p4est
1.0
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The coarse topological description of the forest. More...
Go to the source code of this file.
Data Structures | |
struct | p8est_connectivity_t |
This structure holds the 3D inter-tree connectivity information. More... | |
struct | p8est_edge_transform_t |
struct | p8est_edge_info_t |
struct | p8est_corner_transform_t |
struct | p8est_corner_info_t |
Defines | |
#define | P8EST_DIM 3 |
The spatial dimension. | |
#define | P8EST_FACES (2 * P8EST_DIM) |
The number of faces of an octant. | |
#define | P8EST_CHILDREN 8 |
The number of children of an octant. | |
#define | P8EST_HALF (P8EST_CHILDREN / 2) |
The number of children/corners touching one face. | |
#define | P8EST_EDGES 12 |
The number of edges around an octant. | |
#define | P8EST_INSUL 27 |
The size of insulation layer. | |
#define | P8EST_FTRANSFORM 9 |
#define | P8EST_STRING "p8est" |
p8est identification string | |
#define | P8EST_ONDISK_FORMAT 0x3000009 |
Enumerations | |
enum | p8est_connect_type_t { P8EST_CONNECT_FACE = 31, P8EST_CONNECT_EDGE = 32, P8EST_CONNECT_CORNER = 33, P8EST_CONNECT_FULL = P8EST_CONNECT_CORNER } |
Characterize a type of adjacency. More... | |
enum | p8est_connectivity_encode_t { P8EST_CONN_ENCODE_NONE = SC_IO_ENCODE_NONE, P8EST_CONN_ENCODE_LAST } |
Typedef for serialization method. More... | |
Functions | |
int | p8est_connect_type_int (p8est_connect_type_t btype) |
Convert the p8est_connect_type_t into a number. | |
const char * | p8est_connect_type_string (p8est_connect_type_t btype) |
Convert the p8est_connect_type_t into a const string. | |
size_t | p8est_connectivity_memory_used (p8est_connectivity_t *conn) |
Calculate memory usage of a connectivity structure. | |
p8est_connectivity_t * | p8est_connectivity_new (p4est_topidx_t num_vertices, p4est_topidx_t num_trees, p4est_topidx_t num_edges, p4est_topidx_t num_ett, p4est_topidx_t num_corners, p4est_topidx_t num_ctt) |
Allocate a connectivity structure. | |
p8est_connectivity_t * | p8est_connectivity_new_copy (p4est_topidx_t num_vertices, p4est_topidx_t num_trees, p4est_topidx_t num_edges, p4est_topidx_t num_corners, const double *vertices, const p4est_topidx_t *ttv, const p4est_topidx_t *ttt, const int8_t *ttf, const p4est_topidx_t *tte, const p4est_topidx_t *eoff, const p4est_topidx_t *ett, const int8_t *ete, const p4est_topidx_t *ttc, const p4est_topidx_t *coff, const p4est_topidx_t *ctt, const int8_t *ctc) |
Allocate a connectivity structure and populate from constants. | |
void | p8est_connectivity_destroy (p8est_connectivity_t *connectivity) |
Destroy a connectivity structure. | |
void | p8est_connectivity_set_attr (p8est_connectivity_t *conn, int enable_tree_attr) |
Allocate or free the attribute fields in a connectivity. | |
int | p8est_connectivity_is_valid (p8est_connectivity_t *connectivity) |
Examine a connectivity structure. | |
int | p8est_connectivity_is_equal (p8est_connectivity_t *conn1, p8est_connectivity_t *conn2) |
Check two connectivity structures for equality. | |
int | p8est_connectivity_sink (p8est_connectivity_t *conn, sc_io_sink_t *sink) |
Write connectivity to a sink object. | |
sc_array_t * | p8est_connectivity_deflate (p8est_connectivity_t *conn, p8est_connectivity_encode_t code) |
Allocate memory and store the connectivity information there. | |
int | p8est_connectivity_save (const char *filename, p8est_connectivity_t *connectivity) |
Save a connectivity structure to disk. | |
p8est_connectivity_t * | p8est_connectivity_source (sc_io_source_t *source) |
Read connectivity from a source object. | |
p8est_connectivity_t * | p8est_connectivity_inflate (sc_array_t *buffer) |
Create new connectivity from a memory buffer. | |
p8est_connectivity_t * | p8est_connectivity_load (const char *filename, size_t *bytes) |
Load a connectivity structure from disk. | |
p8est_connectivity_t * | p8est_connectivity_new_unitcube (void) |
Create a connectivity structure for the unit cube. | |
p8est_connectivity_t * | p8est_connectivity_new_periodic (void) |
Create a connectivity structure for an all-periodic unit cube. | |
p8est_connectivity_t * | p8est_connectivity_new_rotwrap (void) |
Create a connectivity structure for a mostly periodic unit cube. | |
p8est_connectivity_t * | p8est_connectivity_new_twocubes (void) |
Create a connectivity structure that contains two cubes. | |
p8est_connectivity_t * | p8est_connectivity_new_twowrap (void) |
Create a connectivity structure that contains two cubes where the two far ends are identified periodically. | |
p8est_connectivity_t * | p8est_connectivity_new_rotcubes (void) |
Create a connectivity structure that contains a few cubes. | |
p8est_connectivity_t * | p8est_connectivity_new_brick (int m, int n, int p, int periodic_a, int periodic_b, int periodic_c) |
An m by n by p array with periodicity in x, y, and z if periodic_a, periodic_b, and periodic_c are true, respectively. | |
p8est_connectivity_t * | p8est_connectivity_new_shell (void) |
Create a connectivity structure that builds a spherical shell. | |
p8est_connectivity_t * | p8est_connectivity_new_sphere (void) |
Create a connectivity structure that builds a solid sphere. | |
p8est_connectivity_t * | p8est_connectivity_new_byname (const char *name) |
Create connectivity structure from predefined catalogue. | |
void | p8est_expand_face_transform (int iface, int nface, int ftransform[]) |
Fill an array with the axis combination of a face neighbor transform. | |
p4est_topidx_t | p8est_find_face_transform (p8est_connectivity_t *connectivity, p4est_topidx_t itree, int iface, int ftransform[]) |
Fill an array with the axis combination of a face neighbor transform. | |
void | p8est_find_edge_transform (p8est_connectivity_t *connectivity, p4est_topidx_t itree, int iedge, p8est_edge_info_t *ei) |
Fills an array with information about edge neighbors. | |
void | p8est_find_corner_transform (p8est_connectivity_t *connectivity, p4est_topidx_t itree, int icorner, p8est_corner_info_t *ci) |
Fills an array with information about corner neighbors. | |
void | p8est_connectivity_complete (p8est_connectivity_t *conn) |
Internally connect a connectivity based on tree_to_vertex information. | |
void | p8est_connectivity_permute (p8est_connectivity_t *conn, sc_array_t *perm, int is_current_to_new) |
p8est_connectivity_permute Given a permutation perm of the trees in a connectivity conn, permute the trees of conn in place and update conn to match. | |
void | p8est_connectivity_reorder (MPI_Comm comm, int k, p8est_connectivity_t *conn, p8est_connect_type_t ctype) |
p8est_connectivity_reorder This function takes a connectivity conn and a parameter k, which will typically be the number of processes, and reorders the trees such that if every processes is assigned (num_trees / k) trees, the communication volume will be minimized. | |
void | p8est_connectivity_join_faces (p8est_connectivity_t *conn, p4est_topidx_t tree_left, p4est_topidx_t tree_right, int face_left, int face_right, int orientation) |
p8est_connectivity_join_faces This function takes an existing valid connectivity conn and modifies it by joining two tree faces that are currently boundary faces. | |
int | p8est_connectivity_is_equivalent (p8est_connectivity_t *conn1, p8est_connectivity_t *conn2) |
p8est_connectivity_is_equivalent This function compares two connectivities for equivalence: it returns true if they are the same connectivity, or if they have the same topology. | |
static p8est_edge_transform_t * | p8est_edge_array_index (sc_array_t *array, size_t it) |
Return a pointer to a p8est_edge_transform_t array element. | |
static p8est_corner_transform_t * | p8est_corner_array_index (sc_array_t *array, size_t it) |
Return a pointer to a p8est_corner_transform_t array element. | |
int | p8est_connectivity_read_inp_stream (FILE *stream, p4est_topidx_t *num_vertices, p4est_topidx_t *num_trees, double *vertices, p4est_topidx_t *tree_to_vertex) |
p8est_connectivity_t * | p8est_connectivity_read_inp (const char *filename) |
Variables | |
const int | p8est_face_corners [6][4] |
Store the corner numbers 0..7 for each tree face. | |
const int | p8est_face_edges [6][4] |
Store the face numbers 0..12 for each tree face. | |
const int | p8est_face_dual [6] |
Store the face numbers in the face neighbor's system. | |
const int | p8est_face_permutations [8][4] |
Store only the 8 out of 24 possible permutations that occur. | |
const int | p8est_face_permutation_sets [3][4] |
Store the 3 occurring sets of 4 permutations per face. | |
const int | p8est_face_permutation_refs [6][6] |
For each face combination store the permutation set. | |
const int | p8est_edge_faces [12][2] |
Store the face numbers 0..5 for each tree edge. | |
const int | p8est_edge_corners [12][2] |
Store the corner numbers 0..8 for each tree edge. | |
const int | p8est_edge_face_corners [12][6][2] |
Store the face corner numbers for the faces touching a tree edge. | |
const int | p8est_corner_faces [8][3] |
Store the face numbers 0..5 for each tree corner. | |
const int | p8est_corner_edges [8][3] |
Store the edge numbers 0..11 for each tree corner. | |
const int | p8est_corner_face_corners [8][6] |
Store the face corner numbers for the faces touching a tree corner. | |
const int | p8est_child_edge_faces [8][12] |
Store the faces for each child and edge, can be -1. | |
const int | p8est_child_corner_faces [8][8] |
Store the faces for each child and corner, can be -1. | |
const int | p8est_child_corner_edges [8][8] |
Store the edges for each child and corner, can be -1. |
The coarse topological description of the forest.
#define P8EST_CHILDREN 8 |
The number of children of an octant.
also the nmber of corners
#define P8EST_FACES (2 * P8EST_DIM) |
The number of faces of an octant.
enum p8est_connect_type_t |
Characterize a type of adjacency.
Several functions involve relationships between neighboring trees and/or quadrants, and their behavior depends on how one defines adjacency: 1) entities are adjacent if they share a face, or 2) entities are adjacent if they share a face or corner, or 3) entities are adjacent if they share a face, corner or edge. p8est_connect_type_t is used to choose the desired behavior. This enum must fit into an int8_t.
int p8est_connect_type_int | ( | p8est_connect_type_t | btype | ) |
Convert the p8est_connect_type_t into a number.
[in] | btype | The balance type to convert. |
const char* p8est_connect_type_string | ( | p8est_connect_type_t | btype | ) |
Convert the p8est_connect_type_t into a const string.
[in] | btype | The balance type to convert. |
void p8est_connectivity_complete | ( | p8est_connectivity_t * | conn | ) |
Internally connect a connectivity based on tree_to_vertex information.
Periodicity that is not inherent in the list of vertices will be lost.
[in,out] | conn | The connectivity needs to have proper vertices and tree_to_vertex fields. The tree_to_tree and tree_to_face fields must be allocated and satisfy p8est_connectivity_is_valid (conn) but will be overwritten. The edge and corner fields will be freed and allocated anew. |
sc_array_t* p8est_connectivity_deflate | ( | p8est_connectivity_t * | conn, |
p8est_connectivity_encode_t | code | ||
) |
Allocate memory and store the connectivity information there.
[in] | conn | The connectivity structure to be exported to memory. |
[in] | code | Encoding and compression method for serialization. |
void p8est_connectivity_destroy | ( | p8est_connectivity_t * | connectivity | ) |
Destroy a connectivity structure.
Also destroy all attributes.
p8est_connectivity_t* p8est_connectivity_inflate | ( | sc_array_t * | buffer | ) |
Create new connectivity from a memory buffer.
[in] | buffer | The connectivity is created from this memory buffer. |
int p8est_connectivity_is_equal | ( | p8est_connectivity_t * | conn1, |
p8est_connectivity_t * | conn2 | ||
) |
Check two connectivity structures for equality.
int p8est_connectivity_is_equivalent | ( | p8est_connectivity_t * | conn1, |
p8est_connectivity_t * | conn2 | ||
) |
p8est_connectivity_is_equivalent This function compares two connectivities for equivalence: it returns true if they are the same connectivity, or if they have the same topology.
The definition of topological sameness is strict: there is no attempt made to determine whether permutation and/or rotation of the trees makes the connectivities equivalent.
[in] | conn1 | a valid connectivity |
[out] | conn2 | a valid connectivity |
int p8est_connectivity_is_valid | ( | p8est_connectivity_t * | connectivity | ) |
Examine a connectivity structure.
void p8est_connectivity_join_faces | ( | p8est_connectivity_t * | conn, |
p4est_topidx_t | tree_left, | ||
p4est_topidx_t | tree_right, | ||
int | face_left, | ||
int | face_right, | ||
int | orientation | ||
) |
p8est_connectivity_join_faces This function takes an existing valid connectivity conn and modifies it by joining two tree faces that are currently boundary faces.
[in,out] | conn | connectivity that will be altered. |
[in] | tree_left | tree that will be on the left side of the joined faces. |
[in] | tree_right | tree that will be on the right side of the joined faces. |
[in] | face_left | face of tree_left that will be joined. |
[in] | face_right | face of tree_right that will be joined. |
[in] | orientation | the orientation of face_left and face_right once joined (see the description of p8est_connectivity_t to understand orientation). |
p8est_connectivity_t* p8est_connectivity_load | ( | const char * | filename, |
size_t * | bytes | ||
) |
Load a connectivity structure from disk.
[in] | filename | Name of the file to read. |
[out] | bytes | Size in bytes of connectivity on disk or NULL. |
size_t p8est_connectivity_memory_used | ( | p8est_connectivity_t * | conn | ) |
Calculate memory usage of a connectivity structure.
[in] | conn | Connectivity structure. |
p8est_connectivity_t* p8est_connectivity_new | ( | p4est_topidx_t | num_vertices, |
p4est_topidx_t | num_trees, | ||
p4est_topidx_t | num_edges, | ||
p4est_topidx_t | num_ett, | ||
p4est_topidx_t | num_corners, | ||
p4est_topidx_t | num_ctt | ||
) |
Allocate a connectivity structure.
The attribute fields are initialized to NULL.
[in] | num_vertices | Number of total vertices (i.e. geometric points). |
[in] | num_trees | Number of trees in the forest. |
[in] | num_edges | Number of tree-connecting edges. |
[in] | num_ett | Number of total trees in edge_to_tree array. |
[in] | num_corners | Number of tree-connecting corners. |
[in] | num_ctt | Number of total trees in corner_to_tree array. |
p8est_connectivity_t* p8est_connectivity_new_byname | ( | const char * | name | ) |
Create connectivity structure from predefined catalogue.
[in] | name | Invokes connectivity_new_* function. brick235 brick (2, 3, 5, 0, 0, 0) periodic periodic rotcubes rotcubes rotwrap rotwrap shell shell sphere sphere twocubes twocubes twowrap twowrap unit unitcube |
p8est_connectivity_t* p8est_connectivity_new_copy | ( | p4est_topidx_t | num_vertices, |
p4est_topidx_t | num_trees, | ||
p4est_topidx_t | num_edges, | ||
p4est_topidx_t | num_corners, | ||
const double * | vertices, | ||
const p4est_topidx_t * | ttv, | ||
const p4est_topidx_t * | ttt, | ||
const int8_t * | ttf, | ||
const p4est_topidx_t * | tte, | ||
const p4est_topidx_t * | eoff, | ||
const p4est_topidx_t * | ett, | ||
const int8_t * | ete, | ||
const p4est_topidx_t * | ttc, | ||
const p4est_topidx_t * | coff, | ||
const p4est_topidx_t * | ctt, | ||
const int8_t * | ctc | ||
) |
Allocate a connectivity structure and populate from constants.
The attribute fields are initialized to NULL.
[in] | num_vertices | Number of total vertices (i.e. geometric points). |
[in] | num_trees | Number of trees in the forest. |
[in] | num_edges | Number of tree-connecting edges. |
[in] | num_corners | Number of tree-connecting corners. |
[in] | eoff | Edge-to-tree offsets (num_edges + 1 values). |
[in] | coff | Corner-to-tree offsets (num_corners + 1 values). |
Create a connectivity structure that contains a few cubes.
These are rotated against each other to stress the topology routines.
Create a connectivity structure for a mostly periodic unit cube.
The left and right faces are identified, and bottom and top rotated. Front and back are not identified.
Create a connectivity structure that builds a spherical shell.
It is made up of six connected parts [-1,1]x[-1,1]x[1,2]. This connectivity reuses vertices and relies on a geometry transformation. It is thus not suitable for p8est_connectivity_complete.
Create a connectivity structure that builds a solid sphere.
It is made up of two layers and a cube in the center. This connectivity reuses vertices and relies on a geometry transformation. It is thus not suitable for p8est_connectivity_complete.
void p8est_connectivity_permute | ( | p8est_connectivity_t * | conn, |
sc_array_t * | perm, | ||
int | is_current_to_new | ||
) |
p8est_connectivity_permute Given a permutation perm of the trees in a connectivity conn, permute the trees of conn in place and update conn to match.
[in,out] | conn | The connectivity whose trees are permuted. |
[in] | perm | A permutation array, whose elements are size_t's. |
[in] | is_current_to_new | if true, the jth entry of perm is the new index for the entry whose current index is j, otherwise the jth entry of perm is the current index of the tree whose index will be j after the permutation. |
void p8est_connectivity_reorder | ( | MPI_Comm | comm, |
int | k, | ||
p8est_connectivity_t * | conn, | ||
p8est_connect_type_t | ctype | ||
) |
p8est_connectivity_reorder This function takes a connectivity conn and a parameter k, which will typically be the number of processes, and reorders the trees such that if every processes is assigned (num_trees / k) trees, the communication volume will be minimized.
This is intended for use with connectivities that contain a large number of trees. This should be done BEFORE a p8est is created using the connectivity. This is done in place: any data structures that use indices to refer to trees before this procedure will be invalid. Note that this routine calls metis and not parmetis because the connectivity is copied on every process. A communicator is required because I'm not positive that metis is deterministic. ctype determines when an edge exist between two trees in the dual graph used by metis in the reordering.
[in] | comm | MPI communicator. |
[in] | k | if k > 0, the number of pieces metis will use to guide the reordering; if k = 0, the number of pieces will be determined from the MPI communicator. |
[in,out] | conn | connectivity that will be reordered. |
[in] | ctype | determines when an edge exists in the dual graph of the connectivity structure. |
int p8est_connectivity_save | ( | const char * | filename, |
p8est_connectivity_t * | connectivity | ||
) |
Save a connectivity structure to disk.
[in] | filename | Name of the file to write. |
[in] | connectivity | Valid connectivity structure. |
void p8est_connectivity_set_attr | ( | p8est_connectivity_t * | conn, |
int | enable_tree_attr | ||
) |
Allocate or free the attribute fields in a connectivity.
[in,out] | conn | The conn->*_to_attr fields must either be NULL or previously be allocated by this function. |
[in] | enable_tree_attr | If false, tree_to_attr is freed (NULL is ok). If true, it must be NULL and is allocated. |
int p8est_connectivity_sink | ( | p8est_connectivity_t * | conn, |
sc_io_sink_t * | sink | ||
) |
Write connectivity to a sink object.
[in] | conn | The connectivity to be written. |
[in,out] | sink | The connectivity is written into this sink. |
p8est_connectivity_t* p8est_connectivity_source | ( | sc_io_source_t * | source | ) |
Read connectivity from a source object.
[in,out] | source | The connectivity is read from this source. |
static p8est_corner_transform_t* p8est_corner_array_index | ( | sc_array_t * | array, |
size_t | it | ||
) | [inline, static] |
Return a pointer to a p8est_corner_transform_t array element.
static p8est_edge_transform_t* p8est_edge_array_index | ( | sc_array_t * | array, |
size_t | it | ||
) | [inline, static] |
Return a pointer to a p8est_edge_transform_t array element.
void p8est_expand_face_transform | ( | int | iface, |
int | nface, | ||
int | ftransform[] | ||
) |
Fill an array with the axis combination of a face neighbor transform.
[in] | iface | The number of the originating face. |
[in] | nface | Encoded as nface = r * 6 + nf, where nf = 0..5 is the neigbbor's connecting face number and r = 0..3 is the relative orientation to the neighbor's face. This encoding matches p8est_connectivity_t. |
[out] | ftransform | This array holds 9 integers. [0]..[2] The coordinate axis sequence of the origin face, the first two referring to the tangentials and the third to the normal. A permutation of (0, 1, 2). [3]..[5] The coordinate axis sequence of the target face. [6]..[8] Edge reversal flags for tangential axes (boolean); face code in [0, 3] for the normal coordinate q: 0: q' = -q 1: q' = q + 1 2: q' = q - 1 3: q' = 2 - q |
void p8est_find_corner_transform | ( | p8est_connectivity_t * | connectivity, |
p4est_topidx_t | itree, | ||
int | icorner, | ||
p8est_corner_info_t * | ci | ||
) |
Fills an array with information about corner neighbors.
[in] | itree | The number of the originating tree. |
[in] | icorner | The number of the originating corner. |
[in,out] | ci | A p8est_corner_info_t structure with initialized array. |
void p8est_find_edge_transform | ( | p8est_connectivity_t * | connectivity, |
p4est_topidx_t | itree, | ||
int | iedge, | ||
p8est_edge_info_t * | ei | ||
) |
Fills an array with information about edge neighbors.
[in] | itree | The number of the originating tree. |
[in] | iedge | The number of the originating edge. |
[in,out] | ei | A p8est_edge_info_t structure with initialized array. |
p4est_topidx_t p8est_find_face_transform | ( | p8est_connectivity_t * | connectivity, |
p4est_topidx_t | itree, | ||
int | iface, | ||
int | ftransform[] | ||
) |
Fill an array with the axis combination of a face neighbor transform.
[in] | itree | The number of the originating tree. |
[in] | iface | The number of the originating tree's face. |
[out] | ftransform | This array holds 9 integers. [0]..[2] The coordinate axis sequence of the origin face. [3]..[5] The coordinate axis sequence of the target face. [6]..[8] Edge reverse flag for axes t1, t2; face code for n. |
const int p8est_child_corner_edges[8][8] |
Store the edges for each child and corner, can be -1.
const int p8est_child_corner_faces[8][8] |
Store the faces for each child and corner, can be -1.
const int p8est_child_edge_faces[8][12] |
Store the faces for each child and edge, can be -1.
const int p8est_corner_edges[8][3] |
Store the edge numbers 0..11 for each tree corner.
const int p8est_corner_face_corners[8][6] |
Store the face corner numbers for the faces touching a tree corner.
const int p8est_corner_faces[8][3] |
Store the face numbers 0..5 for each tree corner.
const int p8est_edge_corners[12][2] |
Store the corner numbers 0..8 for each tree edge.
const int p8est_edge_face_corners[12][6][2] |
Store the face corner numbers for the faces touching a tree edge.
const int p8est_edge_faces[12][2] |
Store the face numbers 0..5 for each tree edge.
const int p8est_face_corners[6][4] |
Store the corner numbers 0..7 for each tree face.
const int p8est_face_dual[6] |
Store the face numbers in the face neighbor's system.
const int p8est_face_edges[6][4] |
Store the face numbers 0..12 for each tree face.
const int p8est_face_permutation_refs[6][6] |
For each face combination store the permutation set.
The order is [my_face][neighbor_face]
const int p8est_face_permutation_sets[3][4] |
Store the 3 occurring sets of 4 permutations per face.
const int p8est_face_permutations[8][4] |
Store only the 8 out of 24 possible permutations that occur.