libMesh::TetGenMeshInterface Class Reference

#include <mesh_tetgen_interface.h>

Public Member Functions
	TetGenMeshInterface (UnstructuredMesh &mesh)
	~TetGenMeshInterface ()
void	set_switches (const std::string &)
void	triangulate_pointset ()
void	pointset_convexhull ()
void	triangulate_conformingDelaunayMesh (double quality_constraint=0., double volume_constraint=0.)
void	triangulate_conformingDelaunayMesh_carvehole (const std::vector< Point > &holes, double quality_constraint=0., double volume_constraint=0.)

Protected Member Functions
void	fill_pointlist (TetGenWrapper &wrapper)
void	assign_nodes_to_elem (unsigned *node_labels, Elem *elem)
unsigned	check_hull_integrity ()
void	process_hull_integrity_result (unsigned result)
void	delete_2D_hull_elements ()

Protected Attributes
UnstructuredMesh &	_mesh
std::vector< unsigned >	_sequential_to_libmesh_node_map
MeshSerializer	_serializer
std::string	_switches

Detailed Description

Class TetGenMeshInterface provides an interface for tetrahedralization of meshes using the TetGen library. For information about TetGen cf. TetGen home page.

Author

Steffen Petersen

Date

2004

Author

John W. Peterson

Date

2011

Definition at line 54 of file mesh_tetgen_interface.h.

Constructor & Destructor Documentation

TetGenMeshInterface()

libMesh::TetGenMeshInterface::TetGenMeshInterface ( UnstructuredMesh &  mesh )

explicit

Constructor. Takes a reference to the mesh.

Definition at line 38 of file mesh_tetgen_interface.C.

                                                                 :
  _mesh(mesh),
  _serializer(_mesh),
  _switches("Q")
{
}

~TetGenMeshInterface()

libMesh::TetGenMeshInterface::~TetGenMeshInterface ( )

inline

Empty destructor.

Definition at line 67 of file mesh_tetgen_interface.h.

{}

Member Function Documentation

assign_nodes_to_elem()

void libMesh::TetGenMeshInterface::assign_nodes_to_elem ( unsigned *  node_labels, Elem *  elem  )

protected

Assigns the node IDs contained in the 'node_labels' array to 'elem'.

Definition at line 372 of file mesh_tetgen_interface.C.

References _mesh, _sequential_to_libmesh_node_map, libMesh::Elem::n_nodes(), libMesh::MeshBase::node_ptr(), and libMesh::Elem::set_node().

Referenced by pointset_convexhull(), triangulate_conformingDelaunayMesh_carvehole(), and triangulate_pointset().

{
  for (unsigned int j=0; j<elem->n_nodes(); ++j)
    {
      // Get the mapped node index to ask the Mesh for
      unsigned mapped_node_id = _sequential_to_libmesh_node_map[ node_labels[j] ];

      Node * current_node = this->_mesh.node_ptr( mapped_node_id );

      elem->set_node(j) = current_node;
    }
}

check_hull_integrity()

unsigned libMesh::TetGenMeshInterface::check_hull_integrity ( )

protected

This function checks the integrity of the current set of elements in the Mesh to see if they comprise a convex hull, that is:

• If they are all TRI3 elements
• They all have non-nullptr neighbors

Returns

• 0 if the mesh forms a valid convex hull
• 1 if a non-TRI3 element is found
• 2 if an element with a nullptr-neighbor is found

Definition at line 389 of file mesh_tetgen_interface.C.

References _mesh, libMesh::MeshBase::element_ptr_range(), libMesh::MeshBase::n_elem(), and libMesh::TRI3.

Referenced by triangulate_conformingDelaunayMesh_carvehole().

{
  // Check for easy return: if the Mesh is empty (i.e. if
  // somebody called triangulate_conformingDelaunayMesh on
  // a Mesh with no elements, then hull integrity check must
  // fail...
  if (_mesh.n_elem() == 0)
    return 3;

  for (auto & elem : this->_mesh.element_ptr_range())
    {
      // Check for proper element type
      if (elem->type() != TRI3)
        {
          //libmesh_error_msg("ERROR: Some of the elements in the original mesh were not TRI3!");
          return 1;
        }

      for (auto neigh : elem->neighbor_ptr_range())
        {
          if (neigh == nullptr)
            {
              // libmesh_error_msg("ERROR: Non-convex hull, cannot be tetrahedralized.");
              return 2;
            }
        }
    }

  // If we made it here, return success!
  return 0;
}

delete_2D_hull_elements()

void libMesh::TetGenMeshInterface::delete_2D_hull_elements ( )

protected

Delete original convex hull elements from the Mesh after performing a Delaunay tetrahedralization.

Definition at line 444 of file mesh_tetgen_interface.C.

References _mesh, libMesh::MeshBase::delete_elem(), libMesh::MeshBase::element_ptr_range(), libMesh::MeshBase::get_boundary_info(), libMesh::BoundaryInfo::regenerate_id_sets(), and libMesh::TRI3.

Referenced by triangulate_conformingDelaunayMesh_carvehole().

{
  for (auto & elem : this->_mesh.element_ptr_range())
    {
      // Check for proper element type. Yes, we legally delete elements while
      // iterating over them because no entries from the underlying container
      // are actually erased.
      if (elem->type() == TRI3)
        _mesh.delete_elem(elem);
    }

  // We just removed any boundary info associated with hull element
  // edges, so let's update the boundary id caches.
  this->_mesh.get_boundary_info().regenerate_id_sets();
}

fill_pointlist()

void libMesh::TetGenMeshInterface::fill_pointlist ( TetGenWrapper &  wrapper )

protected

This function copies nodes from the _mesh into TetGen's pointlist. Takes some pains to ensure that non-sequential node numberings (which can happen with e.g. DistributedMesh) are handled.

Definition at line 347 of file mesh_tetgen_interface.C.

References _mesh, _sequential_to_libmesh_node_map, libMesh::TetGenWrapper::allocate_pointlist(), libMesh::MeshBase::n_nodes(), libMesh::MeshBase::node_ptr_range(), and libMesh::TetGenWrapper::set_node().

Referenced by pointset_convexhull(), triangulate_conformingDelaunayMesh_carvehole(), and triangulate_pointset().

{
  // fill input structure with point set data:
  wrapper.allocate_pointlist( this->_mesh.n_nodes() );

  // Make enough space to store a mapping between the implied sequential
  // node numbering used in tetgen and libmesh's (possibly) non-sequential
  // numbering scheme.
  _sequential_to_libmesh_node_map.clear();
  _sequential_to_libmesh_node_map.resize( this->_mesh.n_nodes() );

  {
    unsigned index = 0;
    for (auto & node : this->_mesh.node_ptr_range())
      {
        _sequential_to_libmesh_node_map[index] = node->id();
        wrapper.set_node(index++, (*node)(0), (*node)(1), (*node)(2));
      }
  }
}

pointset_convexhull()

void libMesh::TetGenMeshInterface::pointset_convexhull

(

)

Method invokes TetGen library to compute a Delaunay tetrahedralization from the nodes point set. Stores only 2D hull surface elements.

Definition at line 113 of file mesh_tetgen_interface.C.

References _mesh, _switches, libMesh::MeshBase::add_elem(), assign_nodes_to_elem(), libMesh::MeshBase::delete_elem(), libMesh::MeshBase::element_ptr_range(), fill_pointlist(), libMesh::MeshBase::get_boundary_info(), libMesh::TetGenWrapper::get_numberoftrifaces(), libMesh::TetGenWrapper::get_triface_node(), libMesh::Elem::n_nodes(), libMesh::BoundaryInfo::regenerate_id_sets(), libMesh::TetGenWrapper::run_tetgen(), and libMesh::TetGenWrapper::set_switches().

{
  // class tetgen_wrapper allows library access on a basic level
  TetGenWrapper tetgen_wrapper;

  // Copy Mesh's node points into TetGen data structure
  this->fill_pointlist(tetgen_wrapper);

  // Run TetGen triangulation method:
  // Q = quiet, no terminal output
  // Note: if no switch is used, the input must be a list of 3D points
  // (.node file) and the Delaunay tetrahedralization of this point set
  // will be generated.  In this particular function, we are throwing
  // away the tetrahedra generated by TetGen, and keeping only the
  // convex hull...
  tetgen_wrapper.set_switches(_switches);
  tetgen_wrapper.run_tetgen();
  unsigned int num_elements   = tetgen_wrapper.get_numberoftrifaces();

  // Delete *all* old elements.  Yes, we legally delete elements while
  // iterating over them because no entries from the underlying container
  // are actually erased.
  for (auto & elem : this->_mesh.element_ptr_range())
    this->_mesh.delete_elem (elem);

  // We just removed any boundary info associated with element faces
  // or edges, so let's update the boundary id caches.
  this->_mesh.get_boundary_info().regenerate_id_sets();

  // Add the 2D elements which comprise the convex hull back to the mesh.
  // Vector that temporarily holds the node labels defining element.
  unsigned int node_labels[3];

  for (unsigned int i=0; i<num_elements; ++i)
    {
      Elem * elem = new Tri3;

      // Get node labels associated with this element
      for (unsigned int j=0; j<elem->n_nodes(); ++j)
        node_labels[j] = tetgen_wrapper.get_triface_node(i,j);

      this->assign_nodes_to_elem(node_labels, elem);

      // Finally, add this element to the mesh.
      this->_mesh.add_elem(elem);
    }
}

process_hull_integrity_result()

void libMesh::TetGenMeshInterface::process_hull_integrity_result ( unsigned  result )

protected

This function prints an informative message and crashes based on the output of the check_hull_integrity() function. It is a separate function so that you can check hull integrity without crashing if you desire.

Definition at line 425 of file mesh_tetgen_interface.C.

References libMesh::err.

Referenced by triangulate_conformingDelaunayMesh_carvehole().

{
  if (result != 0)
    {
      libMesh::err << "Error! Conforming Delaunay mesh tetrahedralization requires a convex hull." << std::endl;

      if (result==1)
        {
          libMesh::err << "Non-TRI3 elements were found in the input Mesh.  ";
          libMesh::err << "A constrained Delaunay triangulation requires a convex hull of TRI3 elements." << std::endl;
        }

      libmesh_error_msg("Consider calling TetGenMeshInterface::pointset_convexhull() followed by Mesh::find_neighbors() first.");
    }
}

set_switches()

void libMesh::TetGenMeshInterface::set_switches

(

const std::string &

switches

)

Method to set switches to tetgen, allowing for different behaviours

Definition at line 45 of file mesh_tetgen_interface.C.

References _switches.

{
  // set the tetgen switch manually:
  // p = tetrahedralizes a piecewise linear complex (see definition in user manual)
  // Q = quiet, no terminal output
  // q = specify a minimum radius/edge ratio
  // a = tetrahedron volume constraint
  // V = verbose output
  // for full list of options and their meaning: see the tetgen manual
  // (http://wias-berlin.de/software/tetgen/1.5/doc/manual/manual005.html)
  _switches = switches;
}

triangulate_conformingDelaunayMesh()

void libMesh::TetGenMeshInterface::triangulate_conformingDelaunayMesh	(	double	quality_constraint = 0.,
		double	volume_constraint = 0.
	)

Method invokes TetGen library to compute a Delaunay tetrahedralization from the nodes point set. Boundary constraints are taken from elements array.

Definition at line 165 of file mesh_tetgen_interface.C.

References triangulate_conformingDelaunayMesh_carvehole().

{
  // start triangulation method with empty holes list:
  std::vector<Point> noholes;
  triangulate_conformingDelaunayMesh_carvehole(noholes, quality_constraint, volume_constraint);
}

triangulate_conformingDelaunayMesh_carvehole()

void libMesh::TetGenMeshInterface::triangulate_conformingDelaunayMesh_carvehole	(	const std::vector< Point > &	holes,
		double	quality_constraint = 0.,
		double	volume_constraint = 0.
	)

Method invokes TetGen library to compute a Delaunay tetrahedralization from the nodes point set. Boundary constraints are taken from elements array. Include carve-out functionality.

Definition at line 175 of file mesh_tetgen_interface.C.

References _mesh, _sequential_to_libmesh_node_map, _switches, libMesh::MeshBase::add_elem(), libMesh::MeshBase::add_point(), libMesh::TetGenWrapper::allocate_facet_polygonlist(), libMesh::TetGenWrapper::allocate_facetlist(), libMesh::TetGenWrapper::allocate_polygon_vertexlist(), assign_nodes_to_elem(), libMesh::Utility::binary_find(), check_hull_integrity(), delete_2D_hull_elements(), libMesh::MeshBase::element_ptr_range(), fill_pointlist(), libMesh::TetGenWrapper::get_element_node(), libMesh::TetGenWrapper::get_numberofpoints(), libMesh::TetGenWrapper::get_numberoftetrahedra(), libMesh::TetGenWrapper::get_output_node(), libMesh::DofObject::id(), libMesh::MeshBase::n_elem(), libMesh::MeshBase::n_nodes(), libMesh::Elem::n_nodes(), process_hull_integrity_result(), libMesh::TetGenWrapper::run_tetgen(), libMesh::TetGenWrapper::set_hole(), libMesh::TetGenWrapper::set_switches(), and libMesh::TetGenWrapper::set_vertex().

Referenced by triangulate_conformingDelaunayMesh().

{
  // Before calling this function, the Mesh must contain a convex hull
  // of TRI3 elements which define the boundary.
  unsigned hull_integrity_check = check_hull_integrity();

  // Possibly die if hull integrity check failed
  this->process_hull_integrity_result(hull_integrity_check);

  // class tetgen_wrapper allows library access on a basic level
  TetGenWrapper tetgen_wrapper;

  // Copy Mesh's node points into TetGen data structure
  this->fill_pointlist(tetgen_wrapper);

  // >>> fill input structure "tetgenio" with facet data:
  int facet_num = this->_mesh.n_elem();

  // allocate memory in "tetgenio" structure:
  tetgen_wrapper.allocate_facetlist
    (facet_num, cast_int<int>(holes.size()));


  // Set up tetgen data structures with existing facet information
  // from the convex hull.
  {
    int insertnum = 0;
    for (auto & elem : this->_mesh.element_ptr_range())
      {
        tetgen_wrapper.allocate_facet_polygonlist(insertnum, 1);
        tetgen_wrapper.allocate_polygon_vertexlist(insertnum, 0, 3);

        for (unsigned int j=0; j<elem->n_nodes(); ++j)
          {
            // We need to get the sequential index of elem->node_ptr(j), but
            // it should already be stored in _sequential_to_libmesh_node_map...
            unsigned libmesh_node_id = elem->node_id(j);

            // The libmesh node IDs may not be sequential, but can we assume
            // they are at least in order???  We will do so here.
            std::vector<unsigned>::iterator node_iter =
              Utility::binary_find(_sequential_to_libmesh_node_map.begin(),
                                   _sequential_to_libmesh_node_map.end(),
                                   libmesh_node_id);

            // Check to see if not found: this could also indicate the sequential
            // node map is not sorted...
            if (node_iter == _sequential_to_libmesh_node_map.end())
              libmesh_error_msg("Global node " << libmesh_node_id << " not found in sequential node map!");

            int sequential_index = cast_int<int>
              (std::distance(_sequential_to_libmesh_node_map.begin(),
                             node_iter));

            // Debugging:
            //    libMesh::out << "libmesh_node_id=" << libmesh_node_id
            //         << ", sequential_index=" << sequential_index
            //         << std::endl;

            tetgen_wrapper.set_vertex(insertnum, // facet number
                                      0,         // polygon (always 0)
                                      j,         // local vertex index in tetgen input
                                      sequential_index);
          }

        // Go to next facet in polygonlist
        insertnum++;
      }
  }



  // fill hole list (if there are holes):
  if (holes.size() > 0)
    {
      std::vector<Point>::const_iterator ihole;
      unsigned hole_index = 0;
      for (ihole=holes.begin(); ihole!=holes.end(); ++ihole)
        tetgen_wrapper.set_hole(hole_index++, (*ihole)(0), (*ihole)(1), (*ihole)(2));
    }


  // Run TetGen triangulation method

  // Assemble switches: we append the user's switches (if any) to 'p',
  // which tetrahedralizes a piecewise linear complex (see definition
  // in user manual)
  std::ostringstream oss;
  oss << "p";
  oss << _switches;

  if (quality_constraint != 0)
    oss << "q" << std::fixed << quality_constraint;

  if (volume_constraint != 0)
    oss << "a" << std::fixed << volume_constraint;

  std::string params = oss.str();

  tetgen_wrapper.set_switches(params); // TetGen switches: Piecewise linear complex, Quiet mode
  tetgen_wrapper.run_tetgen();

  // => nodes:
  unsigned int old_nodesnum = this->_mesh.n_nodes();
  REAL x=0., y=0., z=0.;
  const unsigned int num_nodes = tetgen_wrapper.get_numberofpoints();

  // Debugging:
  // libMesh::out << "Original mesh had " << old_nodesnum << " nodes." << std::endl;
  // libMesh::out << "Reserving space for " << num_nodes << " total nodes." << std::endl;

  // Reserve space for additional nodes in the node map
  _sequential_to_libmesh_node_map.reserve(num_nodes);

  // Add additional nodes to the Mesh.
  // Original code had i<=num_nodes here (Note: the indexing is:
  // foo[3*i], [3*i+1], [3*i+2]) But according to the TetGen docs, "In
  // all cases, the first item in any array is stored starting at
  // index [0]."
  for (unsigned int i=old_nodesnum; i<num_nodes; i++)
    {
      // Fill in x, y, z values
      tetgen_wrapper.get_output_node(i, x,y,z);

      // Catch the node returned by add_point()... this will tell us the ID
      // assigned by the Mesh.
      Node * new_node = this->_mesh.add_point ( Point(x,y,z) );

      // Store this new ID in our sequential-to-libmesh node mapping array
      _sequential_to_libmesh_node_map.push_back( new_node->id() );
    }

  // Debugging:
  //  std::copy(_sequential_to_libmesh_node_map.begin(),
  //    _sequential_to_libmesh_node_map.end(),
  //    std::ostream_iterator<unsigned>(std::cout, " "));
  //  std::cout << std::endl;


  // => tetrahedra:
  const unsigned int num_elements = tetgen_wrapper.get_numberoftetrahedra();

  // Vector that temporarily holds the node labels defining element connectivity.
  unsigned int node_labels[4];

  for (unsigned int i=0; i<num_elements; i++)
    {
      // TetGen only supports Tet4 elements.
      Elem * elem = new Tet4;

      // Fill up the the node_labels vector
      for (unsigned int j=0; j<elem->n_nodes(); j++)
        node_labels[j] = tetgen_wrapper.get_element_node(i,j);

      // Associate nodes with this element
      this->assign_nodes_to_elem(node_labels, elem);

      // Finally, add this element to the mesh
      this->_mesh.add_elem(elem);
    }

  // Delete original convex hull elements.  Is there ever a case where
  // we should not do this?
  this->delete_2D_hull_elements();
}

triangulate_pointset()

void libMesh::TetGenMeshInterface::triangulate_pointset

(

)

Method invokes TetGen library to compute a Delaunay tetrahedralization from the nodes point set.

Definition at line 59 of file mesh_tetgen_interface.C.

References _mesh, _switches, libMesh::MeshBase::add_elem(), assign_nodes_to_elem(), fill_pointlist(), libMesh::TetGenWrapper::get_element_node(), libMesh::TetGenWrapper::get_numberoftetrahedra(), libMesh::Elem::n_nodes(), libMesh::TetGenWrapper::run_tetgen(), and libMesh::TetGenWrapper::set_switches().

{
  // class tetgen_wrapper allows library access on a basic level:
  TetGenWrapper tetgen_wrapper;

  // fill input structure with point set data:
  this->fill_pointlist(tetgen_wrapper);

  // Run TetGen triangulation method:
  // Q = quiet, no terminal output
  // V = verbose, more terminal output
  // Note: if no switch is used, the input must be a list of 3D points
  // (.node file) and the Delaunay tetrahedralization of this point set
  // will be generated.

  // Can we apply quality and volume constraints in
  // triangulate_pointset()?.  On at least one test problem,
  // specifying any quality or volume constraints here causes tetgen
  // to segfault down in the insphere method: a nullptr is passed
  // to the routine.
  std::ostringstream oss;
  oss << _switches;
  // oss << "V"; // verbose operation
  //oss  << "q" << std::fixed << 2.0;  // quality constraint
  //oss  << "a" << std::fixed << 100.; // volume constraint
  tetgen_wrapper.set_switches(oss.str());

  // Run tetgen
  tetgen_wrapper.run_tetgen();

  // save elements to mesh structure, nodes will not be changed:
  const unsigned int num_elements   = tetgen_wrapper.get_numberoftetrahedra();

  // Vector that temporarily holds the node labels defining element.
  unsigned int node_labels[4];

  for (unsigned int i=0; i<num_elements; ++i)
    {
      Elem * elem = new Tet4;

      // Get the nodes associated with this element
      for (unsigned int j=0; j<elem->n_nodes(); ++j)
        node_labels[j] = tetgen_wrapper.get_element_node(i,j);

      // Associate the nodes with this element
      this->assign_nodes_to_elem(node_labels, elem);

      // Finally, add this element to the mesh.
      this->_mesh.add_elem(elem);
    }
}

Member Data Documentation

_mesh

UnstructuredMesh& libMesh::TetGenMeshInterface::_mesh

protected

Local reference to the mesh we are working with.

Definition at line 151 of file mesh_tetgen_interface.h.

Referenced by assign_nodes_to_elem(), check_hull_integrity(), delete_2D_hull_elements(), fill_pointlist(), pointset_convexhull(), triangulate_conformingDelaunayMesh_carvehole(), and triangulate_pointset().

_sequential_to_libmesh_node_map

std::vector<unsigned> libMesh::TetGenMeshInterface::_sequential_to_libmesh_node_map

protected

We should not assume libmesh nodes are numbered sequentially... This is not the default behavior of DistributedMesh, for example, unless you specify node IDs explicitly. So this array allows us to keep a mapping between the sequential numbering in tetgen_data.pointlist.

Definition at line 160 of file mesh_tetgen_interface.h.

Referenced by assign_nodes_to_elem(), fill_pointlist(), and triangulate_conformingDelaunayMesh_carvehole().

_serializer

MeshSerializer libMesh::TetGenMeshInterface::_serializer

protected

Tetgen only operates on serial meshes.

Definition at line 165 of file mesh_tetgen_interface.h.

_switches

std::string libMesh::TetGenMeshInterface::_switches

protected

Parameter controlling the behaviour of tetgen. By default quiet.

Definition at line 171 of file mesh_tetgen_interface.h.

Referenced by pointset_convexhull(), set_switches(), triangulate_conformingDelaunayMesh_carvehole(), and triangulate_pointset().

---

The documentation for this class was generated from the following files:

• mesh_tetgen_interface.h
• mesh_tetgen_interface.C