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// Copyright (c) 2010-2024, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#ifndef MFEM_MESH
#define MFEM_MESH
#include "../config/config.hpp"
#include "../general/stable3d.hpp"
#include "../general/globals.hpp"
#include "attribute_sets.hpp"
#include "triangle.hpp"
#include "tetrahedron.hpp"
#include "vertex.hpp"
#include "vtk.hpp"
#include "ncmesh.hpp"
#include "../fem/eltrans.hpp"
#include "../fem/coefficient.hpp"
#include "../general/zstr.hpp"
#ifdef MFEM_USE_ADIOS2
#include "../general/adios2stream.hpp"
#endif
#include <iostream>
#include <array>
#include <map>
#include <memory>
namespace mfem
{
class GeometricFactors;
class FaceGeometricFactors;
class KnotVector;
class NURBSExtension;
class FiniteElementSpace;
class GridFunction;
struct Refinement;
/** An enum type to specify if interior or boundary faces are desired. */
enum class FaceType : bool {Interior, Boundary};
#ifdef MFEM_USE_MPI
class ParMesh;
class ParNCMesh;
#endif
/// Mesh data type
class Mesh
{
friend class NCMesh;
friend class NURBSExtension;
#ifdef MFEM_USE_MPI
friend class ParMesh;
friend class ParNCMesh;
#endif
#ifdef MFEM_USE_ADIOS2
friend class adios2stream;
#endif
protected:
int Dim;
int spaceDim;
int NumOfVertices, NumOfElements, NumOfBdrElements;
int NumOfEdges, NumOfFaces;
/** These variables store the number of Interior and Boundary faces. Calling
fes->GetMesh()->GetNBE() doesn't return the expected value in 3D because
periodic meshes in 3D have some of their faces marked as boundary for
visualization purpose in GLVis. */
mutable int nbInteriorFaces, nbBoundaryFaces;
// see MeshGenerator(); global in parallel
int meshgen;
// sum of (1 << geom) for all geom of all dimensions; local in parallel
int mesh_geoms;
// Counter for Mesh transformations: refinement, derefinement, rebalancing.
// Used for checking during Update operations on objects depending on the
// Mesh, such as FiniteElementSpace, GridFunction, etc.
long sequence;
/// Counter for geometric factor invalidation
long nodes_sequence;
Array<Element *> elements;
// Vertices are only at the corners of elements, where you would expect them
// in the lowest-order mesh. In some cases, e.g. in a Mesh that defines the
// patch topology for a NURBS mesh (see LoadPatchTopo()) the vertices may be
// empty while NumOfVertices is positive.
Array<Vertex> vertices;
Array<Element *> boundary;
Array<Element *> faces;
/** @brief This structure stores the low level information necessary to
interpret the configuration of elements on a specific face. This
information can be accessed using methods like GetFaceElements(),
GetFaceInfos(), FaceIsInterior(), etc.
For accessing higher level deciphered information look at
Mesh::FaceInformation, and its accessor Mesh::GetFaceInformation().
Each face contains information on the indices, local reference faces,
orientations, and potential nonconformity for the two neighboring
elements on a face.
Each face can either be an interior, boundary, or shared interior face.
Each interior face is shared by two elements referred as Elem1 and Elem2.
For boundary faces only the information on Elem1 is relevant.
Shared interior faces correspond to faces where Elem1 and Elem2 are
distributed on different MPI ranks.
Regarding conformity, three cases are distinguished, conforming faces,
nonconforming slave faces, and nonconforming master faces. Master and
slave referring to the coarse and fine elements respectively on a
nonconforming face.
Nonconforming slave faces always have the slave element as Elem1 and
the master element as Elem2. On the other side, nonconforming master
faces always have the master element as Elem1, and one of the slave
element as Elem2. Except for ghost nonconforming slave faces, where
Elem1 is the master side and Elem2 is the slave side.
The indices of Elem1 and Elem2 can be indirectly extracted from
FaceInfo::Elem1No and FaceInfo::Elem2No, read the note below for special
cases on the index of Elem2.
The local face identifiers are deciphered from FaceInfo::Elem1Inf and
FaceInfo::Elem2Inf through the formula: LocalFaceIndex = ElemInf/64,
the semantic of the computed local face identifier can be found in
fem/geom.cpp. The local face identifier corresponds to an index
in the Constants<Geometry>::Edges arrays for 2D element geometries, and
to an index in the Constants<Geometry>::FaceVert arrays for 3D element
geometries.
The orientation of each element relative to a face is obtained through
the formula: Orientation = ElemInf%64, the semantic of the orientation
can also be found in fem/geom.cpp. The orientation corresponds to
an index in the Constants<Geometry>::Orient arrays, providing the
sequence of vertices identifying the orientation of an edge/face. By
convention the orientation of Elem1 is always set to 0, serving as the
reference orientation. The orientation of Elem2 relatively to Elem1 is
therefore determined just by using the orientation of Elem2. An important
special case is the one of nonconforming faces, the orientation should
be composed with the PointMatrix, which also contains orientation
information. A special treatment should be done for 2D, the orientation
in the PointMatrix is not included, therefore when applying the
PointMatrix transformation, the PointMatrix should be flipped, except for
shared nonconforming slave faces where the transformation can be applied
as is.
Another special case is the case of shared nonconforming faces. Ghost
faces use a different design based on so called "ghost" faces.
Ghost faces, as their name suggest are very well hidden, and they
usually have a separate interface from "standard" faces.
*/
struct FaceInfo
{
// Inf = 64 * LocalFaceIndex + FaceOrientation
int Elem1No, Elem2No, Elem1Inf, Elem2Inf;
int NCFace; /* -1 if this is a regular conforming/boundary face;
index into 'nc_faces_info' if >= 0. */
};
// NOTE: in NC meshes, master faces have Elem2No == -1. Slave faces on the
// other hand have Elem2No and Elem2Inf set to the master face's element and
// its local face number.
//
// A local face is one generated from a local element and has index i in
// faces_info such that i < GetNumFaces(). Also, Elem1No always refers to the
// element (slave or master, in the nonconforming case) that generated the
// face.
// Classification of a local (non-ghost) face based on its FaceInfo:
// - Elem2No >= 0 --> local interior face; can be either:
// - NCFace == -1 --> conforming face, or
// - NCFace >= 0 --> nonconforming slave face; Elem2No is the index of
// the master volume element; Elem2Inf%64 is 0, see the note in
// Mesh::GenerateNCFaceInfo().
// - Elem2No < 0 --> local "boundary" face; can be one of:
// - NCFace == -1 --> conforming face; can be either:
// - Elem2Inf < 0 --> true boundary face (no element on side 2)
// - Elem2Inf >= 0 --> shared face where element 2 is a face-neighbor
// element with index -1-Elem2No. This state is initialized by
// ParMesh::ExchangeFaceNbrData().
// - NCFace >= 0 --> nonconforming face; can be one of:
// - Elem2Inf < 0 --> master nonconforming face, interior or shared;
// In this case, Elem2No is -1; see GenerateNCFaceInfo().
// - Elem2Inf >= 0 --> shared slave nonconforming face where element 2
// is the master face-neighbor element with index -1-Elem2No; see
// ParNCMesh::GetFaceNeighbors().
//
// A ghost face is a nonconforming face that is generated by a non-local,
// i.e. ghost, element. A ghost face has index i in faces_info such that
// i >= GetNumFaces().
// Classification of a ghost (non-local) face based on its FaceInfo:
// - Elem1No == -1 --> master ghost face? These ghost faces also have:
// Elem2No == -1, Elem1Inf == Elem2Inf == -1, and NCFace == -1.
// - Elem1No >= 0 --> slave ghost face; Elem1No is the index of the local
// master side element, i.e. side 1 IS NOT the side that generated the
// face. Elem2No is < 0 and -1-Elem2No is the index of the ghost
// face-neighbor element that generated this slave ghost face. In this
// case, Elem2Inf >= 0 and NCFace >= 0.
// Relevant methods: GenerateFaces(), GenerateNCFaceInfo(),
// ParNCMesh::GetFaceNeighbors(),
// ParMesh::ExchangeFaceNbrData()
struct NCFaceInfo
{
bool Slave; // true if this is a slave face, false if master face
int MasterFace; // if Slave, this is the index of the master face
// If not Slave, 'MasterFace' is the local face index of this master face
// as a face in the unique adjacent element.
const DenseMatrix* PointMatrix; // if Slave, position within master face
// (NOTE: PointMatrix points to a matrix owned by NCMesh.)
NCFaceInfo() = default;
NCFaceInfo(bool slave, int master, const DenseMatrix* pm)
: Slave(slave), MasterFace(master), PointMatrix(pm) {}
};
Array<FaceInfo> faces_info;
Array<NCFaceInfo> nc_faces_info;
Table *el_to_edge;
Table *el_to_face;
Table *el_to_el;
Array<int> be_to_face; // faces = vertices (1D), edges (2D), faces (3D)
Table *bel_to_edge; // for 3D only
// Note that the following tables are owned by this class and should not be
// deleted by the caller. Of these three tables, only face_edge and
// edge_vertex are returned by access functions.
mutable Table *face_to_elem; // Used by FindFaceNeighbors, not returned.
mutable Table *face_edge; // Returned by GetFaceEdgeTable().
mutable Table *edge_vertex; // Returned by GetEdgeVertexTable().
IsoparametricTransformation Transformation, Transformation2;
IsoparametricTransformation BdrTransformation;
IsoparametricTransformation FaceTransformation, EdgeTransformation;
FaceElementTransformations FaceElemTr;
// refinement embeddings for forward compatibility with NCMesh
mutable CoarseFineTransformations CoarseFineTr;
// Nodes are only active for higher order meshes, and share locations with
// the vertices, plus all the higher- order control points within the
// element and along the edges and on the faces.
GridFunction *Nodes;
int own_nodes;
static const int vtk_quadratic_tet[10];
static const int vtk_quadratic_pyramid[13];
static const int vtk_quadratic_wedge[18];
static const int vtk_quadratic_hex[27];
#ifdef MFEM_USE_MEMALLOC
friend class Tetrahedron;
MemAlloc <Tetrahedron, 1024> TetMemory;
#endif
// used during NC mesh initialization only
Array<Triple<int, int, int> > tmp_vertex_parents;
public:
typedef Geometry::Constants<Geometry::SEGMENT> seg_t;
typedef Geometry::Constants<Geometry::TRIANGLE> tri_t;
typedef Geometry::Constants<Geometry::SQUARE> quad_t;
typedef Geometry::Constants<Geometry::TETRAHEDRON> tet_t;
typedef Geometry::Constants<Geometry::CUBE> hex_t;
typedef Geometry::Constants<Geometry::PRISM> pri_t;
typedef Geometry::Constants<Geometry::PYRAMID> pyr_t;
enum Operation { NONE, REFINE, DEREFINE, REBALANCE };
/// A list of all unique element attributes used by the Mesh.
Array<int> attributes;
/// A list of all unique boundary attributes used by the Mesh.
Array<int> bdr_attributes;
/// Named sets of element attributes
AttributeSets attribute_sets;
/// Named sets of boundary element attributes
AttributeSets bdr_attribute_sets;
NURBSExtension *NURBSext; ///< Optional NURBS mesh extension.
NCMesh *ncmesh; ///< Optional nonconforming mesh extension.
Array<GeometricFactors*> geom_factors; ///< Optional geometric factors.
Array<FaceGeometricFactors*> face_geom_factors; /**< Optional face geometric
factors. */
// Global parameter that can be used to control the removal of unused
// vertices performed when reading a mesh in MFEM format. The default value
// (true) is set in mesh_readers.cpp.
static bool remove_unused_vertices;
protected:
Operation last_operation;
void Init();
void InitTables();
void SetEmpty(); // Init all data members with empty values
void DestroyTables();
void DeleteTables() { DestroyTables(); InitTables(); }
void DestroyPointers(); // Delete data specifically allocated by class Mesh.
void Destroy(); // Delete all owned data.
void ResetLazyData();
Element *ReadElementWithoutAttr(std::istream &input);
static void PrintElementWithoutAttr(const Element *el, std::ostream &os);
Element *ReadElement(std::istream &input);
static void PrintElement(const Element *el, std::ostream &os);
// Readers for different mesh formats, used in the Load() method.
// The implementations of these methods are in mesh_readers.cpp.
void ReadMFEMMesh(std::istream &input, int version, int &curved);
void ReadLineMesh(std::istream &input);
void ReadNetgen2DMesh(std::istream &input, int &curved);
void ReadNetgen3DMesh(std::istream &input);
void ReadTrueGridMesh(std::istream &input);
void CreateVTKMesh(const Vector &points, const Array<int> &cell_data,
const Array<int> &cell_offsets,
const Array<int> &cell_types,
const Array<int> &cell_attributes,
int &curved, int &read_gf, bool &finalize_topo);
void ReadVTKMesh(std::istream &input, int &curved, int &read_gf,
bool &finalize_topo);
void ReadXML_VTKMesh(std::istream &input, int &curved, int &read_gf,
bool &finalize_topo, const std::string &xml_prefix="");
void ReadNURBSMesh(std::istream &input, int &curved, int &read_gf,
bool spacing=false);
void ReadInlineMesh(std::istream &input, bool generate_edges = false);
void ReadGmshMesh(std::istream &input, int &curved, int &read_gf);
/* Note NetCDF (optional library) is used for reading cubit files */
#ifdef MFEM_USE_NETCDF
/// @brief Load a mesh from a Genesis file.
void ReadCubit(const std::string &filename, int &curved, int &read_gf);
#endif
/// Determine the mesh generator bitmask #meshgen, see MeshGenerator().
/** Also, initializes #mesh_geoms. */
void SetMeshGen();
/// Return the length of the segment from node i to node j.
real_t GetLength(int i, int j) const;
void MarkForRefinement();
void MarkTriMeshForRefinement();
void GetEdgeOrdering(const DSTable &v_to_v, Array<int> &order);
virtual void MarkTetMeshForRefinement(const DSTable &v_to_v);
// Methods used to prepare and apply permutation of the mesh nodes assuming
// that the mesh elements may be rotated (e.g. to mark triangle or tet edges
// for refinement) between the two calls - PrepareNodeReorder() and
// DoNodeReorder(). The latter method assumes that the 'faces' have not been
// updated after the element rotations.
void PrepareNodeReorder(DSTable **old_v_to_v, Table **old_elem_vert);
void DoNodeReorder(DSTable *old_v_to_v, Table *old_elem_vert);
STable3D *GetFacesTable();
STable3D *GetElementToFaceTable(int ret_ftbl = 0);
/** Red refinement. Element with index i is refined. The default
red refinement for now is Uniform. */
void RedRefinement(int i, const DSTable &v_to_v,
int *edge1, int *edge2, int *middle)
{ UniformRefinement(i, v_to_v, edge1, edge2, middle); }
/** Green refinement. Element with index i is refined. The default
refinement for now is Bisection. */
void GreenRefinement(int i, const DSTable &v_to_v,
int *edge1, int *edge2, int *middle)
{ Bisection(i, v_to_v, edge1, edge2, middle); }
/// Bisect a triangle: element with index @a i is bisected.
void Bisection(int i, const DSTable &, int *, int *, int *);
/// Bisect a tetrahedron: element with index @a i is bisected.
void Bisection(int i, HashTable<Hashed2> &);
/// Bisect a boundary triangle: boundary element with index @a i is bisected.
void BdrBisection(int i, const HashTable<Hashed2> &);
/** Uniform Refinement. Element with index i is refined uniformly. */
void UniformRefinement(int i, const DSTable &, int *, int *, int *);
/** @brief Averages the vertices with given @a indexes and saves the result
in #vertices[result]. */
void AverageVertices(const int *indexes, int n, int result);
void InitRefinementTransforms();
int FindCoarseElement(int i);
/** @brief Update the nodes of a curved mesh after the topological part of a
Mesh::Operation, such as refinement, has been performed. */
/** If Nodes GridFunction is defined, i.e. not NULL, this method calls
NodesUpdated().
@note Unlike the similarly named public method NodesUpdated() this
method modifies the mesh nodes (if they exist) and calls NodesUpdated().
*/
void UpdateNodes();
/// Helper to set vertex coordinates given a high-order curvature function.
void SetVerticesFromNodes(const GridFunction *nodes);
void UniformRefinement2D_base(bool update_nodes = true);
/// Refine a mixed 2D mesh uniformly.
virtual void UniformRefinement2D() { UniformRefinement2D_base(); }
/* If @a f2qf is not NULL, adds all quadrilateral faces to @a f2qf which
represents a "face-to-quad-face" index map. When all faces are quads, the
array @a f2qf is kept empty since it is not needed. */
void UniformRefinement3D_base(Array<int> *f2qf = NULL,
DSTable *v_to_v_p = NULL,
bool update_nodes = true);
/// Refine a mixed 3D mesh uniformly.
virtual void UniformRefinement3D() { UniformRefinement3D_base(); }
/// This function is not public anymore. Use GeneralRefinement instead.
virtual void LocalRefinement(const Array<int> &marked_el, int type = 3);
/// This function is not public anymore. Use GeneralRefinement instead.
virtual void NonconformingRefinement(const Array<Refinement> &refinements,
int nc_limit = 0);
/// NC version of GeneralDerefinement.
virtual bool NonconformingDerefinement(Array<real_t> &elem_error,
real_t threshold, int nc_limit = 0,
int op = 1);
/// Derefinement helper.
real_t AggregateError(const Array<real_t> &elem_error,
const int *fine, int nfine, int op);
/// Read NURBS patch/macro-element mesh
void LoadPatchTopo(std::istream &input, Array<int> &edge_to_knot);
void UpdateNURBS();
/** @brief Write the beginning of a NURBS mesh to @a os, specifying the NURBS
patch topology. Optional file comments can be provided in @a comments.
@param[in] os Output stream to which to write.
@param[in] e_to_k Map from edge to signed knotvector indices.
@param[in] version NURBS mesh version number times 10 (e.g. 11 for v1.1).
@param[in] comment Optional comment string, written after version line.
*/
void PrintTopo(std::ostream &os, const Array<int> &e_to_k,
const int version,
const std::string &comment = "") const;
/// Used in GetFaceElementTransformations (...)
void GetLocalPtToSegTransformation(IsoparametricTransformation &,
int i) const;
void GetLocalSegToTriTransformation(IsoparametricTransformation &loc,
int i) const;
void GetLocalSegToQuadTransformation(IsoparametricTransformation &loc,
int i) const;
void GetLocalTriToTetTransformation(IsoparametricTransformation &loc,
int i) const;
void GetLocalTriToWdgTransformation(IsoparametricTransformation &loc,
int i) const;
void GetLocalTriToPyrTransformation(IsoparametricTransformation &loc,
int i) const;
void GetLocalQuadToHexTransformation(IsoparametricTransformation &loc,
int i) const;
void GetLocalQuadToWdgTransformation(IsoparametricTransformation &loc,
int i) const;
void GetLocalQuadToPyrTransformation(IsoparametricTransformation &loc,
int i) const;
/** Used in GetFaceElementTransformations to account for the fact that a
slave face occupies only a portion of its master face. */
void ApplyLocalSlaveTransformation(FaceElementTransformations &FT,
const FaceInfo &fi, bool is_ghost) const;
bool IsSlaveFace(const FaceInfo &fi) const;
/// Returns the orientation of "test" relative to "base"
static int GetTriOrientation(const int *base, const int *test);
/// Returns the orientation of "base" relative to "test"
/// In other words: GetTriOrientation(test, base) should equal
/// InvertTriOrientation(GetTriOrientation(base, test))
static int InvertTriOrientation(int ori);
/// Returns the orientation of "c" relative to "a" by composing
/// previously computed orientations relative to an intermediate
/// set "b".
static int ComposeTriOrientations(int ori_a_b, int ori_b_c);
/// Returns the orientation of "test" relative to "base"
static int GetQuadOrientation(const int *base, const int *test);
/// Returns the orientation of "base" relative to "test"
/// In other words: GetQuadOrientation(test, base) should equal
/// InvertQuadOrientation(GetQuadOrientation(base, test))
static int InvertQuadOrientation(int ori);
/// Returns the orientation of "c" relative to "a" by composing
/// previously computed orientations relative to an intermediate
/// set "b".
static int ComposeQuadOrientations(int ori_a_b, int ori_b_c);
/// Returns the orientation of "test" relative to "base"
static int GetTetOrientation(const int *base, const int *test);
static void GetElementArrayEdgeTable(const Array<Element*> &elem_array,
const DSTable &v_to_v,
Table &el_to_edge);
/** Return element to edge table and the indices for the boundary edges.
The entries in the table are ordered according to the order of the
nodes in the elements. For example, if T is the element to edge table
T(i, 0) gives the index of edge in element i that connects vertex 0
to vertex 1, etc. Returns the number of the edges. */
int GetElementToEdgeTable(Table &);
/// Used in GenerateFaces()
void AddPointFaceElement(int lf, int gf, int el);
void AddSegmentFaceElement (int lf, int gf, int el, int v0, int v1);
void AddTriangleFaceElement (int lf, int gf, int el,
int v0, int v1, int v2);
void AddQuadFaceElement (int lf, int gf, int el,
int v0, int v1, int v2, int v3);
/** For a serial Mesh, return true if the face is interior. For a parallel
ParMesh return true if the face is interior or shared. In parallel, this
method only works if the face neighbor data is exchanged. */
bool FaceIsTrueInterior(int FaceNo) const
{
return FaceIsInterior(FaceNo) || (faces_info[FaceNo].Elem2Inf >= 0);
}
void FreeElement(Element *E);
void GenerateFaces();
void GenerateNCFaceInfo();
/// Begin construction of a mesh
void InitMesh(int Dim_, int spaceDim_, int NVert, int NElem, int NBdrElem);
// Used in the methods FinalizeXXXMesh() and FinalizeTopology()
void FinalizeCheck();
void Loader(std::istream &input, int generate_edges = 0,
std::string parse_tag = "");
/** If NURBS mesh, write NURBS format. If NCMesh, write mfem v1.1 format.
If section_delimiter is empty, write mfem v1.0 format. Otherwise, write
mfem v1.2 format with the given section_delimiter at the end.
If @a comments is non-empty, it will be printed after the first line of
the file, and each line should begin with '#'. */
void Printer(std::ostream &os = mfem::out,
std::string section_delimiter = "",
const std::string &comments = "") const;
/// @brief Creates a mesh for the parallelepiped [0,sx]x[0,sy]x[0,sz],
/// divided into nx*ny*nz hexahedra if @a type = HEXAHEDRON or into
/// 6*nx*ny*nz tetrahedrons if @a type = TETRAHEDRON.
///
/// The parameter @a sfc_ordering controls how the elements
/// (when @a type = HEXAHEDRON) are ordered: true - use space-filling curve
/// ordering, or false - use lexicographic ordering.
void Make3D(int nx, int ny, int nz, Element::Type type,
real_t sx, real_t sy, real_t sz, bool sfc_ordering);
/// @brief Creates a mesh for the parallelepiped [0,sx]x[0,sy]x[0,sz],
/// divided into nx*ny*nz*24 tetrahedrons.
///
/// The mesh is generated by taking nx*ny*nz hexahedra and splitting each
/// hexahedron into 24 tetrahedrons. Each face of the hexahedron is split
/// into 4 triangles (face edges are connected to a face-centered point),
/// and the triangles are connected to a hex-centered point.
void Make3D24TetsFromHex(int nx, int ny, int nz,
real_t sx, real_t sy, real_t sz);
/// @brief Creates mesh for the rectangle [0,sx]x[0,sy], divided into nx*ny*4
/// triangles.
///
/// The mesh is generated by taking nx*ny quadrilaterals and splitting each
/// quadrilateral into 4 triangles by connecting the vertices to a
/// quad-centered point.
void Make2D4TrisFromQuad(int nx, int ny, real_t sx, real_t sy);
/// @brief Creates mesh for the rectangle [0,sx]x[0,sy], divided into nx*ny*5
/// quadrilaterals.
///
/// The mesh is generated by taking nx*ny quadrilaterals and splitting
/// each quadrilateral into 5 quadrilaterals. Each quadrilateral is projected
/// inwards and connected to the original quadrilateral.
void Make2D5QuadsFromQuad(int nx, int ny, real_t sx, real_t sy);
/// @brief Creates mesh for the rectangle [0,sx]x[0,sy], divided into nx*ny
/// quadrilaterals if @a type = QUADRILATERAL or into 2*nx*ny triangles if
/// @a type = TRIANGLE.
///
/// If generate_edges = 0 (default) edges are not generated, if 1 edges are
/// generated. The parameter @a sfc_ordering controls how the elements (when
/// @a type = QUADRILATERAL) are ordered: true - use space-filling curve
/// ordering, or false - use lexicographic ordering.
void Make2D(int nx, int ny, Element::Type type, real_t sx, real_t sy,
bool generate_edges, bool sfc_ordering);
/// @a brief Creates a 1D mesh for the interval [0,sx] divided into n equal
/// intervals.
void Make1D(int n, real_t sx = 1.0);
/// Internal function used in Mesh::MakeRefined
void MakeRefined_(Mesh &orig_mesh, const Array<int> &ref_factors,
int ref_type);
/// Initialize vertices/elements/boundary/tables from a nonconforming mesh.
void InitFromNCMesh(const NCMesh &ncmesh);
/// Create from a nonconforming mesh.
explicit Mesh(const NCMesh &ncmesh);
// used in GetElementData() and GetBdrElementData()
void GetElementData(const Array<Element*> &elem_array, int geom,
Array<int> &elem_vtx, Array<int> &attr) const;
// Internal helper used in MakeSimplicial (and ParMesh::MakeSimplicial).
void MakeSimplicial_(const Mesh &orig_mesh, int *vglobal);
public:
/// @anchor mfem_Mesh_ctors
/// @name Standard Mesh constructors and related methods
///
/// These constructors and assignment operators accept mesh information in
/// a variety of common forms. For more specialized constructors see
/// @ref mfem_Mesh_named_ctors "Named mesh constructors".
/// @{
Mesh() : attribute_sets(attributes), bdr_attribute_sets(bdr_attributes)
{ SetEmpty(); }
/** Copy constructor. Performs a deep copy of (almost) all data, so that the
source mesh can be modified (e.g. deleted, refined) without affecting the
new mesh. If 'copy_nodes' is false, use a shallow (pointer) copy for the
nodes, if present. */
explicit Mesh(const Mesh &mesh, bool copy_nodes = true);
/// Move constructor, useful for using a Mesh as a function return value.
Mesh(Mesh &&mesh);
/// Move assignment operator.
Mesh& operator=(Mesh &&mesh);
/// Explicitly delete the copy assignment operator.
Mesh& operator=(const Mesh &mesh) = delete;
/// Construct a Mesh from the given primary data.
/** The array @a vertices is used as external data, i.e. the Mesh does not
copy the data and will not delete the pointer.
The data from the other arrays is copied into the internal Mesh data
structures.
This method calls the method FinalizeTopology(). The method Finalize()
may be called after this constructor and after optionally setting the
Mesh nodes. */
Mesh(real_t *vertices, int num_vertices,
int *element_indices, Geometry::Type element_type,
int *element_attributes, int num_elements,
int *boundary_indices, Geometry::Type boundary_type,
int *boundary_attributes, int num_boundary_elements,
int dimension, int space_dimension = -1);
/** @anchor mfem_Mesh_init_ctor
@brief _Init_ constructor: begin the construction of a Mesh object.
Construct a shell of a mesh object allocating space to store pointers to
the vertices, elements, and boundary elements. The vertices and elements
themselves can later be added using methods from the
@ref mfem_Mesh_construction "Mesh construction" group. */
Mesh(int Dim_, int NVert, int NElem, int NBdrElem = 0, int spaceDim_ = -1)
: attribute_sets(attributes), bdr_attribute_sets(bdr_attributes)
{
if (spaceDim_ == -1) { spaceDim_ = Dim_; }
InitMesh(Dim_, spaceDim_, NVert, NElem, NBdrElem);
}
/** Creates mesh by reading a file in MFEM, Netgen, or VTK format. If
generate_edges = 0 (default) edges are not generated, if 1 edges are
generated. See also @a Mesh::LoadFromFile. See @a Mesh::Finalize for the
meaning of @a refine. */
explicit Mesh(const std::string &filename, int generate_edges = 0,
int refine = 1, bool fix_orientation = true);
/** Creates mesh by reading data stream in MFEM, Netgen, or VTK format. If
generate_edges = 0 (default) edges are not generated, if 1 edges are
generated. */
explicit Mesh(std::istream &input, int generate_edges = 0, int refine = 1,
bool fix_orientation = true);
/// Create a disjoint mesh from the given mesh array
///
/// @note Data is copied from the meshes in @a mesh_array.
Mesh(Mesh *mesh_array[], int num_pieces);
/** This is similar to the mesh constructor with the same arguments, but here
the current mesh is destroyed and another one created based on the data
stream again given in MFEM, Netgen, or VTK format. If generate_edges = 0
(default) edges are not generated, if 1 edges are generated. */
/// \see mfem::ifgzstream() for on-the-fly decompression of compressed ascii
/// inputs.
virtual void Load(std::istream &input, int generate_edges = 0,
int refine = 1, bool fix_orientation = true)
{
Loader(input, generate_edges);
Finalize(refine, fix_orientation);
}
/// Swaps internal data with another mesh. By default, non-geometry members
/// like 'ncmesh' and 'NURBSExt' are only swapped when 'non_geometry' is set.
void Swap(Mesh& other, bool non_geometry);
/// Clear the contents of the Mesh.
void Clear() { Destroy(); SetEmpty(); }
/// Destroys Mesh.
virtual ~Mesh() { DestroyPointers(); }
/// @}
/** @anchor mfem_Mesh_named_ctors @name Named mesh constructors.
Each of these constructors uses the move constructor, and can be used as
the right-hand side of an assignment when creating new meshes. For more
general mesh constructors see
@ref mfem_Mesh_ctors "Standard mesh constructors".*/
///@{
/** Creates mesh by reading a file in MFEM, Netgen, or VTK format. If
generate_edges = 0 (default) edges are not generated, if 1 edges are
generated.
@note @a filename is not cached by the Mesh object and can be
safely deleted following this function call.
*/
static Mesh LoadFromFile(const std::string &filename,
int generate_edges = 0, int refine = 1,
bool fix_orientation = true);
/// Creates 1D mesh, divided into n equal intervals.
static Mesh MakeCartesian1D(int n, real_t sx = 1.0);
/// @brief Creates mesh for the rectangle [0,sx]x[0,sy], divided into nx*ny
/// quadrilaterals if @a type = QUADRILATERAL or into 2*nx*ny triangles if
/// @a type = TRIANGLE.
///
/// If generate_edges = 0 (default) edges are not generated, if 1 edges are
/// generated. The parameter @a sfc_ordering controls how the elements (when
/// @a type = QUADRILATERAL) are ordered: true - use space-filling curve
/// ordering, or false - use lexicographic ordering.
static Mesh MakeCartesian2D(
int nx, int ny, Element::Type type, bool generate_edges = false,
real_t sx = 1.0, real_t sy = 1.0, bool sfc_ordering = true);
/// @brief Creates a mesh for the parallelepiped [0,sx]x[0,sy]x[0,sz],
/// divided into nx*ny*nz hexahedra if @a type = HEXAHEDRON or into
/// 6*nx*ny*nz tetrahedrons if @a type = TETRAHEDRON.
///
/// The parameter @a sfc_ordering controls how the elements
/// (when @a type = HEXAHEDRON) are ordered: true - use space-filling curve
/// ordering, or false - use lexicographic ordering.
static Mesh MakeCartesian3D(
int nx, int ny, int nz, Element::Type type,
real_t sx = 1.0, real_t sy = 1.0, real_t sz = 1.0,
bool sfc_ordering = true);
/// @brief Creates a mesh for the parallelepiped [0,sx]x[0,sy]x[0,sz],
/// divided into nx*ny*nz*24 tetrahedrons.
///
/// The mesh is generated by taking nx*ny*nz hexahedra and splitting each
/// hexahedron into 24 tetrahedrons. Each face of the hexahedron is split
/// into 4 triangles (face edges are connected to a face-centered point),
/// and the triangles are connected to a hex-centered point.
static Mesh MakeCartesian3DWith24TetsPerHex(int nx, int ny, int nz,
real_t sx = 1.0, real_t sy = 1.0,
real_t sz = 1.0);
/// @brief Creates mesh for the rectangle [0,sx]x[0,sy], divided into nx*ny*4
/// triangles.
///
/// The mesh is generated by taking nx*ny quadrilaterals and splitting each
/// quadrilateral into 4 triangles by connecting the vertices to a
/// quad-centered point.
static Mesh MakeCartesian2DWith4TrisPerQuad(int nx, int ny, real_t sx = 1.0,
real_t sy = 1.0);
/// @brief Creates mesh for the rectangle [0,sx]x[0,sy], divided into nx*ny*5
/// quadrilaterals.
///
/// The mesh is generated by taking nx*ny quadrilaterals and splitting
/// each quadrilateral into 5 quadrilaterals. Each quadrilateral is projected
/// inwards and connected to the original quadrilateral.
static Mesh MakeCartesian2DWith5QuadsPerQuad(int nx, int ny, real_t sx = 1.0,
real_t sy = 1.0);
/// Create a refined (by any factor) version of @a orig_mesh.
/** @param[in] orig_mesh The starting coarse mesh.
@param[in] ref_factor The refinement factor, an integer > 1.
@param[in] ref_type Specify the positions of the new vertices. The
options are BasisType::ClosedUniform or
BasisType::GaussLobatto.
The refinement data which can be accessed with GetRefinementTransforms()
is set to reflect the performed refinements.
@note The constructed Mesh is straight-sided. */
static Mesh MakeRefined(Mesh &orig_mesh, int ref_factor, int ref_type);
/// Create a refined mesh, where each element of the original mesh may be
/// refined by a different factor.
/** @param[in] orig_mesh The starting coarse mesh.
@param[in] ref_factors An array of integers whose size is the number of
elements of @a orig_mesh. The @a ith element of
@a orig_mesh is refined by refinement factor
@a ref_factors[i].
@param[in] ref_type Specify the positions of the new vertices. The
options are BasisType::ClosedUniform or
BasisType::GaussLobatto.
The refinement data which can be accessed with GetRefinementTransforms()
is set to reflect the performed refinements.
@note The constructed Mesh is straight-sided. */
/// refined @a ref_factors[i] times in each dimension.
static Mesh MakeRefined(Mesh &orig_mesh, const Array<int> &ref_factors,
int ref_type);
/** Create a mesh by splitting each element of @a orig_mesh into simplices.
Quadrilaterals are split into two triangles, prisms are split into
3 tetrahedra, and hexahedra are split into either 5 or 6 tetrahedra
depending on the configuration.
@warning The curvature of the original mesh is not carried over to the
new mesh. Periodic meshes are not supported. */
static Mesh MakeSimplicial(const Mesh &orig_mesh);
/// Create a periodic mesh by identifying vertices of @a orig_mesh.
/** Each vertex @a i will be mapped to vertex @a v2v[i], such that all
vertices that are coincident under the periodic mapping get mapped to
the same index. The mapping @a v2v can be generated from translation
vectors using Mesh::CreatePeriodicVertexMapping.
@note MFEM requires that each edge of the resulting mesh be uniquely
identifiable by a pair of distinct vertices. As a consequence, periodic
boundaries must be separated by at least two interior vertices.
@note The resulting mesh uses a discontinuous nodal function, see
SetCurvature() for further details. */
static Mesh MakePeriodic(const Mesh &orig_mesh, const std::vector<int> &v2v);
///@}
/** @anchor mfem_Mesh_construction
@name Methods for piecewise Mesh construction.
These methods are intended to be used with the @ref mfem_Mesh_init_ctor
"init constructor". */
///@{
/// @note The returned object should be deleted by the caller.
Element *NewElement(int geom);
int AddVertex(real_t x, real_t y = 0.0, real_t z = 0.0);
int AddVertex(const real_t *coords);
int AddVertex(const Vector &coords);
/// Mark vertex @a i as nonconforming, with parent vertices @a p1 and @a p2.
void AddVertexParents(int i, int p1, int p2);
/// Adds a vertex at the mean center of the @a nverts vertex indices given
/// by @a vi.
int AddVertexAtMeanCenter(const int *vi, const int nverts, int dim = 3);
/// Adds a segment to the mesh given by 2 vertices @a v1 and @a v2.
int AddSegment(int v1, int v2, int attr = 1);
/// Adds a segment to the mesh given by 2 vertices @a vi.
int AddSegment(const int *vi, int attr = 1);
/// Adds a triangle to the mesh given by 3 vertices @a v1 through @a v3.
int AddTriangle(int v1, int v2, int v3, int attr = 1);
/// Adds a triangle to the mesh given by 3 vertices @a vi.
int AddTriangle(const int *vi, int attr = 1);
/// Adds a triangle to the mesh given by 3 vertices @a vi.
int AddTri(const int *vi, int attr = 1) { return AddTriangle(vi, attr); }
/// Adds a quadrilateral to the mesh given by 4 vertices @a v1 through @a v4.
int AddQuad(int v1, int v2, int v3, int v4, int attr = 1);
/// Adds a quadrilateral to the mesh given by 4 vertices @a vi.
int AddQuad(const int *vi, int attr = 1);
/// Adds a tetrahedron to the mesh given by 4 vertices @a v1 through @a v4.
int AddTet(int v1, int v2, int v3, int v4, int attr = 1);
/// Adds a tetrahedron to the mesh given by 4 vertices @a vi.
int AddTet(const int *vi, int attr = 1);
/// Adds a wedge to the mesh given by 6 vertices @a v1 through @a v6.
int AddWedge(int v1, int v2, int v3, int v4, int v5, int v6, int attr = 1);
/// Adds a wedge to the mesh given by 6 vertices @a vi.
int AddWedge(const int *vi, int attr = 1);
/// Adds a pyramid to the mesh given by 5 vertices @a v1 through @a v5.
int AddPyramid(int v1, int v2, int v3, int v4, int v5, int attr = 1);
/// Adds a pyramid to the mesh given by 5 vertices @a vi.
int AddPyramid(const int *vi, int attr = 1);
/// Adds a hexahedron to the mesh given by 8 vertices @a v1 through @a v8.
int AddHex(int v1, int v2, int v3, int v4, int v5, int v6, int v7, int v8,
int attr = 1);
/// Adds a hexahedron to the mesh given by 8 vertices @a vi.
int AddHex(const int *vi, int attr = 1);
/// @brief Adds 6 tetrahedrons to the mesh by splitting a hexahedron given by
/// 8 vertices @a vi.
void AddHexAsTets(const int *vi, int attr = 1);
/// @brief Adds 2 wedges to the mesh by splitting a hexahedron given by
/// 8 vertices @a vi.
void AddHexAsWedges(const int *vi, int attr = 1);
/// @brief Adds 6 pyramids to the mesh by splitting a hexahedron given by
/// 8 vertices @a vi.
void AddHexAsPyramids(const int *vi, int attr = 1);
/// @brief Adds 24 tetrahedrons to the mesh by splitting a hexahedron.
///
/// @a vi are the 8 vertices of the hexahedron, @a hex_face_verts has the
/// map from the 4 vertices of each face of the hexahedron to the index
/// of the point created at the center of the face, and @a attr is the
/// attribute of the new elements. See @a Make3D24TetsFromHex for usage.
void AddHexAs24TetsWithPoints(int *vi,
std::map<std::array<int, 4>, int>
&hex_face_verts,
int attr = 1);
/// @brief Adds 4 triangles to the mesh by splitting a quadrilateral given by
/// 4 vertices @a vi.
///
/// @a attr is the attribute of the new elements. See @a Make2D4TrisFromQuad
/// for usage.
void AddQuadAs4TrisWithPoints(int *vi, int attr = 1);
/// @brief Adds 5 quadrilaterals to the mesh by splitting a quadrilateral
/// given by 4 vertices @a vi.
///
/// @a attr is the attribute of the new elements. See @a Make2D5QuadsFromQuad
/// for usage.
void AddQuadAs5QuadsWithPoints(int *vi, int attr = 1);
/// The parameter @a elem should be allocated using the NewElement() method
/// @note Ownership of @a elem will pass to the Mesh object
int AddElement(Element *elem);
/// The parameter @a elem should be allocated using the NewElement() method
/// @note Ownership of @a elem will pass to the Mesh object
int AddBdrElement(Element *elem);
int AddBdrSegment(int v1, int v2, int attr = 1);
int AddBdrSegment(const int *vi, int attr = 1);
int AddBdrTriangle(int v1, int v2, int v3, int attr = 1);
int AddBdrTriangle(const int *vi, int attr = 1);
int AddBdrQuad(int v1, int v2, int v3, int v4, int attr = 1);
int AddBdrQuad(const int *vi, int attr = 1);
void AddBdrQuadAsTriangles(const int *vi, int attr = 1);
int AddBdrPoint(int v, int attr = 1);
virtual void GenerateBoundaryElements();
/// Finalize the construction of a triangular Mesh.
void FinalizeTriMesh(int generate_edges = 0, int refine = 0,
bool fix_orientation = true);
/// Finalize the construction of a quadrilateral Mesh.
void FinalizeQuadMesh(int generate_edges = 0, int refine = 0,
bool fix_orientation = true);
/// Finalize the construction of a tetrahedral Mesh.
void FinalizeTetMesh(int generate_edges = 0, int refine = 0,
bool fix_orientation = true);
/// Finalize the construction of a wedge Mesh.
void FinalizeWedgeMesh(int generate_edges = 0, int refine = 0,
bool fix_orientation = true);
/// Finalize the construction of a hexahedral Mesh.
void FinalizeHexMesh(int generate_edges = 0, int refine = 0,
bool fix_orientation = true);
/// Finalize the construction of any type of Mesh.
/** This method calls FinalizeTopology() and Finalize(). */
void FinalizeMesh(int refine = 0, bool fix_orientation = true);
///@}
/// @name Mesh consistency methods
/// @{
/** @brief Finalize the construction of the secondary topology (connectivity)
data of a Mesh. */
/** This method does not require any actual coordinate data (either vertex
coordinates for linear meshes or node coordinates for meshes with nodes)
to be available. However, the data generated by this method is generally
required by the FiniteElementSpace class.
After calling this method, setting the Mesh vertices or nodes, it may be
appropriate to call the method Finalize(). */
void FinalizeTopology(bool generate_bdr = true);
/// Finalize the construction of a general Mesh.
/** This method will:
- check and optionally fix the orientation of regular elements
- check and fix the orientation of boundary elements
- assume that #vertices are defined, if #Nodes == NULL
- assume that #Nodes are defined, if #Nodes != NULL.
@param[in] refine If true, prepare the Mesh for conforming refinement of
triangular or tetrahedral meshes.
@param[in] fix_orientation
If true, fix the orientation of inverted mesh elements
by permuting their vertices.
Before calling this method, call FinalizeTopology() and ensure that the
Mesh vertices or nodes are set. */
virtual void Finalize(bool refine = false, bool fix_orientation = false);
/// @brief Determine the sets of unique attribute values in domain and
/// boundary elements.
///
/// Separately scan the domain and boundary elements to generate unique,
/// sorted sets of the element attribute values present in the mesh and
/// store these in the Mesh::attributes and Mesh::bdr_attributes arrays.
virtual void SetAttributes();
/// Check (and optionally attempt to fix) the orientation of the elements
/** @param[in] fix_it If `true`, attempt to fix the orientations of some
elements: triangles, quads, and tets.
@return The number of elements with wrong orientation.
@note For meshes with nodes (e.g. high-order or periodic meshes), fixing
the element orientations may require additional permutation of the nodal
GridFunction of the mesh which is not performed by this method. Instead,
the method Finalize() should be used with the parameter
@a fix_orientation set to `true`.
@note This method performs a simple check if an element is inverted, e.g.
for most elements types, it checks if the Jacobian of the mapping from
the reference element is non-negative at the center of the element. */
int CheckElementOrientation(bool fix_it = true);
/// Check the orientation of the boundary elements
/** @return The number of boundary elements with wrong orientation. */
int CheckBdrElementOrientation(bool fix_it = true);
/** This method modifies a tetrahedral mesh so that Nedelec spaces of order
greater than 1 can be defined on the mesh. Specifically, we
1) rotate all tets in the mesh so that the vertices {v0, v1, v2, v3}
satisfy: v0 < v1 < min(v2, v3).
2) rotate all boundary triangles so that the vertices {v0, v1, v2}
satisfy: v0 < min(v1, v2).
@note Refinement does not work after a call to this method! */
MFEM_DEPRECATED virtual void ReorientTetMesh();
/// Remove unused vertices and rebuild mesh connectivity.
void RemoveUnusedVertices();
/** Remove boundary elements that lie in the interior of the mesh, i.e. that
have two adjacent faces in 3D, or edges in 2D. */
void RemoveInternalBoundaries();
/// @}
/// @name Element ordering methods
/// @{
/** This is our integration with the Gecko library. The method finds an
element ordering that will increase memory coherency by putting elements
that are in physical proximity closer in memory. It can also be used to
obtain a space-filling curve ordering for ParNCMesh partitioning.
@param[out] ordering Output element ordering.
@param iterations Total number of V cycles. The ordering may improve with
more iterations. The best iteration is returned at the end.
@param window Initial window size. This determines the number of
permutations tested at each multigrid level and strongly influences the
quality of the result, but the cost of increasing 'window' is exponential.
@param period The window size is incremented every 'period' iterations.
@param seed Seed for initial random ordering (0 = skip random reorder).
@param verbose Print the progress of the optimization to mfem::out.
@param time_limit Optional time limit for the optimization, in seconds.
When reached, ordering from the best iteration so far is returned
(0 = no limit).
@return The final edge product cost of the ordering. The function may be
called in an external loop with different seeds, and the best ordering can
then be retained. */
real_t GetGeckoElementOrdering(Array<int> &ordering,
int iterations = 4, int window = 4,
int period = 2, int seed = 0,
bool verbose = false, real_t time_limit = 0);
/** Return an ordering of the elements that approximately follows the Hilbert
curve. The method performs a spatial (Hilbert) sort on the centers of all
elements and returns the resulting sequence, which can then be passed to
ReorderElements. This is a cheap alternative to GetGeckoElementOrdering.*/
void GetHilbertElementOrdering(Array<int> &ordering);
/** Rebuilds the mesh with a different order of elements. For each element i,
the array ordering[i] contains its desired new index. Note that the method
reorders vertices, edges and faces along with the elements. */
void ReorderElements(const Array<int> &ordering, bool reorder_vertices = true);
/// @}
/// @anchor mfem_Mesh_deprecated_ctors @name Deprecated mesh constructors
///
/// These constructors have been deprecated in favor of
/// @ref mfem_Mesh_named_ctors "Named mesh constructors".
/// @{
/// Deprecated: see @a MakeCartesian3D.
MFEM_DEPRECATED
Mesh(int nx, int ny, int nz, Element::Type type, bool generate_edges = false,
real_t sx = 1.0, real_t sy = 1.0, real_t sz = 1.0,
bool sfc_ordering = true)
: attribute_sets(attributes), bdr_attribute_sets(bdr_attributes)
{
Make3D(nx, ny, nz, type, sx, sy, sz, sfc_ordering);
Finalize(true); // refine = true
}
/// Deprecated: see @a MakeCartesian2D.
MFEM_DEPRECATED
Mesh(int nx, int ny, Element::Type type, bool generate_edges = false,
real_t sx = 1.0, real_t sy = 1.0, bool sfc_ordering = true)
: attribute_sets(attributes), bdr_attribute_sets(bdr_attributes)
{
Make2D(nx, ny, type, sx, sy, generate_edges, sfc_ordering);
Finalize(true); // refine = true
}
/// Deprecated: see @a MakeCartesian1D.
MFEM_DEPRECATED
explicit Mesh(int n, real_t sx = 1.0)
: attribute_sets(attributes), bdr_attribute_sets(bdr_attributes)
{
Make1D(n, sx);
// Finalize(); // reminder: not needed
}
/// Deprecated: see @a MakeRefined.
MFEM_DEPRECATED
Mesh(Mesh *orig_mesh, int ref_factor, int ref_type);
/// @}
/// @name Information about the mesh as a whole
/// @{
/// @brief Dimension of the reference space used within the elements
int Dimension() const { return Dim; }
/// @brief Dimension of the physical space containing the mesh
int SpaceDimension() const { return spaceDim; }
/// Equals 1 + num_holes - num_loops
inline int EulerNumber() const
{ return NumOfVertices - NumOfEdges + NumOfFaces - NumOfElements; }
/// Equals 1 - num_holes
inline int EulerNumber2D() const
{ return NumOfVertices - NumOfEdges + NumOfElements; }
/** @brief Get the mesh generator/type.
The purpose of this is to be able to quickly tell what type of elements
one has in the mesh. Examination of this bitmask along with knowledge
of the mesh dimension can be used to identify which element types are
present.
@return A bitmask:
- bit 0 - simplices are present in the mesh (triangles, tets),
- bit 1 - tensor product elements are present in the mesh (quads, hexes),
- bit 2 - the mesh has wedge elements.
- bit 3 - the mesh has pyramid elements.
In parallel, the result takes into account elements on all processors.
*/
inline int MeshGenerator() const { return meshgen; }
/// Checks if the mesh has boundary elements
virtual bool HasBoundaryElements() const { return (NumOfBdrElements > 0); }
/** @brief Return true iff the given @a geom is encountered in the mesh.
Geometries of dimensions lower than Dimension() are counted as well. */
bool HasGeometry(Geometry::Type geom) const
{ return mesh_geoms & (1 << geom); }
/** @brief Return the number of geometries of the given dimension present in
the mesh. */
/** For a parallel mesh only the local geometries are counted. */
int GetNumGeometries(int dim) const;
/// Return all element geometries of the given dimension present in the mesh.
/** For a parallel mesh only the local geometries are returned.
The returned geometries are sorted. */
void GetGeometries(int dim, Array<Geometry::Type> &el_geoms) const;
/// Returns the minimum and maximum corners of the mesh bounding box.
/** For high-order meshes, the geometry is first refined @a ref times. */
void GetBoundingBox(Vector &min, Vector &max, int ref = 2);
void GetCharacteristics(real_t &h_min, real_t &h_max,
real_t &kappa_min, real_t &kappa_max,
Vector *Vh = NULL, Vector *Vk = NULL);
/// @}
/// @name Information concerning numbers of mesh entities
/// @{
/** @brief Returns number of vertices. Vertices are only at the corners of
elements, where you would expect them in the lowest-order mesh. */
inline int GetNV() const { return NumOfVertices; }
/// Returns number of elements.
inline int GetNE() const { return NumOfElements; }
/// Returns number of boundary elements.
inline int GetNBE() const { return NumOfBdrElements; }
/// Return the number of edges.
inline int GetNEdges() const { return NumOfEdges; }
/// Return the number of faces in a 3D mesh.
inline int GetNFaces() const { return NumOfFaces; }
/// Return the number of faces (3D), edges (2D) or vertices (1D).
int GetNumFaces() const;
/** @brief Return the number of faces (3D), edges (2D) or vertices (1D)
including ghost faces. */
int GetNumFacesWithGhost() const;
/** @brief Returns the number of faces according to the requested type, does
not count master nonconforming faces.
If type==Boundary returns only the number of true boundary faces
contrary to GetNBE() that returns all "boundary" elements which may
include actual interior faces.
Similarly, if type==Interior, only the true interior faces are counted
excluding all master nonconforming faces. */
virtual int GetNFbyType(FaceType type) const;
/// Return the total (global) number of elements.
long long GetGlobalNE() const { return ReduceInt(NumOfElements); }
/// @}
/// @name Access to individual mesh entities
/// @{
/// @brief Return pointer to vertex i's coordinates.
/// @warning For high-order meshes (when #Nodes != NULL) vertices may not be
/// updated and should not be used!
const real_t *GetVertex(int i) const { return vertices[i](); }
/// @brief Return pointer to vertex i's coordinates.
///
/// @warning For high-order meshes (when Nodes != NULL) vertices may not
/// being updated and should not be used!
///
/// @note The pointer returned by this function can be used to
/// alter vertex locations but the pointer itself should not be
/// changed by the caller.
real_t *GetVertex(int i) { return vertices[i](); }
/// @brief Return pointer to the i'th element object
///
/// The index @a i should be in the range [0, Mesh::GetNE())
///
/// In parallel, @a i is the local element index which is in the
/// same range mentioned above.
const Element *GetElement(int i) const { return elements[i]; }
/// @brief Return pointer to the i'th element object
///
/// @note Provides read/write access to the i'th element object so
/// that element attributes or connectivity can be adjusted. However,
/// the Element object itself should not be deleted by the caller.
Element *GetElement(int i) { return elements[i]; }
/// @brief Return pointer to the i'th boundary element object
///
/// The index @a i should be in the range [0, Mesh::GetNBE())
///
/// In parallel, @a i is the local boundary element index which is
/// in the same range mentioned above.
const Element *GetBdrElement(int i) const { return boundary[i]; }
/// @brief Return pointer to the i'th boundary element object
///
/// @note Provides read/write access to the i'th boundary element object so
/// that boundary attributes or connectivity can be adjusted. However,
/// the Element object itself should not be deleted by the caller.
Element *GetBdrElement(int i) { return boundary[i]; }
/// @brief Return pointer to the i'th face element object
///
/// The index @a i should be in the range [0, Mesh::GetNFaces())
const Element *GetFace(int i) const { return faces[i]; }
/// @}
/// @name Access to groups of mesh entities
/// @{
const Element* const *GetElementsArray() const
{ return elements.GetData(); }
void GetElementData(int geom, Array<int> &elem_vtx, Array<int> &attr) const
{ GetElementData(elements, geom, elem_vtx, attr); }
void GetBdrElementData(int geom, Array<int> &bdr_elem_vtx,
Array<int> &bdr_attr) const
{ GetElementData(boundary, geom, bdr_elem_vtx, bdr_attr); }
/// @}
/// @name Access information concerning individual mesh entites
/// @{
/// Return the attribute of element i.
int GetAttribute(int i) const { return elements[i]->GetAttribute(); }
/// Set the attribute of element i.
void SetAttribute(int i, int attr) { elements[i]->SetAttribute(attr); }
/// Return the attribute of boundary element i.
int GetBdrAttribute(int i) const { return boundary[i]->GetAttribute(); }
/// Set the attribute of boundary element i.
void SetBdrAttribute(int i, int attr) { boundary[i]->SetAttribute(attr); }
/// Return the attribute of patch i, for a NURBS mesh.
int GetPatchAttribute(int i) const;
/// Set the attribute of patch i, for a NURBS mesh.
void SetPatchAttribute(int i, int attr);
/// Return the attribute of patch boundary element i, for a NURBS mesh.
int GetPatchBdrAttribute(int i) const;
/// Set the attribute of patch boundary element i, for a NURBS mesh.
void SetPatchBdrAttribute(int i, int attr);
/// Returns the type of element i.
Element::Type GetElementType(int i) const;
/// Returns the type of boundary element i.
Element::Type GetBdrElementType(int i) const;
/// Deprecated in favor of Mesh::GetFaceGeometry
MFEM_DEPRECATED Geometry::Type GetFaceGeometryType(int Face) const
{ return GetFaceGeometry(Face); }
Element::Type GetFaceElementType(int Face) const;
/// Return the Geometry::Type associated with face @a i.
Geometry::Type GetFaceGeometry(int i) const;
Geometry::Type GetElementGeometry(int i) const
{
return elements[i]->GetGeometryType();
}
Geometry::Type GetBdrElementGeometry(int i) const
{
return boundary[i]->GetGeometryType();
}
/// Deprecated in favor of Mesh::GetFaceGeometry
MFEM_DEPRECATED Geometry::Type GetFaceBaseGeometry(int i) const
{ return GetFaceGeometry(i); }
Geometry::Type GetElementBaseGeometry(int i) const
{ return GetElementGeometry(i); }
Geometry::Type GetBdrElementBaseGeometry(int i) const
{ return GetBdrElementGeometry(i); }
/// Return true if the given face is interior. @sa FaceIsTrueInterior().
bool FaceIsInterior(int FaceNo) const
{
return (faces_info[FaceNo].Elem2No >= 0);
}
/** @brief Get the size of the i-th element relative to the perfect
reference element. */
real_t GetElementSize(int i, int type = 0);
real_t GetElementSize(int i, const Vector &dir);
real_t GetElementSize(ElementTransformation *T, int type = 0) const;
real_t GetElementVolume(int i);
void GetElementCenter(int i, Vector &center);
/** Compute the Jacobian of the transformation from the perfect
reference element at the given integration point (defaults to the
center of the element if no integration point is specified) */
void GetElementJacobian(int i, DenseMatrix &J,
const IntegrationPoint *ip = NULL);
/// @}
/// List of mesh geometries stored as Array<Geometry::Type>.
class GeometryList : public Array<Geometry::Type>
{
protected:
Geometry::Type geom_buf[Geometry::NumGeom];
public:
/// Construct a GeometryList of all element geometries in @a mesh.
GeometryList(const Mesh &mesh)
: Array<Geometry::Type>(geom_buf, Geometry::NumGeom)
{ mesh.GetGeometries(mesh.Dimension(), *this); }
/** @brief Construct a GeometryList of all geometries of dimension @a dim
in @a mesh. */
GeometryList(const Mesh &mesh, int dim)
: Array<Geometry::Type>(geom_buf, Geometry::NumGeom)
{ mesh.GetGeometries(dim, *this); }
};
/// @name Access connectivity for individual mesh entites
/// @{
/// Returns the indices of the vertices of element i.
void GetElementVertices(int i, Array<int> &v) const
{ elements[i]->GetVertices(v); }
/// Returns the indices of the vertices of boundary element i.
void GetBdrElementVertices(int i, Array<int> &v) const
{ boundary[i]->GetVertices(v); }
/// Return the indices and the orientations of all edges of element i.
void GetElementEdges(int i, Array<int> &edges, Array<int> &cor) const;
/// Return the indices and the orientations of all edges of bdr element i.
void GetBdrElementEdges(int i, Array<int> &edges, Array<int> &cor) const;
/** Return the indices and the orientations of all edges of face i.
Works for both 2D (face=edge) and 3D faces. */
void GetFaceEdges(int i, Array<int> &edges, Array<int> &o) const;
/// Returns the indices of the vertices of face i.
void GetFaceVertices(int i, Array<int> &vert) const
{
if (Dim == 1)
{
vert.SetSize(1); vert[0] = i;
}
else
{
faces[i]->GetVertices(vert);
}
}
/// Returns the indices of the vertices of edge i.
void GetEdgeVertices(int i, Array<int> &vert) const;
/// Return the indices and the orientations of all faces of element i.
void GetElementFaces(int i, Array<int> &faces, Array<int> &ori) const;
/** @brief Returns the sorted, unique indices of elements sharing a face with
element @a elem, including @a elem. */
Array<int> FindFaceNeighbors(const int elem) const;
/** Return the index and the orientation of the vertex of bdr element i. (1D)
Return the index and the orientation of the edge of bdr element i. (2D)
Return the index and the orientation of the face of bdr element i. (3D)
In 2D, the returned edge orientation is 0 or 1, not +/-1 as returned by
GetElementEdges/GetBdrElementEdges. */
void GetBdrElementFace(int i, int *f, int *o) const;
/** @brief For the given boundary element, bdr_el, return its adjacent
element and its info, i.e. 64*local_bdr_index+bdr_orientation.
The returned bdr_orientation is that of the boundary element relative to
the respective face element.
@sa GetBdrElementAdjacentElement2() */
void GetBdrElementAdjacentElement(int bdr_el, int &el, int &info) const;
/** @brief Deprecated.
For the given boundary element, bdr_el, return its adjacent element and
its info, i.e. 64*local_bdr_index+inverse_bdr_orientation.
The returned inverse_bdr_orientation is the inverse of the orientation of
the boundary element relative to the respective face element. In other
words this is the orientation of the face element relative to the
boundary element.
@warning This only differs from GetBdrElementAdjacentElement by returning
the face info with inverted orientation. It does @b not return
information corresponding to a second adjacent face. This function is
deprecated, use Geometry::GetInverseOrientation, Mesh::EncodeFaceInfo,
Mesh::DecodeFaceInfoOrientation, and Mesh::DecodeFaceInfoLocalIndex
instead.
@sa GetBdrElementAdjacentElement() */
MFEM_DEPRECATED
void GetBdrElementAdjacentElement2(int bdr_el, int &el, int &info) const;
/// @brief Return the local face (codimension-1) index for the given boundary
/// element index.
int GetBdrElementFaceIndex(int be_idx) const { return be_to_face[be_idx]; }
/// Deprecated in favor of GetBdrElementFaceIndex().
MFEM_DEPRECATED int GetBdrFace(int i) const { return GetBdrElementFaceIndex(i); }
/** Return the vertex index of boundary element i. (1D)
Return the edge index of boundary element i. (2D)
Return the face index of boundary element i. (3D)
Deprecated in favor of GetBdrElementFaceIndex(). */
MFEM_DEPRECATED int GetBdrElementEdgeIndex(int i) const { return GetBdrElementFaceIndex(i); }
/// @}
/// @name Access connectivity data
/// @{
/// @note The returned Table should be deleted by the caller
Table *GetVertexToElementTable();
/// Return the "face"-element Table. Here "face" refers to face (3D),
/// edge (2D), or vertex (1D).
///
/// @note The returned Table should be deleted by the caller.
Table *GetFaceToElementTable() const;
/// Returns the face-to-edge Table (3D)
///
/// @note The returned object should NOT be deleted by the caller.
Table *GetFaceEdgeTable() const;
/// Returns the edge-to-vertex Table (3D)
///
/// @note The returned object should NOT be deleted by the caller.
Table *GetEdgeVertexTable() const;
/** Return vertex to vertex table. The connections stored in the table
are from smaller to bigger vertex index, i.e. if i<j and (i, j) is
in the table, then (j, i) is not stored.
@note This data is not stored internally as a Table. The Table passed as
an argument is populated using the EdgeVertex Table (see GetEdgeVertexTable)
if available or the element connectivity.
*/
void GetVertexToVertexTable(DSTable &) const;
const Table &ElementToElementTable();
const Table &ElementToFaceTable() const;
const Table &ElementToEdgeTable() const;
Array<int> GetFaceToBdrElMap() const;
///@}
/// @brief Return FiniteElement for reference element of the specified type
///
/// @note The returned object is a pointer to a global object and should not
/// be deleted by the caller.
static FiniteElement *GetTransformationFEforElementType(Element::Type);
/** @brief For the vertex (1D), edge (2D), or face (3D) of a boundary element
with the orientation @a o, return the transformation of the boundary
element integration point @ ip to the face element. In 2D, the
the orientation is 0 or 1 as returned by GetBdrElementFace, not +/-1.
Supports both internal and external boundaries. */
static IntegrationPoint TransformBdrElementToFace(Geometry::Type geom, int o,
const IntegrationPoint &ip);
/// @anchor mfem_Mesh_elem_trans
/// @name Access the coordinate transformation for individual elements
///
/// See also the methods related to
/// @ref mfem_Mesh_geom_factors "Geometric Factors" for accessing
/// information cached at quadrature points.
/// @{
/// @brief Builds the transformation defining the i-th element in @a ElTr.
/// @a ElTr must be allocated in advance and will be owned by the caller.
///
/// @note The provided pointer must not be NULL. In the future this should be
/// changed to a reference parameter consistent with
/// GetFaceElementTransformations.
void GetElementTransformation(int i,
IsoparametricTransformation *ElTr) const;
/// @brief Returns a pointer to the transformation defining the i-th element.
///
/// @note The returned object is owned by the class and is shared, i.e.,
/// calling this function resets pointers obtained from previous calls.
/// Also, this pointer should NOT be deleted by the caller.
ElementTransformation *GetElementTransformation(int i);
/// @brief Builds the transformation defining the i-th element in @a ElTr
/// assuming position of the vertices/nodes are given by @a nodes.
/// @a ElTr must be allocated in advance and will be owned by the caller.
///
/// @note The provided pointer must not be NULL. In the future this should be
/// changed to a reference parameter consistent with
/// GetFaceElementTransformations.
void GetElementTransformation(int i, const Vector &nodes,
IsoparametricTransformation *ElTr) const;
/// @brief Returns a pointer to the transformation defining the i-th boundary
/// element.
///
/// @note The returned object is owned by the class and is shared, i.e.,
/// calling this function resets pointers obtained from previous calls.
/// Also, the returned object should NOT be deleted by the caller.
ElementTransformation *GetBdrElementTransformation(int i);
/// @brief Builds the transformation defining the i-th boundary element in
/// @a ElTr. @a ElTr must be allocated in advance and will be owned by the
/// caller.
///
/// @note The provided pointer must not be NULL. In the future this should be
/// changed to a reference parameter consistent with
/// GetFaceElementTransformations.
void GetBdrElementTransformation(int i,
IsoparametricTransformation *ElTr) const;
/// @brief Returns a pointer to the transformation defining the given face
/// element.
///
/// @note The returned object is owned by the class and is shared, i.e.,
/// calling this function resets pointers obtained from previous calls. Also,
/// the returned object should NOT be deleted by the caller.
ElementTransformation *GetFaceTransformation(int FaceNo);
/// @brief Builds the transformation defining the i-th face element in
/// @a FTr. @a FTr must be allocated in advance and will be owned by the
/// caller.
///
/// @note The provided pointer must not be NULL. In the future this should be
/// changed to a reference parameter consistent with
/// GetFaceElementTransformations.
void GetFaceTransformation(int i, IsoparametricTransformation *FTr) const;
/** @brief A helper method that constructs a transformation from the
reference space of a face to the reference space of an element. */
/** The local index of the face as a face in the element and its orientation
are given by the input parameter @a info, as @a info = 64*loc_face_idx +
loc_face_orientation. */
void GetLocalFaceTransformation(int face_type, int elem_type,
IsoparametricTransformation &Transf,
int info) const;
/// @brief Builds the transformation defining the i-th edge element in
/// @a EdTr. @a EdTr must be allocated in advance and will be owned by the
/// caller.
///
/// @note The provided pointer must not be NULL. In the future this should be
/// changed to a reference parameter consistent with
/// GetFaceElementTransformations.
void GetEdgeTransformation(int i, IsoparametricTransformation *EdTr) const;
/// @brief Returns a pointer to the transformation defining the given edge
/// element.
///
/// @note The returned object is owned by the class and is shared, i.e.,
/// calling this function resets pointers obtained from previous calls.
/// Also, the returned object should NOT be deleted by the caller.
ElementTransformation *GetEdgeTransformation(int EdgeNo);
/// Returns (a pointer to an object containing) the following data:
///
/// 1) Elem1No - the index of the first element that contains this face this
/// is the element that has the same outward unit normal vector as the
/// face;
///
/// 2) Elem2No - the index of the second element that contains this face this
/// element has outward unit normal vector as the face multiplied with -1;
///
/// 3) Elem1, Elem2 - pointers to the ElementTransformation's of the first
/// and the second element respectively;
///
/// 4) Face - pointer to the ElementTransformation of the face;
///
/// 5) Loc1, Loc2 - IntegrationPointTransformation's mapping the face
/// coordinate system to the element coordinate system (both in their
/// reference elements). Used to transform IntegrationPoints from face to
/// element. More formally, let:
/// TL1, TL2 be the transformations represented by Loc1, Loc2,
/// TE1, TE2 - the transformations represented by Elem1, Elem2,
/// TF - the transformation represented by Face, then
/// TF(x) = TE1(TL1(x)) = TE2(TL2(x)) for all x in the reference face.
///
/// 6) FaceGeom - the base geometry for the face.
///
/// The mask specifies which fields in the structure to return:
/// mask & 1 - Elem1, mask & 2 - Elem2
/// mask & 4 - Loc1, mask & 8 - Loc2, mask & 16 - Face.
/// These mask values are defined in the ConfigMasks enum type as part of the
/// FaceElementTransformations class in fem/eltrans.hpp.
///
/// @note The returned object is owned by the class and is shared, i.e.,
/// calling this function resets pointers obtained from previous calls.
/// Also, this pointer should NOT be deleted by the caller.
virtual FaceElementTransformations *
GetFaceElementTransformations(int FaceNo, int mask = 31);
/// @brief Variant of GetFaceElementTransformations using a user allocated
/// FaceElementTransformations object.
virtual void GetFaceElementTransformations(int FaceNo,
FaceElementTransformations &FElTr,
IsoparametricTransformation &ElTr1,
IsoparametricTransformation &ElTr2,
int mask = 31) const;
/// @brief See GetFaceElementTransformations().
///
/// @note The returned object is owned by the class and is shared, i.e.,
/// calling this function resets pointers obtained from previous calls.
/// Also, this pointer should NOT be deleted by the caller.
FaceElementTransformations *GetInteriorFaceTransformations(int FaceNo);
/// @brief Variant of GetInteriorFaceTransformations using a user allocated
/// FaceElementTransformations object.
void GetInteriorFaceTransformations(int FaceNo,
FaceElementTransformations &FElTr,
IsoparametricTransformation &ElTr1,
IsoparametricTransformation &ElTr2) const;
/// @brief Builds the transformation defining the given boundary face.
///
/// @note The returned object is owned by the class and is shared, i.e.,
/// calling this function resets pointers obtained from previous calls.
/// Also, this pointer should NOT be deleted by the caller.
FaceElementTransformations *GetBdrFaceTransformations(int BdrElemNo);
/// @brief Variant of GetBdrFaceTransformations using a user allocated
/// FaceElementTransformations object.
void GetBdrFaceTransformations(int BdrElemNo,
FaceElementTransformations &FElTr,
IsoparametricTransformation &ElTr1,
IsoparametricTransformation &ElTr2) const;
/// @}
/// @anchor mfem_Mesh_geom_factors
/// @name Access the coordinate transformation at quadrature points
///
/// See also methods related to
/// @ref mfem_Mesh_elem_trans "Element-wise coordinate transformation".
/// @{
/** @brief Return the mesh geometric factors corresponding to the given
integration rule.
The IntegrationRule used with GetGeometricFactors needs to remain valid
until the internally stored GeometricFactors objects are destroyed (by
calling Mesh::DeleteGeometricFactors(), Mesh::NodesUpdated(), or the Mesh
destructor).
If the device MemoryType parameter @a d_mt is specified, then the
returned object will use that type unless it was previously allocated
with a different type.
The returned pointer points to an internal object that may be invalidated
by mesh operations such as refinement, vertex/node movement, etc. Since
not all such modifications can be tracked by the Mesh class (e.g. when
using the pointer returned by GetNodes() to change the nodes) one needs
to account for such changes by calling the method NodesUpdated() which,
in particular, will call DeleteGeometricFactors(). */
const GeometricFactors* GetGeometricFactors(
const IntegrationRule& ir,
const int flags,
MemoryType d_mt = MemoryType::DEFAULT);
/** @brief Return the mesh geometric factors for the faces corresponding
to the given integration rule.
The IntegrationRule used with GetFaceGeometricFactors needs to remain
valid until the internally stored FaceGeometricFactors objects are
destroyed (by either calling Mesh::DeleteGeometricFactors(),
Mesh::NodesUpdated(), or the Mesh destructor).
If the device MemoryType parameter @a d_mt is specified, then the
returned object will use that type unless it was previously allocated
with a different type.
The returned pointer points to an internal object that may be invalidated
by mesh operations such as refinement, vertex/node movement, etc. Since
not all such modifications can be tracked by the Mesh class (e.g. when
using the pointer returned by GetNodes() to change the nodes) one needs
to account for such changes by calling the method NodesUpdated() which,
in particular, will call DeleteGeometricFactors(). */
const FaceGeometricFactors* GetFaceGeometricFactors(
const IntegrationRule& ir,
const int flags,
FaceType type,
MemoryType d_mt = MemoryType::DEFAULT);
/// Destroy all GeometricFactors stored by the Mesh.
/** This method can be used to force recomputation of the GeometricFactors,
for example, after the mesh nodes are modified externally.
@note In general, the preferred method for resetting the GeometricFactors
should be to call NodesUpdated(). */
void DeleteGeometricFactors();
/// @}
/** This enumerated type describes the three main face topologies:
- Boundary, for faces on the boundary of the computational domain,
- Conforming, for conforming faces interior to the computational domain,
- Nonconforming, for nonconforming faces interior to the computational
domain. */
enum class FaceTopology { Boundary,
Conforming,
Nonconforming,
NA
};
/** This enumerated type describes the location of the two elements sharing a
face, Local meaning that the element is local to the MPI rank, FaceNbr
meaning that the element is distributed on a different MPI rank, this
typically means that methods with FaceNbr should be used to access the
relevant information, e.g., ParFiniteElementSpace::GetFaceNbrElementVDofs.
*/
enum class ElementLocation { Local, FaceNbr, NA };
/** This enumerated type describes the topological relation of an element to
a face:
- Coincident meaning that the element's face is topologically equal to
the mesh face.
- Superset meaning that the element's face is topologically coarser than
the mesh face, i.e., the element's face contains the mesh face.
- Subset meaning that the element's face is topologically finer than the
mesh face, i.e., the element's face is contained in the mesh face.
Superset and Subset are only relevant for nonconforming faces.
Master nonconforming faces have a conforming element on one side, and a
fine element on the other side. Slave nonconforming faces have a
conforming element on one side, and a coarse element on the other side.
*/
enum class ElementConformity { Coincident, Superset, Subset, NA };
/** This enumerated type describes the corresponding FaceInfo internal
representation (encoded cases), c.f. FaceInfo's documentation:
Classification of a local (non-ghost) face based on its FaceInfo:
- Elem2No >= 0 --> local interior face; can be either:
- NCFace == -1 --> LocalConforming,
- NCFace >= 0 --> LocalSlaveNonconforming,
- Elem2No < 0 --> local "boundary" face; can be one of:
- NCFace == -1 --> conforming face; can be either:
- Elem2Inf < 0 --> Boundary,
- Elem2Inf >= 0 --> SharedConforming,
- NCFace >= 0 --> nonconforming face; can be one of:
- Elem2Inf < 0 --> MasterNonconforming (shared or not shared),
- Elem2Inf >= 0 --> SharedSlaveNonconforming.
Classification of a ghost (non-local) face based on its FaceInfo:
- Elem1No == -1 --> GhostMaster (includes other unused ghost faces),
- Elem1No >= 0 --> GhostSlave.
*/
enum class FaceInfoTag { Boundary,
LocalConforming,
LocalSlaveNonconforming,
SharedConforming,
SharedSlaveNonconforming,
MasterNonconforming,
GhostSlave,
GhostMaster
};
/** @brief This structure is used as a human readable output format that
deciphers the information contained in Mesh::FaceInfo when using the
Mesh::GetFaceInformation() method.
The element indices in this structure don't need further processing,
contrary to the ones obtained through Mesh::GetFacesElements and can
directly be used, e.g., Elem1 and Elem2 indices.
Likewise the orientations for Elem1 and Elem2 already take into account
special cases and can be used as is.
*/
struct FaceInformation
{
FaceTopology topology;
struct
{
ElementLocation location;
ElementConformity conformity;
int index;
int local_face_id;
int orientation;
} element[2];
FaceInfoTag tag;
int ncface;
const DenseMatrix* point_matrix;
/** @brief Return true if the face is a local interior face which is NOT
a master nonconforming face. */
bool IsLocal() const
{
return element[1].location == Mesh::ElementLocation::Local;
}
/** @brief Return true if the face is a shared interior face which is NOT
a master nonconforming face. */
bool IsShared() const
{
return element[1].location == Mesh::ElementLocation::FaceNbr;
}
/** @brief return true if the face is an interior face to the computation
domain, either a local or shared interior face (not a boundary face)
which is NOT a master nonconforming face.
*/
bool IsInterior() const
{
return topology == FaceTopology::Conforming ||
topology == FaceTopology::Nonconforming;
}
/** @brief Return true if the face is a boundary face. */
bool IsBoundary() const
{
return topology == FaceTopology::Boundary;
}
/// @brief Return true if the face is of the same type as @a type.
bool IsOfFaceType(FaceType type) const
{
switch (type)
{
case FaceType::Interior:
return IsInterior();
case FaceType::Boundary:
return IsBoundary();
default:
return false;
}
}
/// @brief Return true if the face is a conforming face.
bool IsConforming() const
{
return topology == FaceTopology::Conforming;
}
/// @brief Return true if the face is a nonconforming fine face.
bool IsNonconformingFine() const
{
return topology == FaceTopology::Nonconforming &&
(element[0].conformity == ElementConformity::Superset ||
element[1].conformity == ElementConformity::Superset);
}
/// @brief Return true if the face is a nonconforming coarse face.
/** Note that ghost nonconforming master faces cannot be clearly
identified as such with the currently available information, so this
method will return false for such faces. */
bool IsNonconformingCoarse() const
{
return topology == FaceTopology::Nonconforming &&
element[1].conformity == ElementConformity::Subset;
}
/// @brief cast operator from FaceInformation to FaceInfo.
operator Mesh::FaceInfo() const;
};
/// Given a "face info int", return the face orientation. @sa FaceInfo.
static int DecodeFaceInfoOrientation(int info) { return info%64; }
/// Given a "face info int", return the local face index. @sa FaceInfo.
static int DecodeFaceInfoLocalIndex(int info) { return info/64; }
/// @brief Given @a local_face_index and @a orientation, return the
/// corresponding encoded "face info int". @sa FaceInfo.
static int EncodeFaceInfo(int local_face_index, int orientation)
{ return orientation + local_face_index*64; }
/// @name More advanced entity information access methods
/// @{
/* Return point matrix of element i of dimension Dim X #v, where for every
vertex we give its coordinates in space of dimension Dim. */
void GetPointMatrix(int i, DenseMatrix &pointmat) const;
/* Return point matrix of boundary element i of dimension Dim X #v, where for
every vertex we give its coordinates in space of dimension Dim. */
void GetBdrPointMatrix(int i, DenseMatrix &pointmat) const;
/** This method aims to provide face information in a deciphered format, i.e.
Mesh::FaceInformation, compared to the raw encoded information returned
by Mesh::GetFaceElements() and Mesh::GetFaceInfos(). */
FaceInformation GetFaceInformation(int f) const;
void GetFaceElements (int Face, int *Elem1, int *Elem2) const;
void GetFaceInfos (int Face, int *Inf1, int *Inf2) const;
void GetFaceInfos (int Face, int *Inf1, int *Inf2, int *NCFace) const;
/// @}
/// @name Methods related to mesh partitioning
/// @{
/// @note The returned array should be deleted by the caller.
int *CartesianPartitioning(int nxyz[]);
/// @note The returned array should be deleted by the caller.
int *GeneratePartitioning(int nparts, int part_method = 1);
/// @todo This method needs a proper description
void CheckPartitioning(int *partitioning_);
/// @}
/// @anchor mfem_Mesh_trans
/// @name Methods related to accessing/altering mesh coordinates
///
/// See also @ref mfem_Mesh_gf_nodes "Coordinates as a GridFunction".
/// @{
// Vertices are only at the corners of elements, where you would expect them
// in the lowest-order mesh.
void MoveVertices(const Vector &displacements);
void GetVertices(Vector &vert_coord) const;
void SetVertices(const Vector &vert_coord);
/** @brief Set the internal Vertex array to point to the given @a vertices
array without assuming ownership of the pointer. */
/** If @a zerocopy is `true`, the vertices must be given as an array of 3
doubles per vertex. If @a zerocopy is `false` then the current Vertex
data is first copied to the @a vertices array. */
void ChangeVertexDataOwnership(real_t *vertices, int len_vertices,
bool zerocopy = false);
// Nodes are only active for higher order meshes, and share locations with
// the vertices, plus all the higher- order control points within the element
// and along the edges and on the faces.
void GetNode(int i, real_t *coord) const;
void SetNode(int i, const real_t *coord);
// Node operations for curved mesh.
// They call the corresponding '...Vertices' method if the
// mesh is not curved (i.e. Nodes == NULL).
void MoveNodes(const Vector &displacements);
void GetNodes(Vector &node_coord) const;
/// Updates the vertex/node locations. Invokes NodesUpdated().
void SetNodes(const Vector &node_coord);
void ScaleSubdomains (real_t sf);
void ScaleElements (real_t sf);
void Transform(void (*f)(const Vector&, Vector&));
void Transform(VectorCoefficient &deformation);
/** @brief This function should be called after the mesh node coordinates
have been updated externally, e.g. by modifying the internal nodal
GridFunction returned by GetNodes(). */
/** It deletes internal quantities derived from the node coordinates,
such as the (Face)GeometricFactors.
@note Unlike the similarly named protected method UpdateNodes() this
method does not modify the nodes. */
void NodesUpdated() { DeleteGeometricFactors(); }
/// @}
/// @anchor mfem_Mesh_gf_nodes
/// @name Methods related to nodal coordinates stored as a GridFunction
///
/// See also @ref mfem_Mesh_trans "Mesh Transformations".
/// @{
/// @brief Return a pointer to the internal node GridFunction (may be NULL).
///
/// If the mesh is straight-sided (low-order), it may not have a GridFunction
/// for the nodes, in which case this function returns NULL. To ensure that
/// the nodal GridFunction exists, first call EnsureNodes().
/// @sa SetCurvature().
///
/// @note The returned object should NOT be deleted by the caller.
GridFunction *GetNodes() { return Nodes; }
const GridFunction *GetNodes() const { return Nodes; }
/// Return the mesh nodes ownership flag.
bool OwnsNodes() const { return own_nodes; }
/// Set the mesh nodes ownership flag.
void SetNodesOwner(bool nodes_owner) { own_nodes = nodes_owner; }
/// Replace the internal node GridFunction with the given GridFunction.
/** Invokes NodesUpdated(). */
void NewNodes(GridFunction &nodes, bool make_owner = false);
/** @brief Swap the internal node GridFunction pointer and ownership flag
members with the given ones. */
/** Invokes NodesUpdated(). */
void SwapNodes(GridFunction *&nodes, int &own_nodes_);
/// Return the mesh nodes/vertices projected on the given GridFunction.
void GetNodes(GridFunction &nodes) const;
/** Replace the internal node GridFunction with a new GridFunction defined
on the given FiniteElementSpace. The new node coordinates are projected
(derived) from the current nodes/vertices. */
virtual void SetNodalFESpace(FiniteElementSpace *nfes);
/** Replace the internal node GridFunction with the given GridFunction. The
given GridFunction is updated with node coordinates projected (derived)
from the current nodes/vertices. */
void SetNodalGridFunction(GridFunction *nodes, bool make_owner = false);
/** Return the FiniteElementSpace on which the current mesh nodes are
defined or NULL if the mesh does not have nodes. */
const FiniteElementSpace *GetNodalFESpace() const;
/** @brief Make sure that the mesh has valid nodes, i.e. its geometry is
described by a vector finite element grid function (even if it is a
low-order mesh with straight edges).
@sa GetNodes(). */
void EnsureNodes();
/// Set the curvature of the mesh nodes using the given polynomial degree.
/** Creates a nodal GridFunction if one doesn't already exist.
@param[in] order Polynomial degree of the nodal FE space. If this
value is <= 0 then the method will remove the
nodal GridFunction and the Mesh will use the
vertices array instead; the other arguments are
ignored in this case.
@param[in] discont Whether to use a discontinuous or continuous
finite element space (continuous is default).
@param[in] space_dim The space dimension (optional).
@param[in] ordering The Ordering of the finite element space
(Ordering::byVDIM is the default). */
virtual void SetCurvature(int order, bool discont = false, int space_dim = -1,
int ordering = 1);
/// @}
/// @name Methods related to mesh refinement
/// @{
/// Refine all mesh elements.
/** @param[in] ref_algo %Refinement algorithm. Currently used only for pure
tetrahedral meshes. If set to zero (default), a tet mesh will be refined
using algorithm A, that produces elements with better quality compared to
algorithm B used when the parameter is non-zero.
For tetrahedral meshes, after using algorithm A, the mesh cannot be
refined locally using methods like GeneralRefinement() unless it is
re-finalized using Finalize() with the parameter @a refine set to true.
Note that calling Finalize() in this way will generally invalidate any
FiniteElementSpace%s and GridFunction%s defined on the mesh. */
void UniformRefinement(int ref_algo = 0);
/** @brief Refine NURBS mesh, with an optional refinement factor, generally
anisotropic.
@param[in] rf Optional refinement factor. If scalar, the factor is used
for all dimensions. If an array, factors can be specified
for each dimension. The factor multiplies the number of
elements in each dimension. Some factors can be 1.
@param[in] tol NURBS geometry deviation tolerance, cf. Algorithm A5.8 of
"The NURBS Book", 2nd ed, Piegl and Tiller. */
virtual void NURBSUniformRefinement(int rf = 2, real_t tol = 1.0e-12);
virtual void NURBSUniformRefinement(const Array<int> &rf, real_t tol=1.e-12);
/// Coarsening for a NURBS mesh, with an optional coarsening factor @a cf > 1
/// which divides the number of elements in each dimension.
void NURBSCoarsening(int cf = 2, real_t tol = 1.0e-12);
/** Refine selected mesh elements. Refinement type can be specified for each
element. The function can do conforming refinement of triangles and
tetrahedra and nonconforming refinement (i.e., with hanging-nodes) of
triangles, quadrilaterals and hexahedra. If 'nonconforming' = -1,
suitable refinement method is selected automatically (namely, conforming
refinement for triangles). Use nonconforming = 0/1 to force the method.
For nonconforming refinements, nc_limit optionally specifies the maximum
level of hanging nodes (unlimited by default). */
void GeneralRefinement(const Array<Refinement> &refinements,
int nonconforming = -1, int nc_limit = 0);
/** Simplified version of GeneralRefinement taking a simple list of elements
to refine, without refinement types. */
void GeneralRefinement(const Array<int> &el_to_refine,
int nonconforming = -1, int nc_limit = 0);
/// Refine each element with given probability. Uses GeneralRefinement.
void RandomRefinement(real_t prob, bool aniso = false,
int nonconforming = -1, int nc_limit = 0);
/// Refine elements sharing the specified vertex. Uses GeneralRefinement.
void RefineAtVertex(const Vertex& vert,
real_t eps = 0.0, int nonconforming = -1);
/** Refine element i if elem_error[i] > threshold, for all i.
Returns true if at least one element was refined, false otherwise. */
bool RefineByError(const Array<real_t> &elem_error, real_t threshold,
int nonconforming = -1, int nc_limit = 0);
/** Refine element i if elem_error(i) > threshold, for all i.
Returns true if at least one element was refined, false otherwise. */
bool RefineByError(const Vector &elem_error, real_t threshold,
int nonconforming = -1, int nc_limit = 0);
/** Derefine the mesh based on an error measure associated with each
element. A derefinement is performed if the sum of errors of its fine
elements is smaller than 'threshold'. If 'nc_limit' > 0, derefinements
that would increase the maximum level of hanging nodes of the mesh are
skipped. Returns true if the mesh changed, false otherwise. */
bool DerefineByError(Array<real_t> &elem_error, real_t threshold,
int nc_limit = 0, int op = 1);
/// Same as DerefineByError for an error vector.
bool DerefineByError(const Vector &elem_error, real_t threshold,
int nc_limit = 0, int op = 1);
/** Make sure that a quad/hex mesh is considered to be nonconforming (i.e.,
has an associated NCMesh object). Simplex meshes can be both conforming
(default) or nonconforming. */
void EnsureNCMesh(bool simplices_nonconforming = false);
bool Conforming() const { return ncmesh == NULL; }
bool Nonconforming() const { return ncmesh != NULL; }
/** Return fine element transformations following a mesh refinement.
Space uses this to construct a global interpolation matrix. */
const CoarseFineTransformations &GetRefinementTransforms() const;
/// Return type of last modification of the mesh.
Operation GetLastOperation() const { return last_operation; }
/** Return update counter. The counter starts at zero and is incremented
each time refinement, derefinement, or rebalancing method is called.
It is used for checking proper sequence of Space:: and GridFunction::
Update() calls. */
long GetSequence() const { return sequence; }
/// @brief Return the nodes update counter.
///
/// This counter starts at zero, and is incremented every time the geometric
/// factors must be recomputed (e.g. on calls to Mesh::Transform,
/// Mesh::NodesUpdated, etc.)
long GetNodesSequence() const { return nodes_sequence; }
/// @}
///@{ @name NURBS mesh refinement methods
/** Refine a NURBS mesh with the knots specified in the file named @a ref_file.
The file has the number of knot vectors on the first line. It is the same
number of knot vectors specified in the NURBS mesh in the section edges. Then
for each knot vector specified in the section edges (with the same ordering),
a line describes (in this order): 1) an integer giving the number of knots
inserted, 2) the knots inserted as a double. The advantage of this method
is that it is possible to specifically refine a coarse NURBS mesh without
changing the mesh file itself. Examples in miniapps/nurbs/meshes. */
void RefineNURBSFromFile(std::string ref_file);
/// For NURBS meshes, insert the new knots in @a kv, for each direction.
void KnotInsert(Array<KnotVector*> &kv);
/// For NURBS meshes, insert the knots in @a kv, for each direction.
void KnotInsert(Array<Vector*> &kv);
/// For NURBS meshes, remove the knots in @a kv, for each direction.
void KnotRemove(Array<Vector*> &kv);
/* For each knot vector:
new_degree = max(old_degree, min(old_degree + rel_degree, degree)). */
void DegreeElevate(int rel_degree, int degree = 16);
///@}
/// @name Print/Save/Export methods
/// @{
/// Print the mesh to the given stream using Netgen/Truegrid format.
virtual void PrintXG(std::ostream &os = mfem::out) const;
/// Print the mesh to the given stream using the default MFEM mesh format.
/// \see mfem::ofgzstream() for on-the-fly compression of ascii outputs. If
/// @a comments is non-empty, it will be printed after the first line of the
/// file, and each line should begin with '#'.
virtual void Print(std::ostream &os = mfem::out,
const std::string &comments = "") const
{ Printer(os, "", comments); }
/// Save the mesh to a file using Mesh::Print. The given @a precision will be
/// used for ASCII output.
virtual void Save(const std::string &fname, int precision=16) const;
/// Print the mesh to the given stream using the adios2 bp format
#ifdef MFEM_USE_ADIOS2
virtual void Print(adios2stream &os) const;
#endif
/// Print the mesh in VTK format (linear and quadratic meshes only).
/// \see mfem::ofgzstream() for on-the-fly compression of ascii outputs
void PrintVTK(std::ostream &os);
/** Print the mesh in VTK format. The parameter ref > 0 specifies an element
subdivision number (useful for high order fields and curved meshes).
If the optional field_data is set, we also add a FIELD section in the
beginning of the file with additional dataset information. */
/// \see mfem::ofgzstream() for on-the-fly compression of ascii outputs
void PrintVTK(std::ostream &os, int ref, int field_data=0);
/** Print the mesh in VTU format. The parameter ref > 0 specifies an element
subdivision number (useful for high order fields and curved meshes).
If @a bdr_elements is true, then output (only) the boundary elements,
otherwise output only the non-boundary elements. */
void PrintVTU(std::ostream &os,
int ref=1,
VTKFormat format=VTKFormat::ASCII,
bool high_order_output=false,
int compression_level=0,
bool bdr_elements=false);
/** Print the mesh in VTU format with file name fname. */
virtual void PrintVTU(std::string fname,
VTKFormat format=VTKFormat::ASCII,
bool high_order_output=false,
int compression_level=0,
bool bdr=false);
/** Print the boundary elements of the mesh in VTU format, and output the
boundary attributes as a data array (useful for boundary conditions). */
void PrintBdrVTU(std::string fname,
VTKFormat format=VTKFormat::ASCII,
bool high_order_output=false,
int compression_level=0);
/** @brief Prints the mesh with boundary elements given by the boundary of
the subdomains, so that the boundary of subdomain i has boundary
attribute i+1. */
/// \see mfem::ofgzstream() for on-the-fly compression of ascii outputs
void PrintWithPartitioning (int *partitioning,
std::ostream &os, int elem_attr = 0) const;
void PrintElementsWithPartitioning (int *partitioning,
std::ostream &os,
int interior_faces = 0);
/// Print set of disjoint surfaces:
/*!
* If Aface_face(i,j) != 0, print face j as a boundary
* element with attribute i+1.
*/
void PrintSurfaces(const Table &Aface_face, std::ostream &os) const;
/// Auxiliary method used by PrintCharacteristics().
/** It is also used in the `mesh-explorer` miniapp. */
static void PrintElementsByGeometry(int dim,
const Array<int> &num_elems_by_geom,
std::ostream &os);
/** @brief Compute and print mesh characteristics such as number of vertices,
number of elements, number of boundary elements, minimal and maximal
element sizes, minimal and maximal element aspect ratios, etc. */
/** If @a Vh or @a Vk are not NULL, return the element sizes and aspect
ratios for all elements in the given Vector%s. */
void PrintCharacteristics(Vector *Vh = NULL, Vector *Vk = NULL,
std::ostream &os = mfem::out);
/** @brief In serial, this method calls PrintCharacteristics(). In parallel,
additional information about the parallel decomposition is also printed.
*/
virtual void PrintInfo(std::ostream &os = mfem::out)
{
PrintCharacteristics(NULL, NULL, os);
}
#ifdef MFEM_DEBUG
/// Output an NCMesh-compatible debug dump.
void DebugDump(std::ostream &os) const;
#endif
/// @}
/// @name Miscellaneous or undocumented methods
/// @{
/// @brief Creates a mapping @a v2v from the vertex indices of the mesh such
/// that coincident vertices under the given @a translations are identified.
/** Each Vector in @a translations should be of size @a sdim (the spatial
dimension of the mesh). Two vertices are considered coincident if the
translated coordinates of one vertex are within the given tolerance (@a
tol, relative to the mesh diameter) of the coordinates of the other
vertex.
@warning This algorithm does not scale well with the number of boundary
vertices in the mesh, and may run slowly on very large meshes. */
std::vector<int> CreatePeriodicVertexMapping(
const std::vector<Vector> &translations, real_t tol = 1e-8) const;
/** @brief Find the ids of the elements that contain the given points, and
their corresponding reference coordinates.
The DenseMatrix @a point_mat describes the given points - one point for
each column; it should have SpaceDimension() rows.
The InverseElementTransformation object, @a inv_trans, is used to attempt
the element transformation inversion. If NULL pointer is given, the
method will use a default constructed InverseElementTransformation. Note
that the algorithms in the base class InverseElementTransformation can be
completely overwritten by deriving custom classes that override the
Transform() method.
If no element is found for the i-th point, elem_ids[i] is set to -1.
In the ParMesh implementation, the @a point_mat is expected to be the
same on all ranks. If the i-th point is found by multiple ranks, only one
of them will mark that point as found, i.e. set its elem_ids[i] to a
non-negative number; the other ranks will set their elem_ids[i] to -2 to
indicate that the point was found but assigned to another rank.
@returns The total number of points that were found.
@note This method is not 100 percent reliable, i.e. it is not guaranteed
to find a point, even if it lies inside a mesh element. */
virtual int FindPoints(DenseMatrix& point_mat, Array<int>& elem_ids,
Array<IntegrationPoint>& ips, bool warn = true,
InverseElementTransformation *inv_trans = NULL);
/** @brief Computes geometric parameters associated with a Jacobian matrix
in 2D/3D. These parameters are
(1) Area/Volume,
(2) Aspect-ratio (1 in 2D, and 2 non-dimensional and 2 dimensional
parameters in 3D. Dimensional parameters are used
for target construction in TMOP),
(3) skewness (1 in 2D and 3 in 3D), and finally
(4) orientation (1 in 2D and 3 in 3D).
*/
void GetGeometricParametersFromJacobian(const DenseMatrix &J,
real_t &volume,
Vector &aspr,
Vector &skew,
Vector &ori) const;
/// Utility function: sum integers from all processors (Allreduce).
virtual long long ReduceInt(int value) const { return value; }
/// @todo This method needs a proper description
void GetElementColoring(Array<int> &colors, int el0 = 0);
/// @todo This method needs a proper description
void MesquiteSmooth(const int mesquite_option = 0);
/// @todo This method needs a proper description
void CheckDisplacements(const Vector &displacements, real_t &tmax);
/// @}
};
/** Overload operator<< for std::ostream and Mesh; valid also for the derived
class ParMesh */
std::ostream &operator<<(std::ostream &os, const Mesh &mesh);
/// @brief Print function for Mesh::FaceInformation.
std::ostream& operator<<(std::ostream &os, const Mesh::FaceInformation& info);
/** @brief Class containing a minimal description of a part (a subset of the
elements) of a Mesh and its connectivity to other parts.
The main purpose of this class is to facilitate the partitioning of serial
meshes (in serial, i.e. on one processor) and save the parts in parallel
MFEM mesh format.
Another potential futrure purpose of this class could be to facilitate
exchange of MeshParts between MPI ranks for repartitioning purposes. It can
also potentially be used to implement parallel mesh I/O functions with
partitionings that have number of parts different from the number of MPI
tasks.
@note Parts of NURBS or non-conforming meshes cannot be fully described by
this class alone with its current data members. Such extensions may be added
in the future.
*/
class MeshPart
{
protected:
struct Entity { int geom; int num_verts; const int *verts; };
struct EntityHelper
{
int dim, num_entities;
int geom_offsets[Geometry::NumGeom+1];
typedef const Array<int> entity_to_vertex_type[Geometry::NumGeom];
entity_to_vertex_type &entity_to_vertex;
EntityHelper(int dim_,
const Array<int> (&entity_to_vertex_)[Geometry::NumGeom]);
Entity FindEntity(int bytype_entity_id);
};
public:
/// Reference space dimension of the elements
int dimension;
/// Dimension of the physical space into which the MeshPart is embedded.
int space_dimension;
/// Number of vertices
int num_vertices;
/// Number of elements with reference space dimension equal to 'dimension'.
int num_elements;
/** @brief Number of boundary elements with reference space dimension equal
to 'dimension'-1. */
int num_bdr_elements;
/**
Each 'entity_to_vertex[geom]' describes the entities of Geometry::Type
'geom' in terms of their vertices. The number of entities of type 'geom'
is:
num_entities[geom] = size('entity_to_vertex[geom]')/num_vertices[geom]
The number of all elements, 'num_elements', is:
'num_elements' = sum_{dim[geom]=='dimension'} num_entities[geom]
and the number of all boundary elements, 'num_bdr_elements' is:
'num_bdr_elements' = sum_{dim[geom]=='dimension'-1} num_entities[geom]
Note that 'entity_to_vertex' does NOT describe all "faces" in the mesh
part (i.e. all 'dimension'-1 entities) but only the boundary elements.
Also, note that lower dimesional entities ('dimension'-2 and lower) are
NOT described by the respective array, i.e. the array will be empty.
*/
Array<int> entity_to_vertex[Geometry::NumGeom];
/** @brief Store the refinement flags for tetraheral elements. If all tets
have zero refinement flags then this array is empty, i.e. has size 0. */
Array<int> tet_refine_flags;
/**
Terminology: "by-type" element/boundary ordering: ordered by
Geometry::Type and within each Geometry::Type 'geom' ordered as in
'entity_to_vertex[geom]'.
Optional re-ordering of the elements that will be used by (Par)Mesh
objects constructed from this MeshPart. This array maps "natural" element
ids (used by the Mesh/ParMesh objects) to "by-type" element ids (see
above):
"by-type" element id = element_map["natural" element id]
The size of the array is either 'num_elements' or 0 when no re-ordering is
needed (then "by-type" id == "natural" id).
*/
Array<int> element_map;
/// Optional re-ordering for the boundary elements, similar to 'element_map'.
Array<int> boundary_map;
/**
Element attributes. Ordered using the "natural" element ordering defined
by the array 'element_map'. The size of this array is 'num_elements'.
*/
Array<int> attributes;
/**
Boundary element attributes. Ordered using the "natural" boundary element
ordering defined by the array 'boundary_map'. The size of this array is
'num_bdr_elements'.
*/
Array<int> bdr_attributes;
/**
Optional vertex coordinates. The size of the array is either
size = 'space_dimension' * 'num_vertices'
or 0 when the vertex coordinates are not used, i.e. when the MeshPart uses
a nodal GridFunction to describe its location in physical space. This
array uses Ordering::byVDIM: "X0,Y0,Z0, X1,Y1,Z1, ...".
*/
Array<real_t> vertex_coordinates;
/**
Optional serial Mesh object constructed on demand using the method
GetMesh(). One use case for it is when one wants to construct FE spaces
and GridFunction%s on the MeshPart for saving or MPI communication.
*/
std::unique_ptr<Mesh> mesh;
/**
Nodal FE space defined on 'mesh' used by the GridFunction 'nodes'. Uses
the FE collection from the global nodal FE space.
*/
std::unique_ptr<FiniteElementSpace> nodal_fes;
/**
'nodes': pointer to a GridFunction describing the physical location of the
MeshPart. Used for describing high-order and periodic meshes. This
GridFunction is defined on the FE space 'nodal_fes' which, in turn, is
defined on the Mesh 'mesh'.
*/
std::unique_ptr<GridFunction> nodes;
/** @name Connectivity to other MeshPart objects */
///@{
/// Total number of MeshParts
int num_parts;
/** @brief Index of the part described by this MeshPart:
0 <= 'my_part_id' < 'num_parts' */
int my_part_id;
/**
A group G is a subset of the set { 0, 1, ..., 'num_parts'-1 } for which
there is a mesh entity E (of any dimension) in the global mesh such that
G is the set of the parts assigned (by the partitioning array) to the
elements adjacent to E. The MeshPart describes only the "neighbor" groups,
i.e. the groups that contain 'my_part_id'. The Table 'my_groups' defines
the "neighbor" groups in terms of their part ids. In other words, it maps
"neighbor" group ids to a (sorted) list of part ids. In particular, the
number of "neighbor" groups is given by 'my_groups.Size()'. The "local"
group { 'my_part_id' } has index 0 in 'my_groups'.
*/
Table my_groups;
/**
Shared entities for this MeshPart are mesh entities of all dimensions less
than 'dimension' that are generated by the elements of this MeshPart and
at least one other MeshPart.
The Table 'group_shared_entity_to_vertex[geom]' defines, for each group,
the shared entities of Geometry::Type 'geom'. Each row (corresponding to a
"neighbor" group, as defined by 'my_groups') in the Table defines the
shared entities in a way similar to the arrays 'entity_to_vertex[geom]'.
The "local" group (with index 0) does not have any shared entities, so the
0-th row in the Table is always empty.
IMPORTANT: the descriptions of the groups in this MeshPart must match
their descriptions in all neighboring MeshParts. This includes the
ordering of the shared entities within the group, as well as the vertex
ordering of each shared entity.
*/
Table group_shared_entity_to_vertex[Geometry::NumGeom];
///@}
/** @brief Write the MeshPart to a stream using the parallel format
"MFEM mesh v1.2". */
void Print(std::ostream &os) const;
/** @brief Construct a serial Mesh object from the MeshPart.
The nodes of 'mesh' are NOT initialized by this method, however, the
nodal FE space and nodal GridFunction can be created and then attached to
the 'mesh'. The Mesh is constructed only if 'mesh' is empty, otherwise
the method simply returns the object held by 'mesh'.
*/
Mesh &GetMesh();
};
/** @brief Class that allows serial meshes to be partitioned into MeshPart
objects, typically one MeshPart at a time, which can then be used to write
the local mesh in parallel MFEM mesh format.
Sample usage of this class: partition a serial mesh and save it in parallel
MFEM format:
\code
// The array 'partitioning' can be obtained e.g. from
// mesh->GeneratePartitioning():
void usage1(Mesh *mesh, int num_parts, int *partitioning)
{
MeshPartitioner partitioner(*mesh, num_parts, partitioning);
MeshPart mesh_part;
for (int i = 0; i < num_parts; i++)
{
partitioner.ExtractPart(i, mesh_part);
ofstream omesh(MakeParFilename("my-mesh.", i));
mesh_part.Print(omesh);
}
}
\endcode
This class can also be used to partition a mesh and GridFunction(s) and save
them in parallel:
\code
// The array 'partitioning' can be obtained e.g. from
// mesh->GeneratePartitioning():
void usage2(Mesh *mesh, int num_parts, int *partitioning,
GridFunction *gf)
{
MeshPartitioner partitioner(*mesh, num_parts, partitioning);
MeshPart mesh_part;
for (int i = 0; i < num_parts; i++)
{
partitioner.ExtractPart(i, mesh_part);
ofstream omesh(MakeParFilename("my-mesh.", i));
mesh_part.Print(omesh);
auto lfes = partitioner.ExtractFESpace(mesh_part, *gf->FESpace());
auto lgf = partitioner.ExtractGridFunction(mesh_part, *gf, *lfes);
ofstream ofield(MakeParFilename("my-field.", i));
lgf->Save(ofield);
}
}
\endcode
*/
class MeshPartitioner
{
protected:
Mesh &mesh;
Array<int> partitioning;
Table part_to_element;
Table part_to_boundary;
Table edge_to_element;
Table vertex_to_element;
public:
/** @brief Construct a MeshPartitioner.
@param[in] mesh_ Mesh to be partitioned into MeshPart%s.
@param[in] num_parts_ Number of parts to partition the mesh into.
@param[in] partitioning_ Partitioning array: for every element in the
mesh gives the partition it belongs to; if NULL,
partitioning will be generated internally by
calling Mesh::GeneratePartitioning().
@param[in] part_method Partitioning method to be used in the call to
Mesh::GeneratePartitioning() when the provided
input partitioning is NULL.
*/
MeshPartitioner(Mesh &mesh_, int num_parts_, int *partitioning_ = NULL,
int part_method = 1);
/** @brief Construct a MeshPart corresponding to the given @a part_id.
@param[in] part_id Partition index to extract; valid values are in
the range [0, num_parts).
@param[out] mesh_part Output MeshPart object; its contents is
overwritten, while potentially reusing existing
dynamic memory allocations.
*/
void ExtractPart(int part_id, MeshPart &mesh_part) const;
/** @brief Construct a local version of the given FiniteElementSpace
@a global_fespace corresponding to the given @a mesh_part.
@param[in,out] mesh_part MeshPart on which to construct the local
FiniteElementSpace; this object is
generally modified by this call since it
calls mesh_part.GetMesh() to ensure the
local mesh is constructed.
@param[in] global_fespace The global FiniteElementSpace that should
be restricted to the @a mesh_part.
@returns A FiniteElementSpace pointer stored in a unique_ptr. The
returned local FiniteElementSpace is built on the Mesh object
contained in @a mesh_part (MeshPart::mesh) and it reuses the
FiniteElementCollection of the @a global_fespace.
*/
std::unique_ptr<FiniteElementSpace>
ExtractFESpace(MeshPart &mesh_part,
const FiniteElementSpace &global_fespace) const;
/** @brief Construct a local version of the given GridFunction, @a global_gf,
corresponding to the given @a mesh_part. The respective data is copied
from @a global_gf to the returned local GridFunction.
@param[in] mesh_part MeshPart on which to construct the local
GridFunction.
@param[in] global_gf The global GridFunction that should be
restricted to the @a mesh_part.
@param[in,out] local_fespace The local FiniteElementSpace corresponding
to @a mesh_part, e.g. constructed by the
method ExtractFESpace().
@returns A GridFunction pointer stored in a unique_ptr. The returned
local GridFunction is initialized with data appropriately copied
from @a global_gf.
*/
std::unique_ptr<GridFunction>
ExtractGridFunction(const MeshPart &mesh_part,
const GridFunction &global_gf,
FiniteElementSpace &local_fespace) const;
};
/** @brief Structure for storing mesh geometric factors: coordinates, Jacobians,
and determinants of the Jacobians. */
/** Typically objects of this type are constructed and owned by objects of class
Mesh. See Mesh::GetGeometricFactors(). */
class GeometricFactors
{
private:
void Compute(const GridFunction &nodes,
MemoryType d_mt = MemoryType::DEFAULT);
public:
const Mesh *mesh;
const IntegrationRule *IntRule;
int computed_factors;
enum FactorFlags
{
COORDINATES = 1 << 0,
JACOBIANS = 1 << 1,
DETERMINANTS = 1 << 2,
};
GeometricFactors(const Mesh *mesh, const IntegrationRule &ir, int flags,
MemoryType d_mt = MemoryType::DEFAULT);
GeometricFactors(const GridFunction &nodes, const IntegrationRule &ir,
int flags,
MemoryType d_mt = MemoryType::DEFAULT);
/// Mapped (physical) coordinates of all quadrature points.
/** This array uses a column-major layout with dimensions (NQ x SDIM x NE)
where
- NQ = number of quadrature points per element,
- SDIM = space dimension of the mesh = mesh.SpaceDimension(), and
- NE = number of elements in the mesh. */
Vector X;
/// Jacobians of the element transformations at all quadrature points.
/** This array uses a column-major layout with dimensions (NQ x SDIM x DIM x
NE) where
- NQ = number of quadrature points per element,
- SDIM = space dimension of the mesh = mesh.SpaceDimension(),
- DIM = dimension of the mesh = mesh.Dimension(), and
- NE = number of elements in the mesh. */
Vector J;
/// Determinants of the Jacobians at all quadrature points.
/** This array uses a column-major layout with dimensions (NQ x NE) where
- NQ = number of quadrature points per element, and
- NE = number of elements in the mesh. */
Vector detJ;
};
/** @brief Structure for storing face geometric factors: coordinates, Jacobians,
determinants of the Jacobians, and normal vectors. */
/** Typically objects of this type are constructed and owned by objects of class
Mesh. See Mesh::GetFaceGeometricFactors(). */
class FaceGeometricFactors
{
public:
const Mesh *mesh;
const IntegrationRule *IntRule;
int computed_factors;
FaceType type;
enum FactorFlags
{
COORDINATES = 1 << 0,
JACOBIANS = 1 << 1,
DETERMINANTS = 1 << 2,
NORMALS = 1 << 3,
};
FaceGeometricFactors(const Mesh *mesh, const IntegrationRule &ir, int flags,
FaceType type, MemoryType d_mt = MemoryType::DEFAULT);
/// Mapped (physical) coordinates of all quadrature points.
/** This array uses a column-major layout with dimensions (NQ x SDIM x NF)
where
- NQ = number of quadrature points per face,
- SDIM = space dimension of the mesh = mesh.SpaceDimension(), and
- NF = number of faces in the mesh. */
Vector X;
/// Jacobians of the element transformations at all quadrature points.
/** This array uses a column-major layout with dimensions (NQ x SDIM x DIM x
NF) where
- NQ = number of quadrature points per face,
- SDIM = space dimension of the mesh = mesh.SpaceDimension(),
- DIM = dimension of the mesh = mesh.Dimension(), and
- NF = number of faces in the mesh. */
Vector J;
/// Determinants of the Jacobians at all quadrature points.
/** This array uses a column-major layout with dimensions (NQ x NF) where
- NQ = number of quadrature points per face, and
- NF = number of faces in the mesh. */
Vector detJ;
/// Normals at all quadrature points.
/** This array uses a column-major layout with dimensions (NQ x DIM x NF) where
- NQ = number of quadrature points per face,
- SDIM = space dimension of the mesh = mesh.SpaceDimension(), and
- NF = number of faces in the mesh. */
Vector normal;
};
/// Class used to extrude the nodes of a mesh
class NodeExtrudeCoefficient : public VectorCoefficient
{
private:
int n, layer;
real_t p[2], s;
Vector tip;
public:
NodeExtrudeCoefficient(const int dim, const int n_, const real_t s_);
void SetLayer(const int l) { layer = l; }
using VectorCoefficient::Eval;
virtual void Eval(Vector &V, ElementTransformation &T,
const IntegrationPoint &ip);
virtual ~NodeExtrudeCoefficient() { }
};
/// Extrude a 1D mesh
Mesh *Extrude1D(Mesh *mesh, const int ny, const real_t sy,
const bool closed = false);
/// Extrude a 2D mesh
Mesh *Extrude2D(Mesh *mesh, const int nz, const real_t sz);
// shift cyclically 3 integers left-to-right
inline void ShiftRight(int &a, int &b, int &c)
{
int t = a;
a = c; c = b; b = t;
}
}
#endif
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