unsigned TetGenMeshInterface::check_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 3;
MeshBase::element_iterator it = this->_mesh.elements_begin();
const MeshBase::element_iterator end = this->_mesh.elements_end();
for (; it != end ; ++it)
{
Elem* elem = *it;
// Check for proper element type
if (elem->type() != TRI3)
{
//libMesh::err << "ERROR: Some of the elements in the original mesh were not TRI3!" << std::endl;
//libmesh_error();
return 1;
}
for (unsigned int i=0; i<elem->n_neighbors(); ++i)
{
if (elem->neighbor(i) == NULL)
{
// libMesh::err << "ERROR: Non-convex hull, cannot be tetrahedralized." << std::endl;
// libmesh_error();
return 2;
}
}
}
// If we made it here, return success!
return 0;
}
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// information may be out of date.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
}
bool MeshRefinement::eliminate_unrefined_patches ()
{
// This function must be run on all processors at once
parallel_only();
bool flags_changed = false;
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)
{
Elem* elem = *elem_it;
// First assume that we'll have to flag this element for both h
// and p refinement, then change our minds if we see any
// neighbors that are as coarse or coarser than us.
bool h_flag_me = true,
p_flag_me = true;
// Skip the element if it is already fully flagged for refinement
if (elem->p_refinement_flag() == Elem::REFINE)
p_flag_me = false;
if (elem->refinement_flag() == Elem::REFINE)
{
h_flag_me = false;
if (!p_flag_me)
continue;
}
// Test the parent if that is already flagged for coarsening
else if (elem->refinement_flag() == Elem::COARSEN)
{
libmesh_assert(elem->parent());
elem = elem->parent();
// FIXME - this doesn't seem right - RHS
if (elem->refinement_flag() != Elem::COARSEN_INACTIVE)
continue;
p_flag_me = false;
}
const unsigned int my_level = elem->level();
int my_p_adjustment = 0;
if (elem->p_refinement_flag() == Elem::REFINE)
my_p_adjustment = 1;
else if (elem->p_refinement_flag() == Elem::COARSEN)
{
libmesh_assert_greater (elem->p_level(), 0);
my_p_adjustment = -1;
}
const unsigned int my_new_p_level = elem->p_level() +
my_p_adjustment;
// Check all the element neighbors
for (unsigned int n=0; n<elem->n_neighbors(); n++)
{
const Elem *neighbor = elem->neighbor(n);
// Quit if the element is on a local boundary
if (neighbor == NULL || neighbor == remote_elem)
{
h_flag_me = false;
p_flag_me = false;
break;
}
// if the neighbor will be equally or less refined than
// we are, then we will not become an unrefined island.
// So if we are still considering h refinement:
if (h_flag_me &&
// If our neighbor is already at a lower level,
// it can't end up at a higher level even if it
// is flagged for refinement once
((neighbor->level() < my_level) ||
// If our neighbor is at the same level but isn't
// flagged for refinement, it won't end up at a
// higher level
((neighbor->active()) &&
(neighbor->refinement_flag() != Elem::REFINE)) ||
// If our neighbor is currently more refined but is
// a parent flagged for coarsening, it will end up
// at the same level.
(neighbor->refinement_flag() == Elem::COARSEN_INACTIVE)))
{
// We've proven we won't become an unrefined island,
// so don't h refine to avoid that.
h_flag_me = false;
// If we've also proven we don't need to p refine,
// we don't need to check more neighbors
if (!p_flag_me)
break;
}
if (p_flag_me)
{
// if active neighbors will have a p level
// equal to or lower than ours, then we do not need to p
// refine ourselves.
if (neighbor->active())
{
int p_adjustment = 0;
if (neighbor->p_refinement_flag() == Elem::REFINE)
p_adjustment = 1;
else if (neighbor->p_refinement_flag() == Elem::COARSEN)
{
libmesh_assert_greater (neighbor->p_level(), 0);
p_adjustment = -1;
}
if (my_new_p_level >= neighbor->p_level() + p_adjustment)
{
p_flag_me = false;
if (!h_flag_me)
break;
}
}
// If we have inactive neighbors, we need to
// test all their active descendants which neighbor us
else if (neighbor->ancestor())
{
if (neighbor->min_new_p_level_by_neighbor(elem,
my_new_p_level + 2) <= my_new_p_level)
{
p_flag_me = false;
if (!h_flag_me)
break;
}
}
}
}
if (h_flag_me)
{
// Parents that would create islands should no longer
// coarsen
if (elem->refinement_flag() == Elem::COARSEN_INACTIVE)
{
for (unsigned int c=0; c<elem->n_children(); c++)
{
libmesh_assert_equal_to (elem->child(c)->refinement_flag(),
Elem::COARSEN);
elem->child(c)->set_refinement_flag(Elem::DO_NOTHING);
}
elem->set_refinement_flag(Elem::INACTIVE);
}
else
elem->set_refinement_flag(Elem::REFINE);
flags_changed = true;
}
if (p_flag_me)
{
if (elem->p_refinement_flag() == Elem::COARSEN)
elem->set_p_refinement_flag(Elem::DO_NOTHING);
else
elem->set_p_refinement_flag(Elem::REFINE);
flags_changed = true;
}
}
// If flags changed on any processor then they changed globally
CommWorld.max(flags_changed);
return flags_changed;
}
void unpack(std::vector<largest_id_type>::const_iterator in,
Elem** out,
MeshBase* mesh)
{
#ifndef NDEBUG
const std::vector<largest_id_type>::const_iterator original_in = in;
const largest_id_type incoming_header = *in++;
libmesh_assert_equal_to (incoming_header, elem_magic_header);
#endif
// int 0: level
const unsigned int level =
static_cast<unsigned int>(*in++);
#ifdef LIBMESH_ENABLE_AMR
// int 1: p level
const unsigned int p_level =
static_cast<unsigned int>(*in++);
// int 2: refinement flag
const int rflag = *in++;
libmesh_assert_greater_equal (rflag, 0);
libmesh_assert_less (rflag, Elem::INVALID_REFINEMENTSTATE);
const Elem::RefinementState refinement_flag =
static_cast<Elem::RefinementState>(rflag);
// int 3: p refinement flag
const int pflag = *in++;
libmesh_assert_greater_equal (pflag, 0);
libmesh_assert_less (pflag, Elem::INVALID_REFINEMENTSTATE);
const Elem::RefinementState p_refinement_flag =
static_cast<Elem::RefinementState>(pflag);
#else
in += 3;
#endif // LIBMESH_ENABLE_AMR
// int 4: element type
const int typeint = *in++;
libmesh_assert_greater_equal (typeint, 0);
libmesh_assert_less (typeint, INVALID_ELEM);
const ElemType type =
static_cast<ElemType>(typeint);
const unsigned int n_nodes =
Elem::type_to_n_nodes_map[type];
// int 5: processor id
const processor_id_type processor_id =
static_cast<processor_id_type>(*in++);
libmesh_assert (processor_id < mesh->n_processors() ||
processor_id == DofObject::invalid_processor_id);
// int 6: subdomain id
const subdomain_id_type subdomain_id =
static_cast<subdomain_id_type>(*in++);
// int 7: dof object id
const dof_id_type id =
static_cast<dof_id_type>(*in++);
libmesh_assert_not_equal_to (id, DofObject::invalid_id);
#ifdef LIBMESH_ENABLE_UNIQUE_ID
// int 8: dof object unique id
const unique_id_type unique_id =
static_cast<unique_id_type>(*in++);
#endif
#ifdef LIBMESH_ENABLE_AMR
// int 9: parent dof object id
const dof_id_type parent_id =
static_cast<dof_id_type>(*in++);
libmesh_assert (level == 0 || parent_id != DofObject::invalid_id);
libmesh_assert (level != 0 || parent_id == DofObject::invalid_id);
// int 10: local child id
const unsigned int which_child_am_i =
static_cast<unsigned int>(*in++);
#else
in += 2;
#endif // LIBMESH_ENABLE_AMR
// Make sure we don't miscount above when adding the "magic" header
// plus the real data header
libmesh_assert_equal_to (in - original_in, header_size + 1);
Elem *elem = mesh->query_elem(id);
// if we already have this element, make sure its
// properties match, and update any missing neighbor
// links, but then go on
if (elem)
{
libmesh_assert_equal_to (elem->level(), level);
libmesh_assert_equal_to (elem->id(), id);
//#ifdef LIBMESH_ENABLE_UNIQUE_ID
// No check for unqiue id sanity
//#endif
libmesh_assert_equal_to (elem->processor_id(), processor_id);
libmesh_assert_equal_to (elem->subdomain_id(), subdomain_id);
libmesh_assert_equal_to (elem->type(), type);
libmesh_assert_equal_to (elem->n_nodes(), n_nodes);
#ifndef NDEBUG
// All our nodes should be correct
for (unsigned int i=0; i != n_nodes; ++i)
libmesh_assert(elem->node(i) ==
static_cast<dof_id_type>(*in++));
#else
in += n_nodes;
#endif
#ifdef LIBMESH_ENABLE_AMR
libmesh_assert_equal_to (elem->p_level(), p_level);
libmesh_assert_equal_to (elem->refinement_flag(), refinement_flag);
libmesh_assert_equal_to (elem->p_refinement_flag(), p_refinement_flag);
libmesh_assert (!level || elem->parent() != NULL);
libmesh_assert (!level || elem->parent()->id() == parent_id);
libmesh_assert (!level || elem->parent()->child(which_child_am_i) == elem);
#endif
// Our neighbor links should be "close to" correct - we may have
// to update them, but we can check for some inconsistencies.
for (unsigned int n=0; n != elem->n_neighbors(); ++n)
{
const dof_id_type neighbor_id =
static_cast<dof_id_type>(*in++);
// If the sending processor sees a domain boundary here,
// we'd better agree.
if (neighbor_id == DofObject::invalid_id)
{
libmesh_assert (!(elem->neighbor(n)));
continue;
}
// If the sending processor has a remote_elem neighbor here,
// then all we know is that we'd better *not* have a domain
// boundary.
if (neighbor_id == remote_elem->id())
{
libmesh_assert(elem->neighbor(n));
continue;
}
Elem *neigh = mesh->query_elem(neighbor_id);
// The sending processor sees a neighbor here, so if we
// don't have that neighboring element, then we'd better
// have a remote_elem signifying that fact.
if (!neigh)
{
libmesh_assert_equal_to (elem->neighbor(n), remote_elem);
continue;
}
// The sending processor has a neighbor here, and we have
// that element, but that does *NOT* mean we're already
// linking to it. Perhaps we initially received both elem
// and neigh from processors on which their mutual link was
// remote?
libmesh_assert(elem->neighbor(n) == neigh ||
elem->neighbor(n) == remote_elem);
// If the link was originally remote, we should update it,
// and make sure the appropriate parts of its family link
// back to us.
if (elem->neighbor(n) == remote_elem)
{
elem->set_neighbor(n, neigh);
elem->make_links_to_me_local(n);
}
}
// FIXME: We should add some debug mode tests to ensure that the
// encoded indexing and boundary conditions are consistent.
}
else
{
// We don't already have the element, so we need to create it.
// Find the parent if necessary
Elem *parent = NULL;
#ifdef LIBMESH_ENABLE_AMR
// Find a child element's parent
if (level > 0)
{
// Note that we must be very careful to construct the send
// connectivity so that parents are encountered before
// children. If we get here and can't find the parent that
// is a fatal error.
parent = mesh->elem(parent_id);
}
// Or assert that the sending processor sees no parent
else
libmesh_assert_equal_to (parent_id, static_cast<dof_id_type>(-1));
#else
// No non-level-0 elements without AMR
libmesh_assert_equal_to (level, 0);
#endif
elem = Elem::build(type,parent).release();
libmesh_assert (elem);
#ifdef LIBMESH_ENABLE_AMR
if (level != 0)
{
// Since this is a newly created element, the parent must
// have previously thought of this child as a remote element.
libmesh_assert_equal_to (parent->child(which_child_am_i), remote_elem);
parent->add_child(elem, which_child_am_i);
}
// Assign the refinement flags and levels
elem->set_p_level(p_level);
elem->set_refinement_flag(refinement_flag);
elem->set_p_refinement_flag(p_refinement_flag);
libmesh_assert_equal_to (elem->level(), level);
// If this element definitely should have children, assign
// remote_elem to all of them for now, for consistency. Later
// unpacked elements may overwrite that.
if (!elem->active())
for (unsigned int c=0; c != elem->n_children(); ++c)
elem->add_child(const_cast<RemoteElem*>(remote_elem), c);
#endif // LIBMESH_ENABLE_AMR
// Assign the IDs
elem->subdomain_id() = subdomain_id;
elem->processor_id() = processor_id;
elem->set_id() = id;
#ifdef LIBMESH_ENABLE_UNIQUE_ID
elem->set_unique_id() = unique_id;
#endif
// Assign the connectivity
libmesh_assert_equal_to (elem->n_nodes(), n_nodes);
for (unsigned int n=0; n != n_nodes; n++)
elem->set_node(n) =
mesh->node_ptr
(static_cast<dof_id_type>(*in++));
for (unsigned int n=0; n<elem->n_neighbors(); n++)
{
const dof_id_type neighbor_id =
static_cast<dof_id_type>(*in++);
if (neighbor_id == DofObject::invalid_id)
continue;
// We may be unpacking an element that was a ghost element on the
// sender, in which case the element's neighbors may not all be
// known by the packed element. We'll have to set such
// neighbors to remote_elem ourselves and wait for a later
// packed element to give us better information.
if (neighbor_id == remote_elem->id())
{
elem->set_neighbor(n, const_cast<RemoteElem*>(remote_elem));
continue;
}
// If we don't have the neighbor element, then it's a
// remote_elem until we get it.
Elem *neigh = mesh->query_elem(neighbor_id);
if (!neigh)
{
elem->set_neighbor(n, const_cast<RemoteElem*>(remote_elem));
continue;
}
// If we have the neighbor element, then link to it, and
// make sure the appropriate parts of its family link back
// to us.
elem->set_neighbor(n, neigh);
elem->make_links_to_me_local(n);
}
elem->unpack_indexing(in);
}
in += elem->packed_indexing_size();
// If this is a coarse element,
// add any element side boundary condition ids
if (level == 0)
for (unsigned int s = 0; s != elem->n_sides(); ++s)
{
const int num_bcs = *in++;
libmesh_assert_greater_equal (num_bcs, 0);
for(int bc_it=0; bc_it < num_bcs; bc_it++)
mesh->boundary_info->add_side (elem, s, *in++);
}
// Return the new element
*out = elem;
}
// The actual implementation of building elements.
void InfElemBuilder::build_inf_elem(const Point& origin,
const bool x_sym,
const bool y_sym,
const bool z_sym,
const bool be_verbose,
std::set< std::pair<dof_id_type,
unsigned int> >* inner_faces)
{
if (be_verbose)
{
#ifdef DEBUG
libMesh::out << " Building Infinite Elements:" << std::endl;
libMesh::out << " updating element neighbor tables..." << std::endl;
#else
libMesh::out << " Verbose mode disabled in non-debug mode." << std::endl;
#endif
}
// update element neighbors
this->_mesh.find_neighbors();
START_LOG("build_inf_elem()", "InfElemBuilder");
// A set for storing element number, side number pairs.
// pair.first == element number, pair.second == side number
std::set< std::pair<dof_id_type,unsigned int> > faces;
std::set< std::pair<dof_id_type,unsigned int> > ofaces;
// A set for storing node numbers on the outer faces.
std::set<dof_id_type> onodes;
// The distance to the farthest point in the mesh from the origin
Real max_r=0.;
// The index of the farthest point in the mesh from the origin
int max_r_node = -1;
#ifdef DEBUG
if (be_verbose)
{
libMesh::out << " collecting boundary sides";
if (x_sym || y_sym || z_sym)
libMesh::out << ", skipping sides in symmetry planes..." << std::endl;
else
libMesh::out << "..." << std::endl;
}
#endif
// Iterate through all elements and sides, collect indices of all active
// boundary sides in the faces set. Skip sides which lie in symmetry planes.
// Later, sides of the inner boundary will be sorted out.
{
MeshBase::element_iterator it = this->_mesh.active_elements_begin();
const MeshBase::element_iterator end = this->_mesh.active_elements_end();
for(; it != end; ++it)
{
Elem* elem = *it;
for (unsigned int s=0; s<elem->n_neighbors(); s++)
{
// check if elem(e) is on the boundary
if (elem->neighbor(s) == NULL)
{
// note that it is safe to use the Elem::side() method,
// which gives a non-full-ordered element
AutoPtr<Elem> side(elem->build_side(s));
// bool flags for symmetry detection
bool sym_side=false;
bool on_x_sym=true;
bool on_y_sym=true;
bool on_z_sym=true;
// Loop over the nodes to check whether they are on the symmetry planes,
// and therefore sufficient to use a non-full-ordered side element
for(unsigned int n=0; n<side->n_nodes(); n++)
{
const Point dist_from_origin = this->_mesh.point(side->node(n)) - origin;
if(x_sym)
if( std::abs(dist_from_origin(0)) > 1.e-3 )
on_x_sym=false;
if(y_sym)
if( std::abs(dist_from_origin(1)) > 1.e-3 )
on_y_sym=false;
if(z_sym)
if( std::abs(dist_from_origin(2)) > 1.e-3 )
on_z_sym=false;
// if(x_sym)
// if( std::abs(dist_from_origin(0)) > 1.e-6 )
// on_x_sym=false;
// if(y_sym)
// if( std::abs(dist_from_origin(1)) > 1.e-6 )
// on_y_sym=false;
// if(z_sym)
// if( std::abs(dist_from_origin(2)) > 1.e-6 )
// on_z_sym=false;
//find the node most distant from origin
Real r = dist_from_origin.size();
if (r > max_r)
{
max_r = r;
max_r_node=side->node(n);
}
}
sym_side = (x_sym && on_x_sym) || (y_sym && on_y_sym) || (z_sym && on_z_sym);
if (!sym_side)
faces.insert( std::make_pair(elem->id(), s) );
} // neighbor(s) == NULL
} // sides
} // elems
}
// If a boundary side has one node on the outer boundary,
// all points of this side are on the outer boundary.
// Start with the node most distant from origin, which has
// to be on the outer boundary, then recursively find all
// sides and nodes connected to it. Found sides are moved
// from faces to ofaces, nodes are collected in onodes.
// Here, the search is done iteratively, because, depending on
// the mesh, a very high level of recursion might be necessary.
if (max_r_node > 0)
onodes.insert(max_r_node);
{
std::set< std::pair<dof_id_type,unsigned int> >::iterator face_it = faces.begin();
unsigned int facesfound=0;
while (face_it != faces.end()) {
std::pair<dof_id_type, unsigned int> p;
p = *face_it;
// This has to be a full-ordered side element,
// since we need the correct n_nodes,
AutoPtr<Elem> side(this->_mesh.elem(p.first)->build_side(p.second));
bool found=false;
for(unsigned int sn=0; sn<side->n_nodes(); sn++)
if(onodes.count(side->node(sn)))
{
found=true;
break;
}
// If a new oface is found, include its nodes in onodes
if(found)
{
for(unsigned int sn=0; sn<side->n_nodes(); sn++)
onodes.insert(side->node(sn));
ofaces.insert(p);
face_it++; // iteration is done here
faces.erase(p);
facesfound++;
}
else
face_it++; // iteration is done here
// If at least one new oface was found in this cycle,
// do another search cycle.
if(facesfound>0 && face_it == faces.end())
{
facesfound = 0;
face_it = faces.begin();
}
}
}
#ifdef DEBUG
if (be_verbose)
libMesh::out << " found "
<< faces.size()
<< " inner and "
<< ofaces.size()
<< " outer boundary faces"
<< std::endl;
#endif
// When the user provided a non-null pointer to
// inner_faces, that implies he wants to have
// this std::set. For now, simply copy the data.
if (inner_faces != NULL)
*inner_faces = faces;
// free memory, clear our local variable, no need
// for it any more.
faces.clear();
// outer_nodes maps onodes to their duplicates
std::map<dof_id_type, Node *> outer_nodes;
// We may need to pick our own object ids in parallel
dof_id_type old_max_node_id = _mesh.max_node_id();
dof_id_type old_max_elem_id = _mesh.max_elem_id();
// for each boundary node, add an outer_node with
// double distance from origin.
std::set<dof_id_type>::iterator on_it = onodes.begin();
for( ; on_it != onodes.end(); ++on_it)
{
Point p = (Point(this->_mesh.point(*on_it)) * 2) - origin;
if (_mesh.is_serial())
{
// Add with a default id in serial
outer_nodes[*on_it]=this->_mesh.add_point(p);
}
else
{
// Pick a unique id in parallel
Node &bnode = _mesh.node(*on_it);
dof_id_type new_id = bnode.id() + old_max_node_id;
outer_nodes[*on_it] =
this->_mesh.add_point(p, new_id,
bnode.processor_id());
}
}
#ifdef DEBUG
// for verbose, remember n_elem
dof_id_type n_conventional_elem = this->_mesh.n_elem();
#endif
// build Elems based on boundary side type
std::set< std::pair<dof_id_type,unsigned int> >::iterator face_it = ofaces.begin();
for( ; face_it != ofaces.end(); ++face_it)
{
// Shortcut to the pair being iterated over
std::pair<dof_id_type,unsigned int> p = *face_it;
// build a full-ordered side element to get the base nodes
AutoPtr<Elem> side(this->_mesh.elem(p.first)->build_side(p.second));
// create cell depending on side type, assign nodes,
// use braces to force scope.
bool is_higher_order_elem = false;
{
Elem* el;
switch(side->type())
{
// 3D infinite elements
// TRIs
case TRI3:
el=new InfPrism6;
break;
case TRI6:
el=new InfPrism12;
is_higher_order_elem = true;
break;
// QUADs
case QUAD4:
el=new InfHex8;
break;
case QUAD8:
el=new InfHex16;
is_higher_order_elem = true;
break;
case QUAD9:
el=new InfHex18;
// the method of assigning nodes (which follows below)
// omits in the case of QUAD9 the bubble node; therefore
// we assign these first by hand here.
el->set_node(16) = side->get_node(8);
el->set_node(17) = outer_nodes[side->node(8)];
is_higher_order_elem=true;
break;
// 2D infinite elements
case EDGE2:
el=new InfQuad4;
break;
case EDGE3:
el=new InfQuad6;
el->set_node(4) = side->get_node(2);
break;
// 1D infinite elements not supported
default:
libMesh::out << "InfElemBuilder::build_inf_elem(Point, bool, bool, bool, bool): "
<< "invalid face element "
<< std::endl;
continue;
}
// In parallel, assign unique ids to the new element
if (!_mesh.is_serial())
{
Elem *belem = _mesh.elem(p.first);
el->processor_id() = belem->processor_id();
// We'd better not have elements with more than 6 sides
el->set_id (belem->id() * 6 + p.second + old_max_elem_id);
}
// assign vertices to the new infinite element
const unsigned int n_base_vertices = side->n_vertices();
for(unsigned int i=0; i<n_base_vertices; i++)
{
el->set_node(i ) = side->get_node(i);
el->set_node(i+n_base_vertices) = outer_nodes[side->node(i)];
}
// when this is a higher order element,
// assign also the nodes in between
if (is_higher_order_elem)
{
// n_safe_base_nodes is the number of nodes in \p side
// that may be safely assigned using below for loop.
// Actually, n_safe_base_nodes is _identical_ with el->n_vertices(),
// since for QUAD9, the 9th node was already assigned above
const unsigned int n_safe_base_nodes = el->n_vertices();
for(unsigned int i=n_base_vertices; i<n_safe_base_nodes; i++)
{
el->set_node(i+n_base_vertices) = side->get_node(i);
el->set_node(i+n_safe_base_nodes) = outer_nodes[side->node(i)];
}
}
// add infinite element to mesh
this->_mesh.add_elem(el);
} // el goes out of scope
} // for
#ifdef DEBUG
_mesh.libmesh_assert_valid_parallel_ids();
if (be_verbose)
libMesh::out << " added "
<< this->_mesh.n_elem() - n_conventional_elem
<< " infinite elements and "
<< onodes.size()
<< " nodes to the mesh"
<< std::endl
<< std::endl;
#endif
STOP_LOG("build_inf_elem()", "InfElemBuilder");
}