bool UnstructuredMesh::contract ()
{
LOG_SCOPE ("contract()", "Mesh");
// Flag indicating if this call actually changes the mesh
bool mesh_changed = false;
element_iterator in = elements_begin();
const element_iterator end = elements_end();
#ifdef DEBUG
for ( ; in != end; ++in)
if (*in != libmesh_nullptr)
{
Elem * el = *in;
libmesh_assert(el->active() || el->subactive() || el->ancestor());
}
in = elements_begin();
#endif
// Loop over the elements.
for ( ; in != end; ++in)
if (*in != libmesh_nullptr)
{
Elem * el = *in;
// Delete all the subactive ones
if (el->subactive())
{
// No level-0 element should be subactive.
// Note that we CAN'T test elem->level(), as that
// touches elem->parent()->dim(), and elem->parent()
// might have already been deleted!
libmesh_assert(el->parent());
// Delete the element
// This just sets a pointer to NULL, and doesn't
// invalidate any iterators
this->delete_elem(el);
// the mesh has certainly changed
mesh_changed = true;
}
else
{
// Compress all the active ones
if (el->active())
el->contract();
else
libmesh_assert (el->ancestor());
}
}
// Strip any newly-created NULL voids out of the element array
this->renumber_nodes_and_elements();
// FIXME: Need to understand why deleting subactive children
// invalidates the point locator. For now we will clear it explicitly
this->clear_point_locator();
return mesh_changed;
}
void UnstructuredMesh::find_neighbors (const bool reset_remote_elements,
const bool reset_current_list)
{
// We might actually want to run this on an empty mesh
// (e.g. the boundary mesh for a nonexistant bcid!)
// libmesh_assert_not_equal_to (this->n_nodes(), 0);
// libmesh_assert_not_equal_to (this->n_elem(), 0);
// This function must be run on all processors at once
parallel_object_only();
LOG_SCOPE("find_neighbors()", "Mesh");
const element_iterator el_end = this->elements_end();
//TODO:[BSK] This should be removed later?!
if (reset_current_list)
for (element_iterator el = this->elements_begin(); el != el_end; ++el)
{
Elem * e = *el;
for (unsigned int s=0; s<e->n_neighbors(); s++)
if (e->neighbor_ptr(s) != remote_elem ||
reset_remote_elements)
e->set_neighbor(s, libmesh_nullptr);
}
// Find neighboring elements by first finding elements
// with identical side keys and then check to see if they
// are neighbors
{
// data structures -- Use the hash_multimap if available
typedef unsigned int key_type;
typedef std::pair<Elem *, unsigned char> val_type;
typedef std::pair<key_type, val_type> key_val_pair;
typedef LIBMESH_BEST_UNORDERED_MULTIMAP<key_type, val_type> map_type;
// A map from side keys to corresponding elements & side numbers
map_type side_to_elem_map;
for (element_iterator el = this->elements_begin(); el != el_end; ++el)
{
Elem * element = *el;
for (unsigned char ms=0; ms<element->n_neighbors(); ms++)
{
next_side:
// If we haven't yet found a neighbor on this side, try.
// Even if we think our neighbor is remote, that
// information may be out of date.
if (element->neighbor_ptr(ms) == libmesh_nullptr ||
element->neighbor_ptr(ms) == remote_elem)
{
// Get the key for the side of this element
const unsigned int key = element->key(ms);
// Look for elements that have an identical side key
std::pair <map_type::iterator, map_type::iterator>
bounds = side_to_elem_map.equal_range(key);
// May be multiple keys, check all the possible
// elements which _might_ be neighbors.
if (bounds.first != bounds.second)
{
// Get the side for this element
const UniquePtr<Elem> my_side(element->side_ptr(ms));
// Look at all the entries with an equivalent key
while (bounds.first != bounds.second)
{
// Get the potential element
Elem * neighbor = bounds.first->second.first;
// Get the side for the neighboring element
const unsigned int ns = bounds.first->second.second;
const UniquePtr<Elem> their_side(neighbor->side_ptr(ns));
//libmesh_assert(my_side.get());
//libmesh_assert(their_side.get());
// If found a match with my side
//
// We need special tests here for 1D:
// since parents and children have an equal
// side (i.e. a node), we need to check
// ns != ms, and we also check level() to
// avoid setting our neighbor pointer to
// any of our neighbor's descendants
if( (*my_side == *their_side) &&
(element->level() == neighbor->level()) &&
((element->dim() != 1) || (ns != ms)) )
{
// So share a side. Is this a mixed pair
// of subactive and active/ancestor
// elements?
// If not, then we're neighbors.
// If so, then the subactive's neighbor is
if (element->subactive() ==
neighbor->subactive())
{
// an element is only subactive if it has
// been coarsened but not deleted
element->set_neighbor (ms,neighbor);
neighbor->set_neighbor(ns,element);
}
else if (element->subactive())
{
element->set_neighbor(ms,neighbor);
}
else if (neighbor->subactive())
{
neighbor->set_neighbor(ns,element);
}
side_to_elem_map.erase (bounds.first);
// get out of this nested crap
goto next_side;
}
++bounds.first;
}
}
// didn't find a match...
// Build the map entry for this element
key_val_pair kvp;
kvp.first = key;
kvp.second.first = element;
kvp.second.second = ms;
// use the lower bound as a hint for
// where to put it.
#if defined(LIBMESH_HAVE_UNORDERED_MAP) || defined(LIBMESH_HAVE_TR1_UNORDERED_MAP) || defined(LIBMESH_HAVE_HASH_MAP) || defined(LIBMESH_HAVE_EXT_HASH_MAP)
side_to_elem_map.insert (kvp);
#else
side_to_elem_map.insert (bounds.first,kvp);
#endif
}
}
}
}
#ifdef LIBMESH_ENABLE_AMR
/**
* Here we look at all of the child elements which
* don't already have valid neighbors.
*
* If a child element has a NULL neighbor it is
* either because it is on the boundary or because
* its neighbor is at a different level. In the
* latter case we must get the neighbor from the
* parent.
*
* If a child element has a remote_elem neighbor
* on a boundary it shares with its parent, that
* info may have become out-dated through coarsening
* of the neighbor's parent. In this case, if the
* parent's neighbor is active then the child should
* share it.
*
* Furthermore, that neighbor better be active,
* otherwise we missed a child somewhere.
*
*
* We also need to look through children ordered by increasing
* refinement level in order to add new interior_parent() links in
* boundary elements which have just been generated by refinement,
* and fix links in boundary elements whose previous
* interior_parent() has just been coarsened away.
*/
const unsigned int n_levels = MeshTools::n_levels(*this);
for (unsigned int level = 1; level < n_levels; ++level)
{
element_iterator end = this->level_elements_end(level);
for (element_iterator el = this->level_elements_begin(level);
el != end; ++el)
{
Elem * current_elem = *el;
libmesh_assert(current_elem);
Elem * parent = current_elem->parent();
libmesh_assert(parent);
const unsigned int my_child_num = parent->which_child_am_i(current_elem);
for (unsigned int s=0; s < current_elem->n_neighbors(); s++)
{
if (current_elem->neighbor_ptr(s) == libmesh_nullptr ||
(current_elem->neighbor_ptr(s) == remote_elem &&
parent->is_child_on_side(my_child_num, s)))
{
Elem * neigh = parent->neighbor_ptr(s);
// If neigh was refined and had non-subactive children
// made remote earlier, then a non-subactive elem should
// actually have one of those remote children as a
// neighbor
if (neigh && (neigh->ancestor()) && (!current_elem->subactive()))
{
#ifdef DEBUG
// Let's make sure that "had children made remote"
// situation is actually the case
libmesh_assert(neigh->has_children());
bool neigh_has_remote_children = false;
for (unsigned int c = 0; c != neigh->n_children(); ++c)
{
if (neigh->child_ptr(c) == remote_elem)
neigh_has_remote_children = true;
}
libmesh_assert(neigh_has_remote_children);
// And let's double-check that we don't have
// a remote_elem neighboring a local element
libmesh_assert_not_equal_to (current_elem->processor_id(),
this->processor_id());
#endif // DEBUG
neigh = const_cast<RemoteElem *>(remote_elem);
}
if (!current_elem->subactive())
current_elem->set_neighbor(s, neigh);
#ifdef DEBUG
if (neigh != libmesh_nullptr && neigh != remote_elem)
// We ignore subactive elements here because
// we don't care about neighbors of subactive element.
if ((!neigh->active()) && (!current_elem->subactive()))
{
libMesh::err << "On processor " << this->processor_id()
<< std::endl;
libMesh::err << "Bad element ID = " << current_elem->id()
<< ", Side " << s << ", Bad neighbor ID = " << neigh->id() << std::endl;
libMesh::err << "Bad element proc_ID = " << current_elem->processor_id()
<< ", Bad neighbor proc_ID = " << neigh->processor_id() << std::endl;
libMesh::err << "Bad element size = " << current_elem->hmin()
<< ", Bad neighbor size = " << neigh->hmin() << std::endl;
libMesh::err << "Bad element center = " << current_elem->centroid()
<< ", Bad neighbor center = " << neigh->centroid() << std::endl;
libMesh::err << "ERROR: "
<< (current_elem->active()?"Active":"Ancestor")
<< " Element at level "
<< current_elem->level() << std::endl;
libMesh::err << "with "
<< (parent->active()?"active":
(parent->subactive()?"subactive":"ancestor"))
<< " parent share "
<< (neigh->subactive()?"subactive":"ancestor")
<< " neighbor at level " << neigh->level()
<< std::endl;
NameBasedIO(*this).write ("bad_mesh.gmv");
libmesh_error_msg("Problematic mesh written to bad_mesh.gmv.");
}
#endif // DEBUG
}
}
// We can skip to the next element if we're full-dimension
// and therefore don't have any interior parents
if (current_elem->dim() >= LIBMESH_DIM)
continue;
// We have no interior parents unless we can find one later
current_elem->set_interior_parent(libmesh_nullptr);
Elem * pip = parent->interior_parent();
if (!pip)
continue;
// If there's no interior_parent children, whether due to a
// remote element or a non-conformity, then there's no
// children to search.
if (pip == remote_elem || pip->active())
{
current_elem->set_interior_parent(pip);
continue;
}
// For node comparisons we'll need a sensible tolerance
Real node_tolerance = current_elem->hmin() * TOLERANCE;
// Otherwise our interior_parent should be a child of our
// parent's interior_parent.
for (unsigned int c=0; c != pip->n_children(); ++c)
{
Elem * child = pip->child_ptr(c);
// If we have a remote_elem, that might be our
// interior_parent. We'll set it provisionally now and
// keep trying to find something better.
if (child == remote_elem)
{
current_elem->set_interior_parent
(const_cast<RemoteElem *>(remote_elem));
continue;
}
bool child_contains_our_nodes = true;
for (unsigned int n=0; n != current_elem->n_nodes();
++n)
{
bool child_contains_this_node = false;
for (unsigned int cn=0; cn != child->n_nodes();
++cn)
if (child->point(cn).absolute_fuzzy_equals
(current_elem->point(n), node_tolerance))
{
child_contains_this_node = true;
break;
}
if (!child_contains_this_node)
{
child_contains_our_nodes = false;
break;
}
}
if (child_contains_our_nodes)
{
current_elem->set_interior_parent(child);
break;
}
}
// We should have found *some* interior_parent at this
// point, whether semilocal or remote.
libmesh_assert(current_elem->interior_parent());
}
}
#endif // AMR
#ifdef DEBUG
MeshTools::libmesh_assert_valid_neighbors(*this,
!reset_remote_elements);
MeshTools::libmesh_assert_valid_amr_interior_parents(*this);
#endif
}