libMesh::MeshTetInterface Class Reference

Class MeshTetInterface provides an abstract interface for tetrahedralization of meshes by subclasses. More...

#include <mesh_tet_interface.h>

Inheritance diagram for libMesh::MeshTetInterface:

Public Member Functions
	MeshTetInterface (UnstructuredMesh &mesh)
	Constructor. More...
virtual	~MeshTetInterface ()
	Default destructor in base class. More...
Real &	desired_volume ()
	Sets and/or gets the desired tetrahedron volume. More...
bool &	smooth_after_generating ()
	Sets/gets flag which tells whether to do two steps of Laplace mesh smoothing after generating the grid. More...
ElemType &	elem_type ()
	Sets and/or gets the desired element type. More...
void	attach_hole_list (std::unique_ptr< std::vector< std::unique_ptr< UnstructuredMesh >>> holes)
	Attaches a vector of Mesh pointers defining holes which will be meshed around. More...
virtual void	triangulate ()=0
	This is the main public interface for this function. More...
void	set_verbosity (unsigned int v)
	Sets a verbosity level, defaulting to 0 (print nothing), to be set as high as 100 (print everything). More...

Protected Types
enum	SurfaceIntegrity {   NON_TRI3 = 1, MISSING_NEIGHBOR = 2, EMPTY_MESH = 3, MISSING_BACKLINK = 4,   BAD_NEIGHBOR_NODES = 5, NON_ORIENTED = 6, BAD_NEIGHBOR_LINKS = 7, DEGENERATE_ELEMENT = 8,   DEGENERATE_MESH = 9 }
	Enumeration of possible surface mesh integrity issues. More...

Protected Member Functions
std::set< SurfaceIntegrity >	check_hull_integrity () const
	This function checks the integrity of the current set of elements in the Mesh to see if they comprise a topological manifold that (if it's also geometrically valid) would define valid boundary for a tetrahedralized volume. More...
std::set< SurfaceIntegrity >	improve_hull_integrity ()
	This function checks the integrity of the current set of elements in the Mesh, and corrects what it can. More...
void	process_hull_integrity_result (const std::set< SurfaceIntegrity > &result) const
	This function prints an informative message and throws an exception based on the output of the check_hull_integrity() function. More...
void	delete_2D_hull_elements ()
	Delete original convex hull elements from the Mesh after performing a Delaunay tetrahedralization. More...

Static Protected Member Functions
static BoundingBox	volume_to_surface_mesh (UnstructuredMesh &mesh)
	Remove volume elements from the given mesh, after converting their outer boundary faces to surface elements. More...

Protected Attributes
unsigned int	_verbosity
	verbosity setting More...
Real	_desired_volume
	The desired volume for the elements in the resulting mesh. More...
bool	_smooth_after_generating
	Flag which tells whether we should smooth the mesh after it is generated. More...
ElemType	_elem_type
	The exact type of tetrahedra we intend to construct. More...
UnstructuredMesh &	_mesh
	Local reference to the mesh we are working with. More...
std::unique_ptr< std::vector< std::unique_ptr< UnstructuredMesh > > >	_holes
	A pointer to a vector of meshes each defining a hole. More...

Detailed Description

Class MeshTetInterface provides an abstract interface for tetrahedralization of meshes by subclasses.

Author

Roy H. Stogner

Date

2024

Definition at line 49 of file mesh_tet_interface.h.

Member Enumeration Documentation

SurfaceIntegrity

enum libMesh::MeshTetInterface::SurfaceIntegrity

protected

Enumeration of possible surface mesh integrity issues.

Enumerator
NON_TRI3
MISSING_NEIGHBOR
EMPTY_MESH
MISSING_BACKLINK
BAD_NEIGHBOR_NODES
NON_ORIENTED
BAD_NEIGHBOR_LINKS
DEGENERATE_ELEMENT
DEGENERATE_MESH

Definition at line 124 of file mesh_tet_interface.h.

                        {
    NON_TRI3 = 1,           // a non-TRI3 element is found
    MISSING_NEIGHBOR = 2,   // an element with a nullptr-neighbor is found
    EMPTY_MESH = 3,         // the mesh is empty
    MISSING_BACKLINK = 4,   // an element neighbor isn't linked back to it
    BAD_NEIGHBOR_NODES = 5, // an element neighbor isn't linked to expected nodes
    NON_ORIENTED = 6,       // an element neighbor has inconsistent orientation
    BAD_NEIGHBOR_LINKS = 7, // an element neighbor has other inconsistent links
    DEGENERATE_ELEMENT = 8, // an element has zero area
    DEGENERATE_MESH = 9     // the mesh clearly bounds zero volume
  };

Constructor & Destructor Documentation

MeshTetInterface()

libMesh::MeshTetInterface::MeshTetInterface ( UnstructuredMesh &  mesh )

explicit

Constructor.

Takes a reference to the mesh.

Definition at line 117 of file mesh_tet_interface.C.

                                                           :
  _verbosity(0), _desired_volume(0), _smooth_after_generating(false),
  _elem_type(TET4), _mesh(mesh)
{
}

~MeshTetInterface()

libMesh::MeshTetInterface::~MeshTetInterface ( )

virtualdefault

Default destructor in base class.

Member Function Documentation

attach_hole_list()

void libMesh::MeshTetInterface::attach_hole_list

(

std::unique_ptr< std::vector< std::unique_ptr< UnstructuredMesh >>>

holes

)

Attaches a vector of Mesh pointers defining holes which will be meshed around.

We use unique_ptr here because we expect that we may need to modify these meshes internally.

Definition at line 128 of file mesh_tet_interface.C.

Referenced by MeshTetTest::testHole(), and MeshTetTest::testSphereShell().

{
  _holes = std::move(holes);
}

check_hull_integrity()

std::set< MeshTetInterface::SurfaceIntegrity > libMesh::MeshTetInterface::check_hull_integrity ( ) const

protected

This function checks the integrity of the current set of elements in the Mesh to see if they comprise a topological manifold that (if it's also geometrically valid) would define valid boundary for a tetrahedralized volume.

Named check_hull_integrity() for backward compatibility, but now accepts non-convex manifolds.

Returns

a set of enums describing problems found, or an empty set if no problems are found.

Definition at line 341 of file mesh_tet_interface.C.

References _mesh, _verbosity, libMesh::MeshBase::active_local_element_stored_range(), BAD_NEIGHBOR_LINKS, BAD_NEIGHBOR_NODES, libMesh::ParallelObject::comm(), libMesh::MeshTools::create_bounding_box(), DEGENERATE_ELEMENT, DEGENERATE_MESH, EMPTY_MESH, libMesh::Elem::get_info(), libMesh::DofObject::id(), int, libMesh::Elem::local_node(), libMesh::BoundingBox::max(), libMesh::BoundingBox::min(), MISSING_BACKLINK, MISSING_NEIGHBOR, libMesh::MeshBase::n_elem(), libMesh::Elem::neighbor_ptr(), libMesh::Elem::node_ptr(), NON_ORIENTED, NON_TRI3, libMesh::Threads::parallel_reduce(), libMesh::Real, TIMPI::Communicator::set_union(), libMesh::Elem::side_index_range(), libMesh::TOLERANCE, libMesh::TRI3, libMesh::Elem::type(), libMesh::Elem::volume(), and libMesh::Elem::which_neighbor_am_i().

Referenced by improve_hull_integrity().

{
  // 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 {EMPTY_MESH};

  std::set<MeshTetInterface::SurfaceIntegrity> returnval;

  const BoundingBox bb = MeshTools::create_bounding_box(this->_mesh);
  const Point extents = bb.max() - bb.min();
  if (extents(0) == 0 ||
      extents(1) == 0 ||
      extents(2) == 0)
    returnval.insert(DEGENERATE_MESH);

  // Figure a area to use for relative tolerances when detecting
  // degenerate elements
  const Real ref_area = std::abs(extents(0) * extents(1)) +
                        std::abs(extents(0) * extents(2)) +
                        std::abs(extents(1) * extents(2));

  struct TriChecker {
    std::set<MeshTetInterface::SurfaceIntegrity> my_returnval;
    const Real my_ref_area;
    const unsigned int my_verbosity;

    TriChecker (Real ref_area, unsigned int verbosity) :
      my_returnval(), my_ref_area(ref_area),
      my_verbosity(verbosity) {}
    TriChecker (TriChecker & other, Threads::split) :
      my_returnval(), my_ref_area(other.my_ref_area),
      my_verbosity(other.my_verbosity) {}

    void operator()(const ConstElemRange & range) {

      for (const Elem * elem : range)
        {
          // Check for proper element type
          if (elem->type() != TRI3)
            {
              if (my_verbosity >= 50)
                std::cerr << "Non-Tri3: " << elem->get_info() << std::endl;
              my_returnval.insert(NON_TRI3);
            }

          // Make sure it's a decent element.
          if (elem->volume() < my_ref_area * TOLERANCE * TOLERANCE)
            {
              if (my_verbosity >= 50)
                std::cerr << "Degenerate element: " << elem->get_info() << std::endl;
              my_returnval.insert(DEGENERATE_ELEMENT);
            }

          for (auto s : elem->side_index_range())
            {
              const Elem * const neigh = elem->neighbor_ptr(s);

              if (neigh == nullptr)
                {
                  if (my_verbosity >= 50)
                    std::cerr << "Element missing neighbor " << s << ": " << elem->get_info() << std::endl;
                  my_returnval.insert(MISSING_NEIGHBOR);
                  continue;
                }

              // Make sure our neighbor points back to us
              const unsigned int nn = neigh->which_neighbor_am_i(elem);

              if (nn >= 3)
                {
                  if (my_verbosity >= 50)
                    std::cerr << "Element missing backlink " << s << ": " << elem->get_info() << std::endl;
                  my_returnval.insert(MISSING_BACKLINK);
                  continue;
                }

              // Our neighbor should have the same the edge nodes we do on
              // the neighboring edgei
              const Node * const n1 = elem->node_ptr(s);
              const Node * const n2 = elem->node_ptr((s+1)%3);

              const unsigned int i1 = neigh->local_node(n1->id());
              const unsigned int i2 = neigh->local_node(n2->id());
              if (i1 >= 3 || i2 >= 3)
                {
                  if (my_verbosity >= 50)
                    std::cerr << "Element with bad neighbor " << s << " nodes: " << elem->get_info() << std::endl;
                  my_returnval.insert(BAD_NEIGHBOR_NODES);
                  continue;
                }

              // It should have those edge nodes in the opposite order
              // (because they have the same orientation we do)
              if ((i2 + 1)%3 != i1)
                {
                  if (my_verbosity >= 50)
                    std::cerr << "Element orientation mismatch with neighbor " << s << ": " << elem->get_info() << std::endl;
                  my_returnval.insert(NON_ORIENTED);
                  continue;
                }

              // And it should have those edge nodes in the expected
              // places relative to its neighbor link
              if (i2 != nn)
                {
                  if (my_verbosity >= 50)
                    std::cerr << "Element with bad links on neighbor " << s << ": " << elem->get_info() << std::endl;
                  my_returnval.insert(BAD_NEIGHBOR_LINKS);
                  continue;
                }
            }
        }
    }

    void join(TriChecker & other) {
      my_returnval.merge(other.my_returnval);
    }
  };

  TriChecker checker (ref_area, this->_verbosity);

  Threads::parallel_reduce
    (this->_mesh.active_local_element_stored_range(), checker);

  // Join problems found in threaded loop
  returnval.merge(checker.my_returnval);

  // Join problems found on other ranks
  std::set<char> int_set;
  std::transform
    (returnval.begin(), returnval.end(),
     std::inserter<std::set<char>>(int_set, int_set.end()),
     [](SurfaceIntegrity i){return int(i);});
  _mesh.comm().set_union(int_set);
  std::transform
    (int_set.begin(), int_set.end(),
     std::inserter<std::set<SurfaceIntegrity>>(returnval, returnval.end()),
     [](int i){return SurfaceIntegrity(i);});

  return returnval;
}

delete_2D_hull_elements()

void libMesh::MeshTetInterface::delete_2D_hull_elements ( )

protected

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

Definition at line 685 of file mesh_tet_interface.C.

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

Referenced by libMesh::TetGenMeshInterface::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();
}

desired_volume()

Real& libMesh::MeshTetInterface::desired_volume ( )

inline

Sets and/or gets the desired tetrahedron volume.

Set to zero to disable volume constraint.

Definition at line 68 of file mesh_tet_interface.h.

References _desired_volume.

Referenced by main(), and MeshTetTest::testSphereShell().

{return _desired_volume;}

elem_type()

ElemType& libMesh::MeshTetInterface::elem_type ( )

inline

Sets and/or gets the desired element type.

This should be a Tet type.

Definition at line 81 of file mesh_tet_interface.h.

References _elem_type.

{return _elem_type;}

improve_hull_integrity()

std::set< MeshTetInterface::SurfaceIntegrity > libMesh::MeshTetInterface::improve_hull_integrity ( )

protected

This function checks the integrity of the current set of elements in the Mesh, and corrects what it can.

Returns

A set of SurfaceIntegrity codes from check_hull_integrity() if there are problems it can't fix, or an empty set otherwise.

Definition at line 488 of file mesh_tet_interface.C.

References _mesh, BAD_NEIGHBOR_LINKS, check_hull_integrity(), libMesh::ParallelObject::comm(), libMesh::TypeVector< T >::cross(), libMesh::MeshBase::elem_ptr(), libMesh::MeshBase::elem_ref(), EMPTY_MESH, libMesh::UnstructuredMesh::find_neighbors(), libMesh::Elem::flip(), libMesh::MeshBase::get_boundary_info(), libMesh::DofObject::id(), libMesh::libmesh_assert(), libMesh::Elem::local_node(), MISSING_BACKLINK, MISSING_NEIGHBOR, libMesh::Elem::neighbor_ptr(), libMesh::Elem::node_ptr(), libMesh::Elem::node_ref_range(), NON_ORIENTED, NON_TRI3, libMesh::Elem::point(), libMesh::Real, libMesh::Elem::side_index_range(), and libMesh::Elem::which_neighbor_am_i().

Referenced by libMesh::NetGenMeshInterface::triangulate(), and libMesh::TetGenMeshInterface::triangulate_conformingDelaunayMesh_carvehole().

{
  // We don't really do anything parallel here, but we aspire to.
  libmesh_parallel_only(this->_mesh.comm());

  std::set<MeshTetInterface::SurfaceIntegrity> integrityproblems =
    this->check_hull_integrity();

  // If we have no problem, or a problem we can't fix, we're done.
  if (integrityproblems.empty() ||
      integrityproblems.count(NON_TRI3) ||
      integrityproblems.count(EMPTY_MESH))
    return integrityproblems;

  // Possibly the user gave us an unprepared mesh with missing or bad
  // neighbor links?
  if (integrityproblems.count(MISSING_NEIGHBOR) ||
      integrityproblems.count(MISSING_BACKLINK) ||
      integrityproblems.count(BAD_NEIGHBOR_LINKS))
  {
    this->_mesh.find_neighbors();
    integrityproblems = this->check_hull_integrity();
  }

  // If find_neighbors() doesn't fix these, I give up.
  if (integrityproblems.count(MISSING_NEIGHBOR) ||
      integrityproblems.count(MISSING_BACKLINK) ||
      integrityproblems.count(BAD_NEIGHBOR_LINKS))
    return integrityproblems;

  // find_neighbors() might have fixed everything
  if (integrityproblems.empty())
    return integrityproblems;

  // A non-oriented (but orientable!) surface is the only thing we
  // shouldn't have fixed or given up on by now.
  libmesh_assert_equal_to(integrityproblems.size(), 1);
  libmesh_assert_equal_to(integrityproblems.count(NON_ORIENTED), 1);

  // We need one known-good triangle to start from.  We'll pick the
  // most-negative-x normal among the triangles on the most-negative-x
  // point.

  // We'll just implement this in serial for now.
  MeshSerializer mesh_serializer(this->_mesh);

  // I don't see why we'd need boundary info here, but maybe we'll
  // want to preserve edge/node conditions eventually?
  BoundaryInfo & bi = this->_mesh.get_boundary_info();

  const Node * lowest_point = (*this->_mesh.elements_begin())->node_ptr(0);

  // Index by ids, not pointers, for consistency in parallel
  std::unordered_set<dof_id_type> attached_elements;

  for (Elem * elem : this->_mesh.element_ptr_range())
    {
      for (const Node & node : elem->node_ref_range())
        {
          if (node(0) < (*lowest_point)(0))
            {
              lowest_point = &node;
              attached_elements.clear();
            }
          if (&node == lowest_point)
            attached_elements.insert(elem->id());
        }
    }

  Elem * best_elem = nullptr;
  Real best_abs_normal_0 = 0;

  for (dof_id_type id : attached_elements)
    {
      Elem * elem = this->_mesh.elem_ptr(id);
      const Point e01 = elem->point(1) - elem->point(0);
      const Point e02 = elem->point(2) - elem->point(0);
      const Point normal = e01.cross(e02).unit();
      const Real abs_normal_0 = std::abs(normal(0));

      if (!best_elem || abs_normal_0 > best_abs_normal_0)
        {
          best_elem = elem;
          best_abs_normal_0 = abs_normal_0;

          // Make sure that element is actually a good one, by
          // flipping it if it's not.
          if (abs_normal_0 == normal(0))
            elem->flip(&bi);
        }
    }

  // Now flood-fill from that element to get a consistent orientation
  // for the others.
  std::unordered_set<dof_id_type> frontier_elements{best_elem->id()},
                                  finished_elements{};

  while (!frontier_elements.empty())
    {
      const dof_id_type elem_id = *frontier_elements.begin();
      Elem & elem = this->_mesh.elem_ref(elem_id);
      for (auto s : elem.side_index_range())
        {
          Elem * neigh = elem.neighbor_ptr(s);
          libmesh_assert(neigh);
          libmesh_assert_less(neigh->which_neighbor_am_i(&elem), 3);

          const Node * const n1 = elem.node_ptr(s);
          const Node * const n2 = elem.node_ptr((s+1)%3);
          const unsigned int i1 = neigh->local_node(n1->id());
          const unsigned int i2 = neigh->local_node(n2->id());
          libmesh_assert_less(i1, 3);
          libmesh_assert_less(i2, 3);

          const dof_id_type neigh_id = neigh->id();

          const bool frontier_neigh = frontier_elements.count(neigh_id);
          const bool finished_neigh = finished_elements.count(neigh_id);

          // Are we flipped?
          if ((i2 + 1)%3 != i1)
            {
              // Are we a Moebius strip???  We give up.
              if (frontier_neigh || finished_neigh)
                return integrityproblems;

              neigh->flip(&bi);
            }

          if (!frontier_neigh && !finished_neigh)
            frontier_elements.insert(neigh_id);
        }

      finished_elements.insert(elem_id);
      frontier_elements.erase(elem_id);
    }

  this->_mesh.find_neighbors();

  libmesh_assert(this->check_hull_integrity().empty());

  return {};
}

process_hull_integrity_result()

void libMesh::MeshTetInterface::process_hull_integrity_result ( const std::set< SurfaceIntegrity > &  result ) const

protected

This function prints an informative message and throws an exception based on the output of the check_hull_integrity() function.

It is a separate function so that you can check hull integrity without exiting or catching an exception if desired.

Definition at line 634 of file mesh_tet_interface.C.

Referenced by libMesh::NetGenMeshInterface::triangulate(), and libMesh::TetGenMeshInterface::triangulate_conformingDelaunayMesh_carvehole().

{
  std::ostringstream err_msg;

  if (result.empty()) // success
    return;

  err_msg << "Error! Conforming Delaunay mesh tetrahedralization requires a convex hull." << std::endl;

  if (result.count(NON_TRI3))
    {
      err_msg << "At least one non-Tri3 element was found in the input boundary mesh.  ";
      err_msg << "Our constrained Delaunay tetrahedralization boundary must be a triangulation of Tri3 elements." << std::endl;
    }
  if (result.count(MISSING_NEIGHBOR))
    {
      err_msg << "At least one triangle without three neighbors was found in the input boundary mesh.  ";
      err_msg << "A constrained Delaunay tetrahedralization boundary must be a triangular manifold without boundary." << std::endl;
    }
  if (result.count(EMPTY_MESH))
    {
      err_msg << "The input boundary mesh was empty!" << std::endl;
      err_msg << "Our constrained Delaunay tetrahedralization boundary must be a triangulation of Tri3 elements." << std::endl;
    }
  if (result.count(MISSING_BACKLINK))
    {
      err_msg << "At least one triangle neighbor without a return neighbor link was found in the input boundary mesh.  ";
      err_msg << "A constrained Delaunay tetrahedralization boundary must be a conforming and non-adaptively-refined mesh." << std::endl;
    }
  if (result.count(BAD_NEIGHBOR_NODES))
    {
      err_msg << "At least one triangle neighbor without expected node links was found in the input boundary mesh.  ";
      err_msg << "A constrained Delaunay tetrahedralization boundary must be a conforming and non-adaptively-refined mesh." << std::endl;
    }
  if (result.count(NON_ORIENTED))
    {
      err_msg << "At least one triangle neighbor with an inconsistent orientation was found in the input boundary mesh.  ";
      err_msg << "A constrained Delaunay tetrahedralization boundary must be an oriented Tri3 mesh." << std::endl;
    }
  if (result.count(BAD_NEIGHBOR_LINKS))
    err_msg << "At least one triangle neighbor with inconsistent node and neighbor links was found in the input boundary mesh." << std::endl;
  if (result.count(DEGENERATE_ELEMENT))
    err_msg << "At least one input triangle is degenerate, with near-zero area relative to the manifold." << std::endl;
  if (result.count(DEGENERATE_MESH))
    err_msg << "The input mesh is degenerate, with zero thickness in at least one direction." << std::endl;

  libmesh_error_msg(err_msg.str());
}

set_verbosity()

void libMesh::MeshTetInterface::set_verbosity ( unsigned int  v )

inline

Sets a verbosity level, defaulting to 0 (print nothing), to be set as high as 100 (print everything).

For verbosity >= 50, print all detected surface mesh integrity issues as they're found. Subclasses may add other output at other verbosity levels.

Definition at line 208 of file mesh_tet_interface.h.

References _verbosity.

Referenced by MeshTetTest::testNetGen().

{
  this->_verbosity = v;
}

smooth_after_generating()

bool& libMesh::MeshTetInterface::smooth_after_generating ( )

inline

Sets/gets flag which tells whether to do two steps of Laplace mesh smoothing after generating the grid.

False by default (for compatibility with old TetGenMeshInterface behavior).

Definition at line 75 of file mesh_tet_interface.h.

References _smooth_after_generating.

{return _smooth_after_generating;}

triangulate()

virtual void libMesh::MeshTetInterface::triangulate ( )

pure virtual

This is the main public interface for this function.

Implemented in libMesh::TetGenMeshInterface, and libMesh::NetGenMeshInterface.

Referenced by MeshTetTest::testTetInterfaceBase().

volume_to_surface_mesh()

BoundingBox libMesh::MeshTetInterface::volume_to_surface_mesh ( UnstructuredMesh &  mesh )

staticprotected

Remove volume elements from the given mesh, after converting their outer boundary faces to surface elements.

Returns the bounding box of the mesh; this is useful for detecting misplaced holes later.

Definition at line 134 of file mesh_tet_interface.C.

References libMesh::MeshBase::add_elem(), libMesh::MeshTools::Modification::all_tri(), libMesh::Elem::build_side_ptr(), libMesh::MeshBase::delete_elem(), libMesh::Elem::dim(), libMesh::Elem::flip(), libMesh::MeshBase::get_boundary_info(), libMesh::DofObject::id(), libMesh::MeshBase::is_prepared(), libMesh::MeshBase::is_replicated(), libMesh::Elem::level(), libMesh::libmesh_assert(), libMesh::Elem::low_order_key(), libMesh::make_range(), libMesh::MeshBase::max_elem_id(), mesh, libMesh::Elem::n_sides(), libMesh::Elem::neighbor_ptr(), libMesh::Elem::node_ref_range(), libMesh::MeshBase::parallel_max_unique_id(), libMesh::MeshBase::prepare_for_use(), libMesh::Real, libMesh::remote_elem, libMesh::DofObject::set_id(), libMesh::Elem::set_interior_parent(), libMesh::Elem::set_neighbor(), libMesh::DofObject::set_unique_id(), libMesh::Elem::side_index_range(), libMesh::Elem::side_ptr(), libMesh::BoundingBox::union_with(), and libMesh::MeshTools::valid_is_prepared().

Referenced by libMesh::NetGenMeshInterface::triangulate().

{
  // If we've been handed an unprepared mesh then we need to be made
  // aware of that and fix that; we're relying on neighbor pointers.
  libmesh_assert(MeshTools::valid_is_prepared(mesh));

  if (!mesh.is_prepared())
    mesh.prepare_for_use();

  // We'll return a bounding box for use by subclasses in basic sanity checks.
  BoundingBox surface_bb;

  // First convert all volume boundaries to surface elements; this
  // gives us a manifold bounding the mesh, though it may not be a
  // connected manifold even if the volume mesh was connected.
  {
    // Make sure ids are in sync and valid on a DistributedMesh
    const dof_id_type max_orig_id = mesh.max_elem_id();
#ifdef LIBMESH_ENABLE_UNIQUE_ID
    const unique_id_type max_unique_id = mesh.parallel_max_unique_id();
#endif

    // Change this if we add arbitrary polyhedra...
    const dof_id_type max_sides = 6;

    std::unordered_set<Elem *> elems_to_delete;

    std::vector<std::unique_ptr<Elem>> elems_to_add;

    // Convert all faces to surface elements
    for (auto * elem : mesh.active_element_ptr_range())
      {
        libmesh_error_msg_if (elem->dim() < 2,
          "Cannot use meshes with 0D or 1D elements to define a volume");

        // If we've already got 2D elements then those are (part of)
        // our surface.
        if (elem->dim() == 2)
          continue;

        // 3D elements will be removed after we've extracted their
        // surface faces.
        elems_to_delete.insert(elem);

        for (auto s : make_range(elem->n_sides()))
          {
            // If there's a neighbor on this side then there's not a
            // boundary
            if (elem->neighbor_ptr(s))
              {
                // We're not supporting AMR meshes here yet
                if (elem->level() != elem->neighbor_ptr(s)->level())
                  libmesh_not_implemented_msg
                    ("Tetrahedralizaton of adapted meshes is not currently supported");
                continue;
              }

            elems_to_add.push_back(elem->build_side_ptr(s));
            Elem * side_elem = elems_to_add.back().get();

            // Wipe the interior_parent before it can become a
            // dangling pointer later
            side_elem->set_interior_parent(nullptr);

            // If the mesh is replicated then its automatic id
            // setting is fine.  If not, then we need unambiguous ids
            // independent of element traversal.
            if (!mesh.is_replicated())
              {
                side_elem->set_id(max_orig_id + max_sides*elem->id() + s);
#ifdef LIBMESH_ENABLE_UNIQUE_ID
                side_elem->set_unique_id(max_unique_id + max_sides*elem->id() + s);
#endif
              }
          }
      }

    // If the mesh is replicated then its automatic neighbor finding
    // is fine.  If not, then we need to insert them ourselves, but
    // it's easy because we can use the fact (from our implementation
    // above) that our new elements have no parents or children, plus
    // the fact (from the tiny fraction of homology I understand) that
    // a manifold boundary is a manifold with no boundary.
    //
    // See UnstructuredMesh::find_neighbors() for more explanation of
    // (a more complicated version of) the algorithm here.
    if (!mesh.is_replicated())
      {
        typedef dof_id_type                     key_type;
        typedef std::pair<Elem *, unsigned char> val_type;
        typedef std::unordered_multimap<key_type, val_type> map_type;
        map_type side_to_elem_map;

        std::unique_ptr<Elem> my_side, their_side;

        for (auto & elem : elems_to_add)
          {
            for (auto s : elem->side_index_range())
              {
                if (elem->neighbor_ptr(s))
                  continue;
                const dof_id_type key = elem->low_order_key(s);
                auto bounds = side_to_elem_map.equal_range(key);
                if (bounds.first != bounds.second)
                  {
                    elem->side_ptr(my_side, s);
                    while (bounds.first != bounds.second)
                      {
                        Elem * potential_neighbor = bounds.first->second.first;
                        const unsigned int ns = bounds.first->second.second;
                        potential_neighbor->side_ptr(their_side, ns);
                        if (*my_side == *their_side)
                          {
                            elem->set_neighbor(s, potential_neighbor);
                            potential_neighbor->set_neighbor(ns, elem.get());
                            side_to_elem_map.erase (bounds.first);
                            break;
                          }
                        ++bounds.first;
                      }

                    if (!elem->neighbor_ptr(s))
                      side_to_elem_map.emplace
                        (key, std::make_pair(elem.get(), cast_int<unsigned char>(s)));
                  }
              }
          }

        // At this point we *should* have a match for everything, so
        // anything we don't have a match for is remote.
        for (auto & elem : elems_to_add)
          for (auto s : elem->side_index_range())
            if (!elem->neighbor_ptr(s))
              elem->set_neighbor(s, const_cast<RemoteElem*>(remote_elem));
      }

    // Remove volume and edge elements
    for (Elem * elem : elems_to_delete)
      mesh.delete_elem(elem);

    // Add the new elements outside the loop so we don't risk
    // invalidating iterators.
    for (auto & elem : elems_to_add)
      mesh.add_elem(std::move(elem));
  }

  // Fix up neighbor pointers, element counts, etc.
  mesh.prepare_for_use();

  // We're making tets; we need to start with tris
  MeshTools::Modification::all_tri(mesh);

  // Partition surface into connected components.  At this point I'm
  // finally going to give up and serialize, because at least we got
  // from 3D down to 2D first, and because I don't want to have to
  // turn flood_component into a while loop with a parallel sync in
  // the middle, and because we do have to serialize *eventually*
  // anyways unless we get a parallel tetrahedralizer backend someday.
  MeshSerializer mesh_serializer(mesh);

  std::vector<std::unordered_set<Elem *>> components;
  std::unordered_set<Elem *> in_component;

  for (auto * elem : mesh.element_ptr_range())
    if (!in_component.count(elem))
      components.emplace_back(flood_component(in_component, elem));

  const std::unordered_set<Elem *> * biggest_component = nullptr;
  Real biggest_six_vol = 0;
  for (const auto & component : components)
    {
      Real six_vol = six_times_signed_volume(component);
      if (std::abs(six_vol) > std::abs(biggest_six_vol))
        {
          biggest_six_vol = six_vol;
          biggest_component = &component;
        }
    }

  if (!biggest_component)
    libmesh_error_msg("No non-zero-volume component found among " <<
                      components.size() << " boundary components");

  for (const auto & component : components)
    if (&component != biggest_component)
      {
        for (Elem * elem: component)
          mesh.delete_elem(elem);
      }
    else
      {
        for (Elem * elem: component)
          {
            if (biggest_six_vol < 0)
              elem->flip(&mesh.get_boundary_info());

            for (auto & node : elem->node_ref_range())
              surface_bb.union_with(node);
          }
      }

  mesh.prepare_for_use();

  return surface_bb;
}

Member Data Documentation

_desired_volume

Real libMesh::MeshTetInterface::_desired_volume

protected

The desired volume for the elements in the resulting mesh.

Unlimited (indicated by 0) by default

Definition at line 178 of file mesh_tet_interface.h.

Referenced by desired_volume(), libMesh::NetGenMeshInterface::triangulate(), and libMesh::TetGenMeshInterface::triangulate_pointset().

_elem_type

ElemType libMesh::MeshTetInterface::_elem_type

protected

The exact type of tetrahedra we intend to construct.

Definition at line 189 of file mesh_tet_interface.h.

Referenced by elem_type().

_holes

std::unique_ptr<std::vector<std::unique_ptr<UnstructuredMesh> > > libMesh::MeshTetInterface::_holes

protected

A pointer to a vector of meshes each defining a hole.

If this is nullptr, there are no holes!

Definition at line 200 of file mesh_tet_interface.h.

Referenced by libMesh::NetGenMeshInterface::triangulate().

_mesh

UnstructuredMesh& libMesh::MeshTetInterface::_mesh

protected

Local reference to the mesh we are working with.

Definition at line 194 of file mesh_tet_interface.h.

Referenced by libMesh::TetGenMeshInterface::assign_nodes_to_elem(), check_hull_integrity(), delete_2D_hull_elements(), libMesh::TetGenMeshInterface::fill_pointlist(), improve_hull_integrity(), libMesh::TetGenMeshInterface::pointset_convexhull(), libMesh::NetGenMeshInterface::triangulate(), libMesh::TetGenMeshInterface::triangulate_conformingDelaunayMesh_carvehole(), and libMesh::TetGenMeshInterface::triangulate_pointset().

_smooth_after_generating

bool libMesh::MeshTetInterface::_smooth_after_generating

protected

Flag which tells whether we should smooth the mesh after it is generated.

False by default.

Definition at line 184 of file mesh_tet_interface.h.

Referenced by libMesh::TetGenMeshInterface::pointset_convexhull(), smooth_after_generating(), libMesh::TetGenMeshInterface::triangulate_conformingDelaunayMesh_carvehole(), and libMesh::TetGenMeshInterface::triangulate_pointset().

_verbosity

unsigned int libMesh::MeshTetInterface::_verbosity

protected

verbosity setting

Definition at line 110 of file mesh_tet_interface.h.

Referenced by check_hull_integrity(), and set_verbosity().

---

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

• include/mesh/mesh_tet_interface.h
• src/mesh/mesh_tet_interface.C