void CentroidPartitioner::compute_centroids (MeshBase& mesh)
{
_elem_centroids.clear();
_elem_centroids.reserve(mesh.n_elem());
// elem_iterator it(mesh.elements_begin());
// const elem_iterator it_end(mesh.elements_end());
MeshBase::element_iterator it = mesh.elements_begin();
const MeshBase::element_iterator it_end = mesh.elements_end();
for (; it != it_end; ++it)
{
Elem* elem = *it;
_elem_centroids.push_back(std::make_pair(elem->centroid(), elem));
}
}
// ------------------------------------------------------------
// SFCPartitioner implementation
void SFCPartitioner::_do_partition (MeshBase & mesh,
const unsigned int n)
{
libmesh_assert_greater (n, 0);
// Check for an easy return
if (n == 1)
{
this->single_partition (mesh);
return;
}
// What to do if the sfcurves library IS NOT present
#ifndef LIBMESH_HAVE_SFCURVES
libmesh_here();
libMesh::err << "ERROR: The library has been built without" << std::endl
<< "Space Filling Curve support. Using a linear" << std::endl
<< "partitioner instead!" << std::endl;
LinearPartitioner lp;
lp.partition (mesh, n);
// What to do if the sfcurves library IS present
#else
LOG_SCOPE("sfc_partition()", "SFCPartitioner");
const dof_id_type n_active_elem = mesh.n_active_elem();
const dof_id_type n_elem = mesh.n_elem();
// the forward_map maps the active element id
// into a contiguous block of indices
std::vector<dof_id_type>
forward_map (n_elem, DofObject::invalid_id);
// the reverse_map maps the contiguous ids back
// to active elements
std::vector<Elem *> reverse_map (n_active_elem, libmesh_nullptr);
int size = static_cast<int>(n_active_elem);
std::vector<double> x (size);
std::vector<double> y (size);
std::vector<double> z (size);
std::vector<int> table (size);
// We need to map the active element ids into a
// contiguous range.
{
MeshBase::element_iterator elem_it = mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = mesh.active_elements_end();
dof_id_type el_num = 0;
for (; elem_it != elem_end; ++elem_it)
{
libmesh_assert_less ((*elem_it)->id(), forward_map.size());
libmesh_assert_less (el_num, reverse_map.size());
forward_map[(*elem_it)->id()] = el_num;
reverse_map[el_num] = *elem_it;
el_num++;
}
libmesh_assert_equal_to (el_num, n_active_elem);
}
// Get the centroid for each active element
{
// const_active_elem_iterator elem_it (mesh.const_elements_begin());
// const const_active_elem_iterator elem_end(mesh.const_elements_end());
MeshBase::element_iterator elem_it = mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem * elem = *elem_it;
libmesh_assert_less (elem->id(), forward_map.size());
const Point p = elem->centroid();
x[forward_map[elem->id()]] = p(0);
y[forward_map[elem->id()]] = p(1);
z[forward_map[elem->id()]] = p(2);
}
}
// build the space-filling curve
if (_sfc_type == "Hilbert")
Sfc::hilbert (&x[0], &y[0], &z[0], &size, &table[0]);
else if (_sfc_type == "Morton")
Sfc::morton (&x[0], &y[0], &z[0], &size, &table[0]);
else
{
libmesh_here();
libMesh::err << "ERROR: Unknown type: " << _sfc_type << std::endl
<< " Valid types are" << std::endl
<< " \"Hilbert\"" << std::endl
<< " \"Morton\"" << std::endl
<< " " << std::endl
<< "Proceeding with a Hilbert curve." << std::endl;
Sfc::hilbert (&x[0], &y[0], &z[0], &size, &table[0]);
}
// Assign the partitioning to the active elements
{
// {
// std::ofstream out ("sfc.dat");
// out << "variables=x,y,z" << std::endl;
// out << "zone f=point" << std::endl;
// for (unsigned int i=0; i<n_active_elem; i++)
// out << x[i] << " "
// << y[i] << " "
// << z[i] << std::endl;
// }
const dof_id_type blksize = (n_active_elem+n-1)/n;
for (dof_id_type i=0; i<n_active_elem; i++)
{
libmesh_assert_less (static_cast<unsigned int>(table[i]-1), reverse_map.size());
Elem * elem = reverse_map[table[i]-1];
elem->processor_id() = cast_int<processor_id_type>
(i/blksize);
}
}
#endif
}
//---------------------------------------------------------
// CentroidPartitioner methods
void CentroidPartitioner::_do_partition (MeshBase& mesh,
const unsigned int n)
{
// Check for an easy return
if (n == 1)
{
this->single_partition (mesh);
return;
}
// Possibly reconstruct centroids
if (mesh.n_elem() != _elem_centroids.size())
this->compute_centroids (mesh);
switch (this->sort_method())
{
case X:
{
std::sort(_elem_centroids.begin(),
_elem_centroids.end(),
CentroidPartitioner::sort_x);
break;
}
case Y:
{
std::sort(_elem_centroids.begin(),
_elem_centroids.end(),
CentroidPartitioner::sort_y);
break;
}
case Z:
{
std::sort(_elem_centroids.begin(),
_elem_centroids.end(),
CentroidPartitioner::sort_z);
break;
}
case RADIAL:
{
std::sort(_elem_centroids.begin(),
_elem_centroids.end(),
CentroidPartitioner::sort_radial);
break;
}
default:
libmesh_error();
}
// Make sure the user has not handed us an
// invalid number of partitions.
libmesh_assert_greater (n, 0);
// the number of elements, e.g. 1000
const dof_id_type n_elem = mesh.n_elem();
// the number of elements per processor, e.g 400
const dof_id_type target_size = n_elem / n;
// Make sure the mesh hasn't changed since the
// last time we computed the centroids.
libmesh_assert_equal_to (mesh.n_elem(), _elem_centroids.size());
for (dof_id_type i=0; i<n_elem; i++)
{
Elem* elem = _elem_centroids[i].second;
elem->processor_id() =
std::min (libmesh_cast_int<processor_id_type>(i / target_size),
libmesh_cast_int<processor_id_type>(n-1));
}
}
void MeshTools::Subdivision::all_subdivision(MeshBase & mesh)
{
std::vector<Elem *> new_elements;
new_elements.reserve(mesh.n_elem());
const bool mesh_has_boundary_data =
(mesh.get_boundary_info().n_boundary_ids() > 0);
std::vector<Elem *> new_boundary_elements;
std::vector<short int> new_boundary_sides;
std::vector<boundary_id_type> new_boundary_ids;
MeshBase::const_element_iterator el = mesh.elements_begin();
const MeshBase::const_element_iterator end_el = mesh.elements_end();
for (; el != end_el; ++el)
{
const Elem * elem = *el;
libmesh_assert_equal_to(elem->type(), TRI3);
Elem * tri = new Tri3Subdivision;
tri->set_id(elem->id());
tri->subdomain_id() = elem->subdomain_id();
tri->set_node(0) = (*el)->get_node(0);
tri->set_node(1) = (*el)->get_node(1);
tri->set_node(2) = (*el)->get_node(2);
if (mesh_has_boundary_data)
{
for (unsigned short side = 0; side < elem->n_sides(); ++side)
{
const boundary_id_type boundary_id =
mesh.get_boundary_info().boundary_id(elem, side);
if (boundary_id != BoundaryInfo::invalid_id)
{
// add the boundary id to the list of new boundary ids
new_boundary_ids.push_back(boundary_id);
new_boundary_elements.push_back(tri);
new_boundary_sides.push_back(side);
}
}
// remove the original element from the BoundaryInfo structure
mesh.get_boundary_info().remove(elem);
}
new_elements.push_back(tri);
mesh.insert_elem(tri);
}
mesh.prepare_for_use();
if (mesh_has_boundary_data)
{
// If the old mesh had boundary data, the new mesh better have some too.
libmesh_assert_greater(new_boundary_elements.size(), 0);
// We should also be sure that the lengths of the new boundary data vectors
// are all the same.
libmesh_assert_equal_to(new_boundary_sides.size(), new_boundary_elements.size());
libmesh_assert_equal_to(new_boundary_sides.size(), new_boundary_ids.size());
// Add the new boundary info to the mesh.
for (unsigned int s = 0; s < new_boundary_elements.size(); ++s)
mesh.get_boundary_info().add_side(new_boundary_elements[s],
new_boundary_sides[s],
new_boundary_ids[s]);
}
mesh.prepare_for_use();
}
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);
}