_utils.h.
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Redistribute both element and vertex data of a mesh.
Note: This is more expensive than redistribute_elements. Use that function if you can.
| [in,out] | mesh | The mesh. |
| [in] | part | The partitioning. One process rank per element. |
Definition at line 236 of file SF_mesh_utils.h.
Compute shape function and its derivatives on a reference element.
| type | Element type. |
| order | Order of the Ansatz functions. |
| ip | Integration point. |
| rshape | Reference shape and deriv. matrix. |
Definition at line 383 of file SF_fem_utils.h.
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Further refine a distribution generated by parallel_distribution().
| [in] | gtarget | Global number of entities that need to be assigned to each rank. |
| [in] | cnt | Counts w.r.t. the ranks vector. |
| [in] | dsp | Displacements w.r.t. the ranks vector. |
| [in] | ranks | The ranks which can be assigned to each individual entity. |
| [in] | myrank | The rank of the calling process. |
| [out] | owner | The process index of the owner of each entity. |
| [out] | counts | The number of entities that has been assigned to each process. |
Definition at line 139 of file SF_parallel_layout.h.
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remove parallel duplicates from a hashmap::unordered_map
Definition at line 1262 of file SF_mesh_utils.h.
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remove parallel duplicates from a hashmap::unordered_set
Definition at line 1278 of file SF_mesh_utils.h.
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Definition at line 1581 of file SF_mesh_utils.h.
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count the lines in a ascii file
Definition at line 441 of file SF_parallel_utils.h.
| size_t SF::root_read | ( | FILE * | fd, |
| V * | vec, | ||
| const size_t | vec_size, | ||
| MPI_Comm | comm | ||
| ) |
root_read wrapper that takes array pointers instead of vectors.
Definition at line 479 of file SF_parallel_utils.h.
| size_t SF::root_read | ( | FILE * | fd, |
| vector< V > & | vec, | ||
| MPI_Comm | comm | ||
| ) |
Read binary data into a vector.
Only rank 0 reads, communicates in chunks.
| V | Value type. |
| fd | File descriptor to use for reading. |
| vec | The data vector to read into. Must be already of correct size. |
| comm | MPI communicator to use. |
Definition at line 324 of file SF_parallel_utils.h.
| size_t SF::root_read_ascii | ( | FILE * | fd, |
| V * | vec, | ||
| const size_t | vec_size, | ||
| MPI_Comm | comm, | ||
| bool | int_type | ||
| ) |
root_read_ascii wrapper that takes array pointers instead of vectors.
Definition at line 495 of file SF_parallel_utils.h.
| size_t SF::root_read_ascii | ( | FILE * | fd, |
| vector< V > & | vec, | ||
| MPI_Comm | comm, | ||
| bool | int_data | ||
| ) |
Read binary data into a vector.
Only rank 0 reads, communicates in chunks.
| V | Value type. |
| fd | File descriptor to use for reading. |
| vec | The data vector to read into. Must be already of correct size. |
| comm | MPI communicator to use. |
| int_data | Whether to interpret read data as integer or float type. |
Definition at line 377 of file SF_parallel_utils.h.
| size_t SF::root_write | ( | FILE * | fd, |
| const vector< V > & | vec, | ||
| MPI_Comm | comm | ||
| ) |
Write vector data binary to disk.
Only rank 0 writes, rest communicates in chunks.
| V | Value type. |
| fd | File descriptor to use for writing. |
| vec | The data vector to write. |
| comm | MPI communicator to use. |
Definition at line 252 of file SF_parallel_utils.h.
| size_t SF::root_write | ( | FILE * | fd, |
| V * | vec, | ||
| const size_t | vec_size, | ||
| MPI_Comm | comm | ||
| ) |
root_write wrapper that takes array pointers instead of vectors.
Definition at line 298 of file SF_parallel_utils.h.
| size_t SF::root_write_ordered | ( | FILE * | fd, |
| const vector< T > & | idx, | ||
| const vector< T > & | cnt, | ||
| const vector< V > & | vec, | ||
| MPI_Comm | comm | ||
| ) |
Write index value pairs to disk in ordered permutation.
This function usese sort_parallel before writing with root write.
| T | Integer type. |
| V | Value type. |
| fd | File descriptor to use for writing. |
| idx | The indices of each logical unit |
| cnt | The number of vector entries associated to each logical unit |
| vec | The data vector holding the logical units |
| comm | MPI communicator to use. |
Definition at line 549 of file SF_parallel_utils.h.
| size_t SF::root_write_ordered | ( | FILE * | fd, |
| const vector< T > & | idx, | ||
| const vector< V > & | vec, | ||
| MPI_Comm | comm | ||
| ) |
Write index value pairs to disk in ordered permutation.
This function usese sort_parallel before writing with root write.
| T | Integer type. |
| V | Value type. |
| fd | File descriptor to use for writing. |
| idx | The indices vector |
| vec | The data vector to write. |
| comm | MPI communicator to use. |
Definition at line 523 of file SF_parallel_utils.h.
| size_t SF::root_write_ordered | ( | FILE * | fd, |
| T * | idx, | ||
| T * | cnt, | ||
| V * | vec, | ||
| const size_t | idx_size, | ||
| const size_t | vec_size, | ||
| MPI_Comm | comm | ||
| ) |
root_write_ordered wrapper that takes array pointers instead of vectors.
Definition at line 583 of file SF_parallel_utils.h.
| size_t SF::root_write_ordered | ( | FILE * | fd, |
| T * | idx, | ||
| V * | vec, | ||
| const size_t | vec_size, | ||
| MPI_Comm | comm | ||
| ) |
root_write_ordered wrapper that takes array pointers instead of vectors.
Definition at line 564 of file SF_parallel_utils.h.
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Definition at line 1176 of file SF_fem_utils.h.
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Compute shape derivatives for an element, based on the shape derivatives of the associated reference element.
| iJ | Inverse Jacobian from the reference element to the real element. |
| rshape | Reference shape funciton and derivatives. |
| ndof | Number of d.o.f. |
| shape | Shape derivatives. |
Definition at line 674 of file SF_fem_utils.h.
| void SF::sort_parallel | ( | MPI_Comm | comm, |
| const vector< T > & | idx, | ||
| const vector< T > & | cnt, | ||
| const vector< V > & | val, | ||
| vector< T > & | out_idx, | ||
| vector< T > & | out_cnt, | ||
| vector< V > & | out_val | ||
| ) |
Definition at line 156 of file SF_parallel_utils.h.
| void SF::sort_parallel | ( | MPI_Comm | comm, |
| const vector< T > & | idx, | ||
| const vector< V > & | val, | ||
| vector< T > & | out_idx, | ||
| vector< V > & | out_val | ||
| ) |
Sort index-value tuples parallel ascending across the ranks.
| T | Integer type. |
| V | Value type. |
| comm | MPI communicator to use. |
| idx | Indices vector |
| val | Values vector |
| out_idx | Output indices vector |
| out_val | Output values vector |
Definition at line 108 of file SF_parallel_utils.h.
| void SF::sort_parallel | ( | MPI_Comm | comm, |
| const vector< T > & | idx, | ||
| vector< T > & | out_idx | ||
| ) |
Sort index values parallel ascending across the ranks.
| T | Integer type. |
| V | Value type. |
| comm | MPI communicator to use. |
| idx | Indices vector |
| out_idx | Output indices vector |
Definition at line 54 of file SF_parallel_utils.h.
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Compute sum of a vector's entries.
Definition at line 340 of file SF_vector.h.
| void SF::tensors_to_array | ( | const vector< dmat< S > > & | m, |
| vector< V > & | arr | ||
| ) |
Definition at line 557 of file dense_mat.hpp.
Definition at line 429 of file dense_mat.hpp.
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Transpose CRS matrix graph A into B.
| T | Integer type |
| a_cnt | [in] A matrix counts |
| a_con | [in] A matrix column indices |
| b_cnt | [out] B matrix counts |
| b_con | [out] B matrix column indices |
Definition at line 186 of file SF_linalg_utils.h.
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treat a file open error by displaying the errnum string interpretation and the caller
Definition at line 83 of file SF_io_base.h.
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The unique_accumulate procedure calculates a partial set union of pairs only looking at the first argument and accumulates the values of the second argument of partially matching pairs.
| _P | Input: Vector sorted in ascending order, first argument. Output: Vector sorted in ascending order with only unique elements, first argument. |
| _A | Input: Vector to accumulate, second argument. Output: Vector of accumulated values, second argument. |
Definition at line 409 of file SF_sort.h.
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The unique_accumulate procedure calculates a partial set union of triples only looking at the first and second argument and accumulates the values of the third argument of partially matching triples.
| _P | Input: Vector sorted in lexicographic order, first argument. Output: Vector sorted in lexicographic order with only unique elements, first argument. |
| _U | Input: Vector sorted in lexicographic order, second argument. Output: Vector sorted in lexicographic order with only unique elements, second argument. |
| _A | Input: Vector to accumulate, third argument. Output: Vector of accumulated values, third argument. |
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The unique_resize procedure calculates the set union of an in ascending order sorted vector.
| _P | Input: Vector sorted in ascending order. Output: Vector sorted in ascending order with only unique elements. |
Definition at line 348 of file SF_sort.h.
The unique_resize procedure calculates the set union of an in ascending order sorted vector.
| _P | Input: Vector sorted in ascending order. Output: Vector sorted in ascending order with only unique elements. |
| _U | Input: Vector sorted in ascending order. Output: Vector sorted in ascending order with only unique elements. |
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Assign the values in rhs to lhs. The data-type of rhs is cast to the type of lhs.
Definition at line 371 of file SF_vector.h.
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Write the local element block to a file.
| [in] | fd | The file descriptor. |
| [in] | write_binary | Whether to write in binary format. |
| [in] | mesh | The mesh. |
Definition at line 313 of file SF_mesh_io.h.
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Write the header of the element and fiber files.
The files can be in either text or binary format.
| [in] | ele_fd | File descriptor of the element file. |
| [in] | fib_fd | File descriptor of the fibers file. |
| [in] | binary | Whether to write in binary file format. |
| [in] | numelem | The number of elements. |
| [in] | nFib | Number of fiber directions. |
Definition at line 145 of file SF_mesh_io.h.
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Read the element data (elements and fibers) of a CARP mesh.
The elements are distributed linearly across the process range.
| [out] | mesh | The mesh. |
| [in] | basename | Base of the element file (without file extension). |
Definition at line 739 of file SF_mesh_io.h.
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Write the local chunk of fibers to a file.
| [in] | fd | The file descriptor we write to. |
| [in] | write_binary | Whether to write in binary format. |
| [in] | mesh | The mesh we write. |
Definition at line 465 of file SF_mesh_io.h.
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Write a parallel mesh to harddisk without gathering it on one rank.
| T | Integer type. |
| S | Floating point type. |
| [in] | mesh | The mesh to write. |
| [in] | binary | Whether to write in binary format. |
| [in] | basename | The basename of the mesh files. |
Definition at line 348 of file SF_mesh_utils.h.
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Write a chunk of points to a file.
| [in] | fd | The file descriptor we write to. |
| [in] | write_binary | Whether to write in binary format. |
| [in] | xyz | The points coord vector. |
Definition at line 890 of file SF_mesh_io.h.
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Write the header of the points file.
The files can be in either text or binary format.
| [in] | pts_fd | File descriptor of the points file. |
| [in] | binary | Whether to write in binary file format. |
| [in] | numpts | The number of points. |
Definition at line 182 of file SF_mesh_io.h.
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Write a mesh in binary vtk format.
| mesh | The mesh. |
| file | The output file name. |
Definition at line 1063 of file SF_mesh_io.h.
1.9.1