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...

Protected Member Functions
unsigned	check_hull_integrity ()
	This function checks the integrity of the current set of elements in the Mesh to see if they comprise a hull, that is: More...
void	process_hull_integrity_result (unsigned result)
	This function prints an informative message and crashes 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
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.

Constructor & Destructor Documentation

MeshTetInterface()

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

explicit

Constructor.

Takes a reference to the mesh.

Definition at line 114 of file mesh_tet_interface.C.

                                                           :
  _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 125 of file mesh_tet_interface.C.

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

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

check_hull_integrity()

unsigned libMesh::MeshTetInterface::check_hull_integrity ( )

protected

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

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

Returns

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

Definition at line 338 of file mesh_tet_interface.C.

References _mesh, libMesh::MeshBase::n_elem(), libMesh::Elem::neighbor_ptr_range(), libMesh::TRI3, and libMesh::Elem::type().

Referenced by libMesh::NetGenMeshInterface::triangulate(), and libMesh::TetGenMeshInterface::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::MeshTetInterface::delete_2D_hull_elements ( )

protected

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

Definition at line 390 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;}

process_hull_integrity_result()

void libMesh::MeshTetInterface::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 372 of file mesh_tet_interface.C.

References libMesh::err.

Referenced by libMesh::TetGenMeshInterface::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.");
    }
}

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 131 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 138 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 149 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 160 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 154 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(), 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 144 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().

---

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

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