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tethex.h
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tethex.h
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/*
* tethex - tetrahedra to hexahedra conversion
* Copyright (c) 2013 Mikhail Artemyev
* Report issues: github.com/martemyev/tethex/issues
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to
* deal in the Software without restriction, including without limitation the
* rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
* sell copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
* IN THE SOFTWARE.
*/
#ifndef TETHEX_TETHEX_H
#define TETHEX_TETHEX_H
#include <iostream>
#include <map>
#include <sstream>
#include <stdexcept>
#include <string>
#include <vector>
namespace tethex {
//-------------------------------------------------------
//
// d2s - convert data to string
//
//-------------------------------------------------------
template <typename T>
inline std::string d2s(T data)
{
std::ostringstream o;
if (!(o << data))
throw std::runtime_error("Bad conversion of data to string!");
return o.str();
}
//-------------------------------------------------------
//
// expect and require
// (the idea was firstly discovered in deal.II sources,
// so thanks to its authors for that)
//
//-------------------------------------------------------
#if DEBUG
#define expect(condition, message) \
if (!(condition)) \
requirement_fails(__FILE__, \
__LINE__, \
message)
#else
// in release (or release-like) versions
// nothing happens
#define expect(condition, message) { }
#endif // DEBUG
#define require(condition, message) \
if (!(condition)) \
requirement_fails(__FILE__, \
__LINE__, \
message)
/**
* Throw an informative exception,
* if requirement or expectation fails
*/
void requirement_fails(const char *file,
int line,
std::string message);
//-------------------------------------------------------
//
// Point
//
//-------------------------------------------------------
/**
* Point in 3-dimensional space.
* It's used for 2-dimensional triangles as well, and
* in this case one of the coordinates is 0 (usually it's z-coordinate).
*/
class Point
{
public:
/**
* The number of Cartesian coordinates, that describe the point.
* Here we always use 3 coordinates to describe a point.
*/
static const int n_coord = 3;
/**
* Default constructor.
* Coordinates are initialized by 0.
*/
Point();
/**
* Constructor with parameter.
* Coordinates are initialized by array of numbers.
* @param coordinates - array of point coordinates
*/
Point(const double coordinates[]);
/**
* Constructor with parameters.
* Coordinates are initialized by numbers.
* @param x_coord - x-coordinate of the point
* @param y_coord - y-coordinate of the point
* @param z_coord - z-coordinate of the point
*/
Point(double x_coord,
double y_coord = 0,
double z_coord = 0);
/**
* Copy constructor
*/
Point(const Point &p);
/**
* Copy assignment operator
*/
Point& operator =(const Point &p);
/**
* Get the coordinate of the point
* @param number - the serial number of coordinate [0, n_coord)
*/
double get_coord(int number) const;
/**
* Set the value of specific coordinate
* @param number - the number of coordinate that we want to set
* @param value - new value of coordinate
*/
void set_coord(int number, double value);
private:
/**
* Cartesian coordinates of the point
*/
double coord[n_coord];
};
//-------------------------------------------------------
//
// MeshElement
//
//-------------------------------------------------------
/**
* This class implements the most part of functionality of
* all elements of mesh: triangles, tetrahedra, quadrangles, hexahedra, etc.
* All these elements are declared as pointers to base (this) class.
* It's not an abstract class, because it has no pure virtual functions,
* but you can't create objects of this class, because its constructor is protected.
*/
class MeshElement
{
public:
/**
* Destructor
*/
virtual ~MeshElement();
/**
* Get the number of vertices
*/
int get_n_vertices() const;
/**
* Get the number of edges
*/
int get_n_edges() const;
/**
* Get the number of faces
*/
int get_n_faces() const;
/**
* Get type of the element that is used in Gmsh
*/
int get_gmsh_el_type() const;
/**
* Get the material ID of the element.
* It's a number that describes the physical domain
* to which the element belongs.
*/
int get_material_id() const;
/**
* Get the number of vertex describing the element
* @param number - local number of vertex [0, n_vertices)
* @return global number of vertex (among other mesh vertices)
*/
int get_vertex(int number) const;
/**
* Get the number of edge describing the element
* @param number - local number of edge [0, n_edges)
* @return global number of edge (among other mesh edges)
*/
int get_edge(int number) const;
/**
* Get the number of face describing the element
* @param number - local number of face [0, n_faces)
* @return global number of face (among other mesh faces)
*/
int get_face(int number) const;
/**
* Set the number of vertex
* @param local_number - the number of vertex inside the element [0, n_vertices)
* @param global_number - the number of vertex among other vertices of the mesh
*/
void set_vertex(int local_number, int global_number);
/**
* Set the number of edge
* @param local_number - the number of edge inside the element [0, n_edges)
* @param global_number - the number of edge among other edges of the mesh
*/
void set_edge(int local_number, int global_number);
/**
* Set the number of face
* @param local_number - the number of face inside the element [0, n_faces)
* @param global_number - the number of face among other faces of the mesh
*/
void set_face(int local_number, int global_number);
/**
* Set all faces once at time
* @param face_numbers - the numbers of all cell faces
*/
void set_faces(const std::vector<int> &face_numbers);
/**
* Check - whether the element contains the vertex or not
* @param vertex - the number of vertex that we want to check
*/
bool contains(const int vertex) const;
protected:
/**
* The number of vertices describing the element.
* It must be defined in each derived class,
* because it's 0 by default.
*/
int n_vertices;
/**
* Vertices (i.e. their global numbers) describing the element
*/
std::vector<int> vertices;
/**
* The number of edges describing the element.
* It must be defined in each derived class,
* because it's 0 by default.
*/
int n_edges;
/**
* Edges (i.e. their global numbers) describing the element
* It's not always used.
*/
std::vector<int> edges;
/**
* The number of faces describing the element.
* It must be defined in each derived class,
* because it's 0 by default.
*/
int n_faces;
/**
* Faces (i.e. their global numbers) describing the element
* It's not always used.
*/
std::vector<int> faces;
/**
* ID of the physical domain where the element takes place.
* It's necessary to distinguish media with different physical properties.
*/
int material_id;
/**
* Type of the element (its number actually) like in Gmsh.
* It must be defined in every derived class.
* It's 0 by default.
*/
int gmsh_el_type;
/**
* Constructor is protected to prevent creating MeshElement objects directly
* @param n_ver - number of vertices
* @param n_edg - number of edges
* @param n_fac - number of faces
* @param el_type - type of the element in Gmsh
*/
MeshElement(int n_ver = 0,
int n_edg = 0,
int n_fac = 0,
int el_type = 0);
/**
* Copy constructor
*/
MeshElement(const MeshElement &elem);
/**
* Copy assignment operator
*/
MeshElement& operator =(const MeshElement &elem);
};
//-------------------------------------------------------
//
// PhysPoint (physical entity)
//
//-------------------------------------------------------
/**
* PhysPoint keep 2 numbers - the number of the vertex associated with the point,
* and the number of physical domain
* where this point takes place (material identificator - in other words).
*/
class PhysPoint : public MeshElement
{
public:
/**
* Point is a vertex itself
*/
static const int n_vertices = 1;
/**
* It's 0-dimensional shape, and it's a boundary for edge
*/
static const int n_edges = 0;
/**
* It has no faces
*/
static const int n_faces = 0;
/**
* In Gmsh physical point is defined by number 15
*/
static const int gmsh_el_type = 15;
/**
* Constructor
*/
PhysPoint();
/**
* Constructor with parameters
* @param ver - the list of vertices
* @param mat_id - the material ID
*/
PhysPoint(const std::vector<int> &ver,
int mat_id = 0);
/**
* Constructor with parameters
* @param ver - a vertex
* @param mat_id - material ID
*/
PhysPoint(const int ver,
int mat_id = 0);
};
//-------------------------------------------------------
//
// Line
//
//-------------------------------------------------------
/**
* Line keeps 3 numbers - the number of beginning vertex,
* the number of the ending one, and a number of physical domain
* where this line takes place (material identificator - in other words).
* Line is not oriented.
*/
class Line : public MeshElement
{
public:
/**
* There are 2 vertices to describe a line
*/
static const int n_vertices = 2;
/**
* Line is edge itself, so the number of edges is 1
*/
static const int n_edges = 1;
/**
* It's 1D shape, so there is no faces here
*/
static const int n_faces = 0;
/**
* In Gmsh line (physical line) is defined by number 1
*/
static const int gmsh_el_type = 1;
/**
* Constructor
*/
Line();
/**
* Constructor with parameters
* @param ver - the list of vertices
* @param mat_id - the material ID
*/
Line(const std::vector<int> &ver,
const int mat_id = 0);
/**
* Constructor with parameters
* @param v1 - one vertex
* @param v2 - another vertex
* @param mat_id - material ID
*/
Line(int v1,
int v2,
int mat_id = 0);
/**
* Find common vertex between two lines
* @param line - second line for seeking common vertex
*/
int common_vertex(const Line& line) const;
/**
* Get another vertex (different from that we have)
* @param vertex - we have the number of one vertex (this one),
* and we want to find the number of another vertex
*/
int another_vertex(int vertex) const;
};
//-------------------------------------------------------
//
// Triangle
//
//-------------------------------------------------------
/**
* Triangle - 2-dimensional simplex.
* The simplest shape in 2D.
* It's an element of mesh,
* therefore it inherits the most part of
* functionality from MeshElement class.
*/
class Triangle : public MeshElement
{
public:
/**
* The number of vertices of triangle
*/
static const int n_vertices = 3;
/**
* The number of edges of triangle
*/
static const int n_edges = 3;
/**
* Triangle is 2D shape,
* so it's a face itself (for tetrahedron)
*/
static const int n_faces = 1;
/**
* In Gmsh triangle is defined by number 2
*/
static const int gmsh_el_type = 2;
/**
* Default constructor
*/
Triangle();
/**
* Constructor with parameters
* @param ver - triangle vertices
* @param mat_id - material ID
*/
Triangle(const std::vector<int> &ver,
int mat_id = 0);
/**
* Constructor with parameters
* @param v1 - first vertex
* @param v2 - second vertex
* @param v3 - third vertex
* @param mat_id - material ID
*/
Triangle(int v1,
int v2,
int v3,
int mat_id = 0);
};
//-------------------------------------------------------
//
// Tetrahedron
//
//-------------------------------------------------------
/**
* Tetrahedron - 3-dimensional simplex.
* The simplest shape in 3D.
* It's an element of mesh,
* therefore it inherits the most part of
* functionality from MeshElement class.
*/
class Tetrahedron : public MeshElement
{
public:
/**
* The number of vertices of tetrahedron
*/
static const int n_vertices = 4;
/**
* The number of edges of tetrahedron
*/
static const int n_edges = 6;
/**
* The number of faces of tetrahedron
*/
static const int n_faces = 4;
/**
* In Gmsh triangle is defined by number 2
*/
static const int gmsh_el_type = 4;
/**
* Default constructor.
*/
Tetrahedron();
/**
* Constructor with parameters
* @param ver - triangle vertices
* @param mat_id - material ID
*/
Tetrahedron(const std::vector<int> &ver,
int mat_id = 0);
/**
* Constructor with parameters
* @param v1 - first vertex
* @param v2 - second vertex
* @param v3 - third vertex
* @param v4 - fourth vertex
* @param mat_id - material ID
*/
Tetrahedron(int v1,
int v2,
int v3,
int v4,
int mat_id = 0);
};
//-------------------------------------------------------
//
// Quadrangle
//
//-------------------------------------------------------
/**
* Quadrangle - 2-dimensional shape with 4 straight edges.
* It's an element of mesh,
* therefore it inherits the most part of
* functionality from MeshElement class.
*/
class Quadrangle : public MeshElement
{
public:
/**
* The number of vertices of quadrangle
*/
static const int n_vertices = 4;
/**
* The number of edges of quadrangle
*/
static const int n_edges = 4;
/**
* Quadrangle is 2D shape,
* so it's a face itself (for hexahedron)
*/
static const int n_faces = 1;
/**
* In Gmsh quadrangle is defined by number 3
*/
static const int gmsh_el_type = 3;
/**
* Default constructor.
*/
Quadrangle();
/**
* Constructor with parameters
* @param ver - quadrangle vertices
* @param mat_id - material ID
*/
Quadrangle(const std::vector<int> &ver,
int mat_id = 0);
/**
* Constructor with parameters
* @param v1 - first vertex
* @param v2 - second vertex
* @param v3 - third vertex
* @param v4 - fourth vertex
* @param mat_id - material ID
*/
Quadrangle(int v1,
int v2,
int v3,
int v4,
int mat_id = 0);
};
//-------------------------------------------------------
//
// Hexahedron
//
//-------------------------------------------------------
/**
* Hexahedron - 3-dimensional shape with 6 plane faces.
* It's an element of mesh,
* therefore it inherits the most part of
* functionality from MeshElement class.
*/
class Hexahedron : public MeshElement
{
public:
/**
* The number of vertices of hexahedron
*/
static const int n_vertices = 8;
/**
* The number of edges of hexahedron
*/
static const int n_edges = 12;
/**
* The number of faces of hexahedron
*/
static const int n_faces = 6;
/**
* In Gmsh hexahedron is defined by number 5
*/
static const int gmsh_el_type = 5;
/**
* Default constructor.
*/
Hexahedron();
/**
* Constructor with parameters
* @param ver - hexahedron vertices
* @param mat_id - material ID
*/
Hexahedron(const std::vector<int> &ver,
int mat_id = 0);
/**
* Constructor with parameters
* @param v1 - first vertex of hexahedron
* @param v8 - 8-th vertex of hexahedron
* @param mat_id - material ID
*/
Hexahedron(int v1,
int v2,
int v3,
int v4,
int v5,
int v6,
int v7,
int v8,
int mat_id = 0);
};
//-------------------------------------------------------
//
// IncidenceMatrix
//
//-------------------------------------------------------
/**
* Incidence matrix describes the relations
* (connections) between mesh nodes.
* It's used for edge numeration and for fast
* finding of edge number knowing 2 vertices,
* that define the edge.
* Because this matrix is symmetric
* we consider its lower triangle only.
*/
class IncidenceMatrix
{
public:
/**
* Constructor
* @param n_vertices - the number of all mesh vertices
* @param cells - the list of all mesh cells
*/
IncidenceMatrix(int n_vertices,
const std::vector<MeshElement*> &cells);
/**
* Destructor
*/
~IncidenceMatrix();
/**
* Find a serial number of the non zero element in the matrix.
* This number usually coincides with the number of edge.
* Since we keep only lower triangle of incidence matrix,
* row_number has to be bigger than col_number.
* @param row_number - the number of row where we seek (or one edge vertex)
* @param col_number - the number of column where we seek (or another edge vertex)
* @return Serial number of the non zero element in the matrix.
*/
int find(int row_number, int col_number) const;
/**
* Get the number of non zero elements in the matrix.
* Can be used to know the number of mesh edges.
*/
int get_n_nonzero() const;
private:
/**
* The dimension of the matrix
*/
int dim;
/**
* The number of nonzero elements of lower matrix triangle
*/
int n_non_zero;
/**
* The number of nonzero elements in each row of lower matrix triangle
*/
int *row;
/**
* The numbers of nonzero elements of lower matrix triangle
*/
int *col;
/**
* No copies
*/
IncidenceMatrix(const IncidenceMatrix&);
IncidenceMatrix& operator =(const IncidenceMatrix&);
};
//-------------------------------------------------------
//
// Mesh
//
//-------------------------------------------------------
/**
* Main class that stores all data during program execution.
*/
class Mesh
{
public:
/**
* Constructor - nothing special
*/
Mesh();
/**
* Destructor - to clean the memory
*/
~Mesh();
/**
* Read the mesh from file
* @param file - the name of the mesh file
*/
void read(const std::string &file);
/**
* Conversion from simplices to bricks.
* Specifically, in 2D - conversion from triangles to quadrangles,
* in 3D - conversion from tetrahedra to hexahedra.
*/
void convert();
/**
* Write the resulting brick mesh into the file
* @param file - the name of mesh file where we write the results of conversion
*/
void write(const std::string &file);
/**
* Get the number of vertices
*/
int get_n_vertices() const;
/**
* Get the number of physical points
*/
int get_n_points() const;
/**
* Get the number of lines (physical lines)
*/
int get_n_lines() const;
/**
* Get the number of edges
*/
int get_n_edges() const;
/**
* Get the number of triangles
*/
int get_n_triangles() const;
/**
* Get the number of faces
*/
int get_n_faces() const;
/**
* Get the number of tetrahedra
*/
int get_n_tetrahedra() const;
/**
* Get the number of tetrahedra
*/
int get_n_quadrangles() const;
/**
* Get the number of hexahedra
*/
int get_n_hexahedra() const;
/**
* Print short information
* about mesh into choosing stream.
*/
void info(std::ostream &out = std::cout) const;
/**
* Print some statistics (detailed information)
* about mesh into choosing stream.
*/
void statistics(std::ostream &out = std::cout) const;
/**
* Get the copy of vertex
* @param number - the number of vertex
*/
Point get_vertex(int number) const;
/**
* Get the physical point
* @param number - the number of point
*/
MeshElement& get_point(int number) const;
/**
* Get the mesh edge
* @param number - the number of edge
*/
MeshElement& get_edge(int number) const;
/**
* Get the physical line
* @param number - the number of line
*/
MeshElement& get_line(int number) const;
/**
* Get the mesh face
* @param number - the number of face
*/
MeshElement& get_face(int number) const;
/**
* Get the mesh triangle
* @param number - the number of triangle
*/
MeshElement& get_triangle(int number) const;
/**
* Get the mesh tetrahedron
* @param number - the number of tetrahedron
*/
MeshElement& get_tetrahedron(int number) const;
/**
* Get the mesh quadrangle
* @param number - the number of quadrangle
*/
MeshElement& get_quadrangle(int number) const;
/**
* Get the mesh hexahedron
* @param number - the number of hexahedron
*/
MeshElement& get_hexahedron(int number) const;
private:
/**
* Mesh vertices (nodes in terms of Gmsh)
*/
std::vector<Point> vertices;
/**
* Physical points.
*They are not treated - just copied into new mesh file.
*/
std::vector<MeshElement*> points;
/**
* Mesh lines - mean physical lines
*/
std::vector<MeshElement*> lines;
/**
* Mesh edges (oriented lines)
*/
std::vector<MeshElement*> edges;
/**
* Mesh faces
*/
std::vector<MeshElement*> faces;