void add_cube_convex_hull_to_mesh(MeshBase& mesh, Point lower_limit, Point upper_limit)
{
#ifdef LIBMESH_HAVE_TETGEN
SerialMesh cube_mesh(mesh.comm(),3);
unsigned n_elem = 1;
MeshTools::Generation::build_cube(cube_mesh,
n_elem,n_elem,n_elem, // n. elements in each direction
lower_limit(0), upper_limit(0),
lower_limit(1), upper_limit(1),
lower_limit(2), upper_limit(2),
HEX8);
// The pointset_convexhull() algorithm will ignore the Hex8s
// in the Mesh, and just construct the triangulation
// of the convex hull.
TetGenMeshInterface t(cube_mesh);
t.pointset_convexhull();
// Now add all nodes from the boundary of the cube_mesh to the input mesh.
// Map from "node id in cube_mesh" -> "node id in mesh". Initially inserted
// with a dummy value, later to be assigned a value by the input mesh.
std::map<unsigned,unsigned> node_id_map;
typedef std::map<unsigned,unsigned>::iterator iterator;
{
MeshBase::element_iterator it = cube_mesh.elements_begin();
const MeshBase::element_iterator end = cube_mesh.elements_end();
for ( ; it != end; ++it)
{
Elem* elem = *it;
for (unsigned s=0; s<elem->n_sides(); ++s)
if (elem->neighbor(s) == NULL)
{
// Add the node IDs of this side to the set
AutoPtr<Elem> side = elem->side(s);
for (unsigned n=0; n<side->n_nodes(); ++n)
node_id_map.insert( std::make_pair(side->node(n), /*dummy_value=*/0) );
}
}
}
// For each node in the map, insert it into the input mesh and keep
// track of the ID assigned.
for (iterator it=node_id_map.begin(); it != node_id_map.end(); ++it)
{
// Id of the node in the cube mesh
unsigned id = (*it).first;
// Pointer to node in the cube mesh
Node* old_node = cube_mesh.node_ptr(id);
// Add geometric point to input mesh
Node* new_node = mesh.add_point ( *old_node );
// Track ID value of new_node in map
(*it).second = new_node->id();
}
// With the points added and the map data structure in place, we are
// ready to add each TRI3 element of the cube_mesh to the input Mesh
// with proper node assignments
{
MeshBase::element_iterator el = cube_mesh.elements_begin();
const MeshBase::element_iterator end_el = cube_mesh.elements_end();
for (; el != end_el; ++el)
{
Elem* old_elem = *el;
if (old_elem->type() == TRI3)
{
Elem* new_elem = mesh.add_elem(new Tri3);
// Assign nodes in new elements. Since this is an example,
// we'll do it in several steps.
for (unsigned i=0; i<old_elem->n_nodes(); ++i)
{
// Locate old node ID in the map
iterator it = node_id_map.find(old_elem->node(i));
// Check for not found
if (it == node_id_map.end())
{
libMesh::err << "Node id " << old_elem->node(i) << " not found in map!" << std::endl;
libmesh_error();
}
// Mapping to node ID in input mesh
unsigned new_node_id = (*it).second;
// Node pointer assigned from input mesh
new_elem->set_node(i) = mesh.node_ptr(new_node_id);
}
}
}
}
#endif // LIBMESH_HAVE_TETGEN
}
void MeshTools::Subdivision::add_boundary_ghosts(MeshBase & mesh)
{
static const Real tol = 1e-5;
// add the mirrored ghost elements (without using iterators, because the mesh is modified in the course)
std::vector<Tri3Subdivision *> ghost_elems;
std::vector<Node *> ghost_nodes;
const unsigned int n_elem = mesh.n_elem();
for (unsigned int eid = 0; eid < n_elem; ++eid)
{
Elem * elem = mesh.elem(eid);
libmesh_assert_equal_to(elem->type(), TRI3SUBDIVISION);
// If the triangle happens to be in a corner (two boundary
// edges), we perform a counter-clockwise loop by mirroring the
// previous triangle until we come back to the original
// triangle. This prevents degenerated triangles in the mesh
// corners and guarantees that the node in the middle of the
// loop is of valence=6.
for (unsigned int i = 0; i < elem->n_sides(); ++i)
{
libmesh_assert_not_equal_to(elem->neighbor(i), elem);
if (elem->neighbor(i) == libmesh_nullptr &&
elem->neighbor(next[i]) == libmesh_nullptr)
{
Elem * nelem = elem;
unsigned int k = i;
for (unsigned int l=0;l<4;l++)
{
// this is the vertex to be mirrored
Point point = nelem->point(k) + nelem->point(next[k]) - nelem->point(prev[k]);
// Check if the proposed vertex doesn't coincide
// with one of the existing vertices. This is
// necessary because for some triangulations, it can
// happen that two mirrored ghost vertices coincide,
// which would then lead to a zero size ghost
// element below.
Node * node = libmesh_nullptr;
for (unsigned int j = 0; j < ghost_nodes.size(); ++j)
{
if ((*ghost_nodes[j] - point).size() < tol * (elem->point(k) - point).size())
{
node = ghost_nodes[j];
break;
}
}
// add the new vertex only if no other is nearby
if (node == libmesh_nullptr)
{
node = mesh.add_point(point);
ghost_nodes.push_back(node);
}
Tri3Subdivision * newelem = new Tri3Subdivision();
// add the first new ghost element to the list just as in the non-corner case
if (l == 0)
ghost_elems.push_back(newelem);
newelem->set_node(0) = nelem->get_node(next[k]);
newelem->set_node(1) = nelem->get_node(k);
newelem->set_node(2) = node;
newelem->set_neighbor(0, nelem);
newelem->set_ghost(true);
if (l>0)
newelem->set_neighbor(2, libmesh_nullptr);
nelem->set_neighbor(k, newelem);
mesh.add_elem(newelem);
mesh.get_boundary_info().add_node(nelem->get_node(k), 1);
mesh.get_boundary_info().add_node(nelem->get_node(next[k]), 1);
mesh.get_boundary_info().add_node(nelem->get_node(prev[k]), 1);
mesh.get_boundary_info().add_node(node, 1);
nelem = newelem;
k = 2 ;
}
Tri3Subdivision * newelem = new Tri3Subdivision();
newelem->set_node(0) = elem->get_node(next[i]);
newelem->set_node(1) = nelem->get_node(2);
newelem->set_node(2) = elem->get_node(prev[i]);
newelem->set_neighbor(0, nelem);
nelem->set_neighbor(2, newelem);
newelem->set_ghost(true);
newelem->set_neighbor(2, elem);
elem->set_neighbor(next[i],newelem);
mesh.add_elem(newelem);
break;
}
}
for (unsigned int i = 0; i < elem->n_sides(); ++i)
{
libmesh_assert_not_equal_to(elem->neighbor(i), elem);
if (elem->neighbor(i) == libmesh_nullptr)
{
// this is the vertex to be mirrored
Point point = elem->point(i) + elem->point(next[i]) - elem->point(prev[i]);
// Check if the proposed vertex doesn't coincide with
// one of the existing vertices. This is necessary
// because for some triangulations, it can happen that
// two mirrored ghost vertices coincide, which would
// then lead to a zero size ghost element below.
Node * node = libmesh_nullptr;
for (unsigned int j = 0; j < ghost_nodes.size(); ++j)
{
if ((*ghost_nodes[j] - point).size() < tol * (elem->point(i) - point).size())
{
node = ghost_nodes[j];
break;
}
}
// add the new vertex only if no other is nearby
if (node == libmesh_nullptr)
{
node = mesh.add_point(point);
ghost_nodes.push_back(node);
}
Tri3Subdivision * newelem = new Tri3Subdivision();
ghost_elems.push_back(newelem);
newelem->set_node(0) = elem->get_node(next[i]);
newelem->set_node(1) = elem->get_node(i);
newelem->set_node(2) = node;
newelem->set_neighbor(0, elem);
newelem->set_ghost(true);
elem->set_neighbor(i, newelem);
mesh.add_elem(newelem);
mesh.get_boundary_info().add_node(elem->get_node(i), 1);
mesh.get_boundary_info().add_node(elem->get_node(next[i]), 1);
mesh.get_boundary_info().add_node(elem->get_node(prev[i]), 1);
mesh.get_boundary_info().add_node(node, 1);
}
}
}
// add the missing ghost elements (connecting new ghost nodes)
std::vector<Tri3Subdivision *> missing_ghost_elems;
std::vector<Tri3Subdivision *>::iterator ghost_el = ghost_elems.begin();
const std::vector<Tri3Subdivision *>::iterator end_ghost_el = ghost_elems.end();
for (; ghost_el != end_ghost_el; ++ghost_el)
{
Tri3Subdivision * elem = *ghost_el;
libmesh_assert(elem->is_ghost());
for (unsigned int i = 0; i < elem->n_sides(); ++i)
{
if (elem->neighbor(i) == libmesh_nullptr &&
elem->neighbor(prev[i]) != libmesh_nullptr)
{
// go around counter-clockwise
Tri3Subdivision * nb1 = static_cast<Tri3Subdivision *>(elem->neighbor(prev[i]));
Tri3Subdivision * nb2 = nb1;
unsigned int j = i;
unsigned int n_nb = 0;
while (nb1 != libmesh_nullptr && nb1->id() != elem->id())
{
j = nb1->local_node_number(elem->node(i));
nb2 = nb1;
nb1 = static_cast<Tri3Subdivision *>(nb1->neighbor(prev[j]));
libmesh_assert(nb1 == libmesh_nullptr || nb1->id() != nb2->id());
n_nb++;
}
libmesh_assert_not_equal_to(nb2->id(), elem->id());
// Above, we merged coinciding ghost vertices. Therefore, we need
// to exclude the case where there is no ghost element to add between
// these two (identical) ghost nodes.
if (elem->get_node(next[i])->id() == nb2->get_node(prev[j])->id())
break;
// If the number of already present neighbors is less than 4, we add another extra element
// so that the node in the middle of the loop ends up being of valence=6.
// This case usually happens when the middle node corresponds to a corner of the original mesh,
// and the extra element below prevents degenerated triangles in the mesh corners.
if (n_nb < 4)
{
// this is the vertex to be mirrored
Point point = nb2->point(j) + nb2->point(prev[j]) - nb2->point(next[j]);
// Check if the proposed vertex doesn't coincide with one of the existing vertices.
// This is necessary because for some triangulations, it can happen that two mirrored
// ghost vertices coincide, which would then lead to a zero size ghost element below.
Node * node = libmesh_nullptr;
for (unsigned int k = 0; k < ghost_nodes.size(); ++k)
{
if ((*ghost_nodes[k] - point).size() < tol * (nb2->point(j) - point).size())
{
node = ghost_nodes[k];
break;
}
}
// add the new vertex only if no other is nearby
if (node == libmesh_nullptr)
{
node = mesh.add_point(point);
ghost_nodes.push_back(node);
}
Tri3Subdivision * newelem = new Tri3Subdivision();
newelem->set_node(0) = nb2->get_node(j);
newelem->set_node(1) = nb2->get_node(prev[j]);
newelem->set_node(2) = node;
newelem->set_neighbor(0, nb2);
newelem->set_neighbor(1, libmesh_nullptr);
newelem->set_ghost(true);
nb2->set_neighbor(prev[j], newelem);
mesh.add_elem(newelem);
mesh.get_boundary_info().add_node(nb2->get_node(j), 1);
mesh.get_boundary_info().add_node(nb2->get_node(prev[j]), 1);
mesh.get_boundary_info().add_node(node, 1);
nb2 = newelem;
j = nb2->local_node_number(elem->node(i));
}
Tri3Subdivision * newelem = new Tri3Subdivision();
newelem->set_node(0) = elem->get_node(next[i]);
newelem->set_node(1) = elem->get_node(i);
newelem->set_node(2) = nb2->get_node(prev[j]);
newelem->set_neighbor(0, elem);
newelem->set_neighbor(1, nb2);
newelem->set_neighbor(2, libmesh_nullptr);
newelem->set_ghost(true);
elem->set_neighbor(i, newelem);
nb2->set_neighbor(prev[j], newelem);
missing_ghost_elems.push_back(newelem);
break;
}
} // end side loop
} // end ghost element loop
// add the missing ghost elements to the mesh
std::vector<Tri3Subdivision *>::iterator missing_el = missing_ghost_elems.begin();
const std::vector<Tri3Subdivision *>::iterator end_missing_el = missing_ghost_elems.end();
for (; missing_el != end_missing_el; ++missing_el)
mesh.add_elem(*missing_el);
}