void ElemCutter::find_intersection_points(const Elem & elem,
const std::vector<Real> & vertex_distance_func)
{
_intersection_pts.clear();
for (unsigned int e=0; e<elem.n_edges(); e++)
{
std::unique_ptr<const Elem> edge (elem.build_edge_ptr(e));
// find the element nodes el0, el1 that map
unsigned int
el0 = elem.get_node_index(edge->node_ptr(0)),
el1 = elem.get_node_index(edge->node_ptr(1));
libmesh_assert (elem.is_vertex(el0));
libmesh_assert (elem.is_vertex(el1));
libmesh_assert_less (el0, vertex_distance_func.size());
libmesh_assert_less (el1, vertex_distance_func.size());
const Real
d0 = vertex_distance_func[el0],
d1 = vertex_distance_func[el1];
// if this egde has a 0 crossing
if (d0*d1 < 0.)
{
libmesh_assert_not_equal_to (d0, d1);
// then find d_star in [0,1], the
// distance from el0 to el1 where the 0 lives.
const Real d_star = d0 / (d0 - d1);
// Prevent adding nodes trivially close to existing
// nodes.
const Real endpoint_tol = 0.01;
if ( (d_star > endpoint_tol) &&
(d_star < (1.-endpoint_tol)) )
{
const Point x_star = (edge->point(0)*(1-d_star) +
edge->point(1)*d_star);
std::cout << "adding cut point (d_star, x_star) = "
<< d_star << " , " << x_star << std::endl;
_intersection_pts.push_back (x_star);
}
}
}
}
//-----------------------------------------------------------------
// Mesh refinement methods
bool MeshRefinement::limit_level_mismatch_at_edge (const unsigned int max_mismatch)
{
// This function must be run on all processors at once
parallel_only();
bool flags_changed = false;
// Maps holding the maximum element level that touches an edge
std::map<std::pair<unsigned int, unsigned int>, unsigned char>
max_level_at_edge;
std::map<std::pair<unsigned int, unsigned int>, unsigned char>
max_p_level_at_edge;
// Loop over all the active elements & fill the maps
{
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;
const unsigned char elem_level =
elem->level() + ((elem->refinement_flag() == Elem::REFINE) ? 1 : 0);
const unsigned char elem_p_level =
elem->p_level() + ((elem->p_refinement_flag() == Elem::REFINE) ? 1 : 0);
// Set the max_level at each edge
for (unsigned int n=0; n<elem->n_edges(); n++)
{
AutoPtr<Elem> edge = elem->build_edge(n);
unsigned int childnode0 = edge->node(0);
unsigned int childnode1 = edge->node(1);
if (childnode1 < childnode0)
std::swap(childnode0, childnode1);
for (const Elem *p = elem; p != NULL; p = p->parent())
{
AutoPtr<Elem> pedge = p->build_edge(n);
unsigned int node0 = pedge->node(0);
unsigned int node1 = pedge->node(1);
if (node1 < node0)
std::swap(node0, node1);
// If elem does not share this edge with its ancestor
// p, refinement levels of elements sharing p's edge
// are not restricted by refinement levels of elem.
// Furthermore, elem will not share this edge with any
// of p's ancestors, so we can safely break out of the
// for loop early.
if (node0 != childnode0 && node1 != childnode1)
break;
childnode0 = node0;
childnode1 = node1;
std::pair<unsigned int, unsigned int> edge_key =
std::make_pair(node0, node1);
if (max_level_at_edge.find(edge_key) ==
max_level_at_edge.end())
{
max_level_at_edge[edge_key] = elem_level;
max_p_level_at_edge[edge_key] = elem_p_level;
}
else
{
max_level_at_edge[edge_key] =
std::max (max_level_at_edge[edge_key], elem_level);
max_p_level_at_edge[edge_key] =
std::max (max_p_level_at_edge[edge_key], elem_p_level);
}
}
}
}
}
// Now loop over the active elements and flag the elements
// who violate the requested level mismatch
{
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;
const unsigned int elem_level = elem->level();
const unsigned int elem_p_level = elem->p_level();
// Skip the element if it is already fully flagged
if (elem->refinement_flag() == Elem::REFINE &&
elem->p_refinement_flag() == Elem::REFINE)
continue;
// Loop over the nodes, check for possible mismatch
for (unsigned int n=0; n<elem->n_edges(); n++)
{
AutoPtr<Elem> edge = elem->build_edge(n);
unsigned int node0 = edge->node(0);
unsigned int node1 = edge->node(1);
if (node1 < node0)
std::swap(node0, node1);
std::pair<unsigned int, unsigned int> edge_key =
std::make_pair(node0, node1);
// Flag the element for refinement if it violates
// the requested level mismatch
if ( (elem_level + max_mismatch) < max_level_at_edge[edge_key]
&& elem->refinement_flag() != Elem::REFINE)
{
elem->set_refinement_flag (Elem::REFINE);
flags_changed = true;
}
if ( (elem_p_level + max_mismatch) < max_p_level_at_edge[edge_key]
&& elem->p_refinement_flag() != Elem::REFINE)
{
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 or edge 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++);
}
for (unsigned int e = 0; e != elem->n_edges(); ++e)
{
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_edge (elem, e, *in++);
}
}
// Return the new element
*out = elem;
}