void
FeatureFloodCount::appendPeriodicNeighborNodes(FeatureData & data) const
{
if (_is_elemental)
{
for (auto entity : data._local_ids)
{
Elem * elem = _mesh.elemPtr(entity);
for (unsigned int node_n = 0; node_n < elem->n_nodes(); node_n++)
{
auto iters = _periodic_node_map.equal_range(elem->node(node_n));
for (auto it = iters.first; it != iters.second; ++it)
{
data._periodic_nodes.insert(it->first);
data._periodic_nodes.insert(it->second);
}
}
}
}
else
{
for (auto entity : data._local_ids)
{
auto iters = _periodic_node_map.equal_range(entity);
for (auto it = iters.first; it != iters.second; ++it)
{
data._periodic_nodes.insert(it->first);
data._periodic_nodes.insert(it->second);
}
}
}
}
void
GrainTracker::calculateBubbleVolumes()
{
Moose::perf_log.push("calculateBubbleVolumes()", "GrainTracker");
// The size of the bubble array will be sized to the max index of the unique grains map
unsigned int max_id = _unique_grains.size() ? _unique_grains.rbegin()->first + 1: 0;
_all_feature_volumes.resize(max_id, 0);
const MeshBase::const_element_iterator el_end = _mesh.getMesh().active_local_elements_end();
for (MeshBase::const_element_iterator el = _mesh.getMesh().active_local_elements_begin(); el != el_end; ++el)
{
Elem * elem = *el;
unsigned int elem_n_nodes = elem->n_nodes();
Real curr_volume = elem->volume();
for (std::map<unsigned int, MooseSharedPointer<FeatureData> >::iterator it = _unique_grains.begin(); it != _unique_grains.end(); ++it)
{
if (it->second->_status == INACTIVE)
continue;
if (_is_elemental)
{
dof_id_type elem_id = elem->id();
if (it->second->_local_ids.find(elem_id) != it->second->_local_ids.end())
{
mooseAssert(it->first < _all_feature_volumes.size(), "_all_feature_volumes access out of bounds");
_all_feature_volumes[it->first] += curr_volume;
break;
}
}
else
{
// Count the number of nodes on this element which are flooded.
unsigned int flooded_nodes = 0;
for (unsigned int node = 0; node < elem_n_nodes; ++node)
{
dof_id_type node_id = elem->node(node);
if (it->second->_local_ids.find(node_id) != it->second->_local_ids.end())
++flooded_nodes;
}
// If a majority of the nodes for this element are flooded,
// assign its volume to the current bubble_counter entry.
if (flooded_nodes >= elem_n_nodes / 2)
_all_feature_volumes[it->first] += curr_volume;
}
}
}
// do all the sums!
_communicator.sum(_all_feature_volumes);
Moose::perf_log.pop("calculateBubbleVolumes()", "GrainTracker");
}
void
NodalFloodCount::calculateBubbleVolumes()
{
Moose::perf_log.push("calculateBubbleVolume()", "NodalFloodCount");
// Size our temporary data structure
std::vector<std::vector<Real> > bubble_volumes(_maps_size);
for (unsigned int map_num = 0; map_num < _maps_size; ++map_num)
{
bubble_volumes[map_num].resize(_bubble_sets[map_num].size());
}
std::vector<unsigned int> flood_nodes(_maps_size);
const MeshBase::const_element_iterator el_end = _mesh.getMesh().active_local_elements_end();
for (MeshBase::const_element_iterator el = _mesh.getMesh().active_local_elements_begin(); el != el_end; ++el)
{
Elem *elem = *el;
unsigned int elem_n_nodes = elem->n_nodes();
Real curr_volume = elem->volume();
for (unsigned int map_num = 0; map_num < _maps_size; ++map_num)
{
unsigned int bubble_counter = 0;
std::list<BubbleData>::const_iterator end = _bubble_sets[map_num].end();
for (std::list<BubbleData>::const_iterator bubble_it1 = _bubble_sets[map_num].begin(); bubble_it1 != end; ++bubble_it1)
{
unsigned int flooded_nodes = 0;
for (unsigned int node = 0; node < elem_n_nodes; ++node)
{
unsigned int node_id = elem->node(node);
if (bubble_it1->_nodes.find(node_id) != bubble_it1->_nodes.end())
++flooded_nodes;
}
// Are a majority of the nodes flooded for this element?
if (flooded_nodes >= elem_n_nodes / 2)
bubble_volumes[map_num][bubble_counter] += curr_volume;
++bubble_counter;
}
}
}
// Stick all the partial bubble volumes in one long single vector to be gathered on the root processor
for (unsigned int map_num = 0; map_num < _maps_size; ++map_num)
_all_bubble_volumes.insert(_all_bubble_volumes.end(), bubble_volumes[map_num].begin(), bubble_volumes[map_num].end());
_communicator.sum(_all_bubble_volumes); //do all the sums!
std::sort(_all_bubble_volumes.begin(), _all_bubble_volumes.end(), std::greater<Real>());
Moose::perf_log.pop("calculateBubbleVolume()", "NodalFloodCount");
}
void
FeatureFloodCount::appendPeriodicNeighborNodes(BubbleData & data) const
{
// Using a typedef makes the code easier to understand and avoids repeating information.
typedef std::multimap<dof_id_type, dof_id_type>::const_iterator IterType;
if (_is_elemental)
{
for (std::set<dof_id_type>::iterator entity_it = data._entity_ids.begin(); entity_it != data._entity_ids.end(); ++entity_it)
{
Elem * elem = _mesh.elem(*entity_it);
for (unsigned int node_n = 0; node_n < elem->n_nodes(); node_n++)
{
std::pair<IterType, IterType> iters = _periodic_node_map.equal_range(elem->node(node_n));
for (IterType it = iters.first; it != iters.second; ++it)
{
data._periodic_nodes.insert(it->first);
data._periodic_nodes.insert(it->second);
}
}
}
}
else
{
for (std::set<dof_id_type>::iterator entity_it = data._entity_ids.begin(); entity_it != data._entity_ids.end(); ++entity_it)
{
std::pair<IterType, IterType> iters = _periodic_node_map.equal_range(*entity_it);
for (IterType it = iters.first; it != iters.second; ++it)
{
data._periodic_nodes.insert(it->first);
data._periodic_nodes.insert(it->second);
}
}
}
}
void TetGenMeshInterface::triangulate_conformingDelaunayMesh_carvehole (const std::vector<Point>& holes,
double quality_constraint,
double volume_constraint)
{
// Before calling this function, the Mesh must contain a convex hull
// of TRI3 elements which define the boundary.
unsigned hull_integrity_check = check_hull_integrity();
// Possibly die if hull integrity check failed
this->process_hull_integrity_result(hull_integrity_check);
// class tetgen_wrapper allows library access on a basic level
TetGenWrapper tetgen_wrapper;
// Copy Mesh's node points into TetGen data structure
this->fill_pointlist(tetgen_wrapper);
// >>> fill input structure "tetgenio" with facet data:
int facet_num = this->_mesh.n_elem();
// allocate memory in "tetgenio" structure:
tetgen_wrapper.allocate_facetlist(facet_num, holes.size());
// Set up tetgen data structures with existing facet information
// from the convex hull.
{
int insertnum = 0;
MeshBase::element_iterator it = this->_mesh.elements_begin();
const MeshBase::element_iterator end = this->_mesh.elements_end();
for (; it != end ; ++it)
{
tetgen_wrapper.allocate_facet_polygonlist(insertnum, 1);
tetgen_wrapper.allocate_polygon_vertexlist(insertnum, 0, 3);
Elem* elem = *it;
for (unsigned int j=0; j<elem->n_nodes(); ++j)
{
// We need to get the sequential index of elem->get_node(j), but
// it should already be stored in _sequential_to_libmesh_node_map...
unsigned libmesh_node_id = elem->node(j);
// The libmesh node IDs may not be sequential, but can we assume
// they are at least in order??? We will do so here.
std::vector<unsigned>::iterator node_iter =
Utility::binary_find(_sequential_to_libmesh_node_map.begin(),
_sequential_to_libmesh_node_map.end(),
libmesh_node_id);
// Check to see if not found: this could also indicate the sequential
// node map is not sorted...
if (node_iter == _sequential_to_libmesh_node_map.end())
{
libMesh::err << "Global node " << libmesh_node_id << " not found in sequential node map!" << std::endl;
libmesh_error();
}
std::vector<unsigned>::difference_type
sequential_index = std::distance(_sequential_to_libmesh_node_map.begin(), node_iter);
// Debugging:
// libMesh::out << "libmesh_node_id=" << libmesh_node_id
// << ", sequential_index=" << sequential_index
// << std::endl;
tetgen_wrapper.set_vertex(insertnum, // facet number
0, // polygon (always 0)
j, // local vertex index in tetgen input
sequential_index);
}
// Go to next facet in polygonlist
insertnum++;
}
}
// fill hole list (if there are holes):
if (holes.size() > 0)
{
std::vector<Point>::const_iterator ihole;
unsigned hole_index = 0;
for (ihole=holes.begin(); ihole!=holes.end(); ++ihole)
tetgen_wrapper.set_hole(hole_index++, (*ihole)(0), (*ihole)(1), (*ihole)(2));
}
// Run TetGen triangulation method:
// p = tetrahedralizes a piecewise linear complex (see definition in user manual)
// Q = quiet, no terminal output
// q = specify a minimum radius/edge ratio
// a = tetrahedron volume constraint
// assemble switches:
std::ostringstream oss; // string holding switches
oss << "pQ";
if (quality_constraint != 0)
oss << "q" << std::fixed << quality_constraint;
if (volume_constraint != 0)
oss << "a" << std::fixed << volume_constraint;
std::string params = oss.str();
tetgen_wrapper.set_switches(params); // TetGen switches: Piecewise linear complex, Quiet mode
tetgen_wrapper.run_tetgen();
// => nodes:
unsigned int old_nodesnum = this->_mesh.n_nodes();
REAL x=0., y=0., z=0.;
const unsigned int num_nodes = tetgen_wrapper.get_numberofpoints();
// Debugging:
// libMesh::out << "Original mesh had " << old_nodesnum << " nodes." << std::endl;
// libMesh::out << "Reserving space for " << num_nodes << " total nodes." << std::endl;
// Reserve space for additional nodes in the node map
_sequential_to_libmesh_node_map.reserve(num_nodes);
// Add additional nodes to the Mesh.
// Original code had i<=num_nodes here (Note: the indexing is:
// foo[3*i], [3*i+1], [3*i+2]) But according to the TetGen docs, "In
// all cases, the first item in any array is stored starting at
// index [0]."
for (unsigned int i=old_nodesnum; i<num_nodes; i++)
{
// Fill in x, y, z values
tetgen_wrapper.get_output_node(i, x,y,z);
// Catch the node returned by add_point()... this will tell us the ID
// assigned by the Mesh.
Node* new_node = this->_mesh.add_point ( Point(x,y,z) );
// Store this new ID in our sequential-to-libmesh node mapping array
_sequential_to_libmesh_node_map.push_back( new_node->id() );
}
// Debugging:
// std::copy(_sequential_to_libmesh_node_map.begin(),
// _sequential_to_libmesh_node_map.end(),
// std::ostream_iterator<unsigned>(std::cout, " "));
// std::cout << std::endl;
// => tetrahedra:
const unsigned int num_elements = tetgen_wrapper.get_numberoftetrahedra();
// Vector that temporarily holds the node labels defining element connectivity.
unsigned int node_labels[4];
for (unsigned int i=0; i<num_elements; i++)
{
// TetGen only supports Tet4 elements.
Elem* elem = new Tet4;
// Fill up the the node_labels vector
for (unsigned int j=0; j<elem->n_nodes(); j++)
node_labels[j] = tetgen_wrapper.get_element_node(i,j);
// Associate nodes with this element
this->assign_nodes_to_elem(node_labels, elem);
// Finally, add this element to the mesh
this->_mesh.add_elem(elem);
}
// Delete original convex hull elements. Is there ever a case where
// we should not do this?
this->delete_2D_hull_elements();
}
void SerialMesh::renumber_nodes_and_elements ()
{
START_LOG("renumber_nodes_and_elem()", "Mesh");
// node and element id counters
unsigned int next_free_elem = 0;
unsigned int next_free_node = 0;
// Will hold the set of nodes that are currently connected to elements
LIBMESH_BEST_UNORDERED_SET<Node*> connected_nodes;
// Loop over the elements. Note that there may
// be NULLs in the _elements vector from the coarsening
// process. Pack the elements in to a contiguous array
// and then trim any excess.
{
std::vector<Elem*>::iterator in = _elements.begin();
std::vector<Elem*>::iterator out = _elements.begin();
const std::vector<Elem*>::iterator end = _elements.end();
for (; in != end; ++in)
if (*in != NULL)
{
Elem* elem = *in;
*out = *in;
++out;
// Increment the element counter
elem->set_id (next_free_elem++);
if(_skip_renumber_nodes_and_elements)
{
// Add this elements nodes to the connected list
for (unsigned int n=0; n<elem->n_nodes(); n++)
connected_nodes.insert(elem->get_node(n));
}
else // We DO want node renumbering
{
// Loop over this element's nodes. Number them,
// if they have not been numbered already. Also,
// position them in the _nodes vector so that they
// are packed contiguously from the beginning.
for (unsigned int n=0; n<elem->n_nodes(); n++)
if (elem->node(n) == next_free_node) // don't need to process
next_free_node++; // [(src == dst) below]
else if (elem->node(n) > next_free_node) // need to process
{
// The source and destination indices
// for this node
const unsigned int src_idx = elem->node(n);
const unsigned int dst_idx = next_free_node++;
// ensure we want to swap a valid nodes
libmesh_assert (_nodes[src_idx] != NULL);
// Swap the source and destination nodes
std::swap(_nodes[src_idx],
_nodes[dst_idx] );
// Set proper indices where that makes sense
if (_nodes[src_idx] != NULL)
_nodes[src_idx]->set_id (src_idx);
_nodes[dst_idx]->set_id (dst_idx);
}
}
}
// Erase any additional storage. These elements have been
// copied into NULL voids by the procedure above, and are
// thus repeated and unnecessary.
_elements.erase (out, end);
}
if(_skip_renumber_nodes_and_elements)
{
// Loop over the nodes. Note that there may
// be NULLs in the _nodes vector from the coarsening
// process. Pack the nodes in to a contiguous array
// and then trim any excess.
std::vector<Node*>::iterator in = _nodes.begin();
std::vector<Node*>::iterator out = _nodes.begin();
const std::vector<Node*>::iterator end = _nodes.end();
for (; in != end; ++in)
if (*in != NULL)
{
// This is a reference so that if we change the pointer it will change in the vector
Node* & node = *in;
// If this node is still connected to an elem, put it in the list
if(connected_nodes.find(node) != connected_nodes.end())
{
*out = node;
++out;
// Increment the node counter
node->set_id (next_free_node++);
}
else // This node is orphaned, delete it!
{
this->boundary_info->remove (node);
// delete the node
delete node;
node = NULL;
}
}
// Erase any additional storage. Whatever was
_nodes.erase (out, end);
}
else // We really DO want node renumbering
{
// Any nodes in the vector >= _nodes[next_free_node]
// are not connected to any elements and may be deleted
// if desired.
// (This code block will erase the unused nodes)
// Now, delete the unused nodes
{
std::vector<Node*>::iterator nd = _nodes.begin();
const std::vector<Node*>::iterator end = _nodes.end();
std::advance (nd, next_free_node);
for (std::vector<Node*>::iterator it=nd;
it != end; ++it)
{
// Mesh modification code might have already deleted some
// nodes
if (*it == NULL)
continue;
// remove any boundary information associated with
// this node
this->boundary_info->remove (*it);
// delete the node
delete *it;
*it = NULL;
}
_nodes.erase (nd, end);
}
}
libmesh_assert (next_free_elem == _elements.size());
libmesh_assert (next_free_node == _nodes.size());
STOP_LOG("renumber_nodes_and_elem()", "Mesh");
}
void VTKIO::cells_to_vtk()
{
const MeshBase& mesh = MeshOutput<MeshBase>::mesh();
vtkSmartPointer<vtkCellArray> cells = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkIdList> pts = vtkSmartPointer<vtkIdList>::New();
std::vector<int> types(mesh.n_active_local_elem());
unsigned active_element_counter = 0;
vtkSmartPointer<vtkIntArray> elem_id = vtkSmartPointer<vtkIntArray>::New();
elem_id->SetName("libmesh_elem_id");
elem_id->SetNumberOfComponents(1);
vtkSmartPointer<vtkIntArray> subdomain_id = vtkSmartPointer<vtkIntArray>::New();
subdomain_id->SetName("subdomain_id");
subdomain_id->SetNumberOfComponents(1);
MeshBase::const_element_iterator it = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end = mesh.active_local_elements_end();
for (; it != end; ++it, ++active_element_counter)
{
Elem *elem = *it;
pts->SetNumberOfIds(elem->n_nodes());
// get the connectivity for this element
std::vector<dof_id_type> conn;
elem->connectivity(0, VTK, conn);
for (unsigned int i=0; i<conn.size(); ++i)
{
// If the node ID is not found in the _local_node_map, we'll
// add it to the _vtk_grid. NOTE[JWP]: none of the examples
// I have actually enters this section of code...
if (_local_node_map.find(conn[i]) == _local_node_map.end())
{
dof_id_type global_node_id = elem->node(i);
const Node* the_node = mesh.node_ptr(global_node_id);
// Error checking...
if (the_node == NULL)
{
libMesh::err << "Error getting pointer to node "
<< global_node_id
<< "!" << std::endl;
libmesh_error();
}
// InsertNextPoint accepts either a double or float array of length 3.
Real pt[3] = {0., 0., 0.};
for (unsigned int d=0; d<LIBMESH_DIM; ++d)
pt[d] = (*the_node)(d);
// Insert the point into the _vtk_grid
vtkIdType local = _vtk_grid->GetPoints()->InsertNextPoint(pt);
// Update the _local_node_map with the ID returned by VTK
_local_node_map[global_node_id] = local;
}
// Otherwise, the node ID was found in the _local_node_map, so
// insert it into the vtkIdList.
pts->InsertId(i, _local_node_map[conn[i]]);
}
vtkIdType vtkcellid = cells->InsertNextCell(pts);
types[active_element_counter] = this->get_elem_type(elem->type());
elem_id->InsertTuple1(vtkcellid, elem->id());
subdomain_id->InsertTuple1(vtkcellid, elem->subdomain_id());
} // end loop over active elements
_vtk_grid->SetCells(&types[0], cells);
_vtk_grid->GetCellData()->AddArray(elem_id);
_vtk_grid->GetCellData()->AddArray(subdomain_id);
}
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;
}
void
FeatureFloodCount::calculateBubbleVolumes()
{
Moose::perf_log.push("calculateBubbleVolume()", "FeatureFloodCount");
// Figure out which bubbles intersect the boundary if the user has enabled that capability.
if (_compute_boundary_intersecting_volume)
{
// Create a std::set of node IDs which are on the boundary called all_boundary_node_ids.
std::set<dof_id_type> all_boundary_node_ids;
// Iterate over the boundary nodes, putting them into the std::set data structure
MooseMesh::bnd_node_iterator
boundary_nodes_it = _mesh.bndNodesBegin(),
boundary_nodes_end = _mesh.bndNodesEnd();
for (; boundary_nodes_it != boundary_nodes_end; ++boundary_nodes_it)
{
BndNode * boundary_node = *boundary_nodes_it;
all_boundary_node_ids.insert(boundary_node->_node->id());
}
// For each of the _maps_size BubbleData lists, determine if the set
// of nodes includes any boundary nodes.
for (unsigned int map_num = 0; map_num < _maps_size; ++map_num)
{
std::list<BubbleData>::iterator
bubble_it = _bubble_sets[map_num].begin(),
bubble_end = _bubble_sets[map_num].end();
// Determine boundary intersection for each BubbleData object
for (; bubble_it != bubble_end; ++bubble_it)
bubble_it->_intersects_boundary = setsIntersect(all_boundary_node_ids.begin(), all_boundary_node_ids.end(),
bubble_it->_entity_ids.begin(), bubble_it->_entity_ids.end());
}
}
// Size our temporary data structure
std::vector<std::vector<Real> > bubble_volumes(_maps_size);
for (unsigned int map_num = 0; map_num < _maps_size; ++map_num)
bubble_volumes[map_num].resize(_bubble_sets[map_num].size());
// Clear pre-existing values and allocate space to store the volume
// of the boundary-intersecting grains for each variable.
_total_volume_intersecting_boundary.clear();
_total_volume_intersecting_boundary.resize(_maps_size);
// Loop over the active local elements. For each variable, and for
// each BubbleData object, check whether a majority of the element's
// nodes belong to that Bubble, and if so assign the element's full
// volume to that bubble.
const MeshBase::const_element_iterator el_end = _mesh.getMesh().active_local_elements_end();
for (MeshBase::const_element_iterator el = _mesh.getMesh().active_local_elements_begin(); el != el_end; ++el)
{
Elem * elem = *el;
unsigned int elem_n_nodes = elem->n_nodes();
Real curr_volume = elem->volume();
for (unsigned int map_num = 0; map_num < _maps_size; ++map_num)
{
std::list<BubbleData>::const_iterator
bubble_it = _bubble_sets[map_num].begin(),
bubble_end = _bubble_sets[map_num].end();
for (unsigned int bubble_counter = 0; bubble_it != bubble_end; ++bubble_it, ++bubble_counter)
{
// Count the number of nodes on this element which are flooded.
unsigned int flooded_nodes = 0;
for (unsigned int node = 0; node < elem_n_nodes; ++node)
{
dof_id_type node_id = elem->node(node);
if (bubble_it->_entity_ids.find(node_id) != bubble_it->_entity_ids.end())
++flooded_nodes;
}
// If a majority of the nodes for this element are flooded,
// assign its volume to the current bubble_counter entry.
if (flooded_nodes >= elem_n_nodes / 2)
{
bubble_volumes[map_num][bubble_counter] += curr_volume;
// If the current bubble also intersects the boundary, also
// accumlate the volume into the total volume of bubbles
// which intersect the boundary.
if (bubble_it->_intersects_boundary)
_total_volume_intersecting_boundary[map_num] += curr_volume;
}
}
}
}
// If we're calculating boundary-intersecting volumes, we have to normalize it by the
// volume of the entire domain.
if (_compute_boundary_intersecting_volume)
{
// Compute the total area using a bounding box. FIXME: this
// assumes the domain is rectangular and 2D, and is probably a
// little expensive so we should only do it once if possible.
MeshTools::BoundingBox bbox = MeshTools::bounding_box(_mesh);
Real total_volume = (bbox.max()(0)-bbox.min()(0))*(bbox.max()(1)-bbox.min()(1));
// Sum up the partial boundary grain volume contributions from all processors
_communicator.sum(_total_volume_intersecting_boundary);
// Scale the boundary intersecting grain volumes by the total domain volume
for (unsigned int i = 0; i<_total_volume_intersecting_boundary.size(); ++i)
_total_volume_intersecting_boundary[i] /= total_volume;
}
// Stick all the partial bubble volumes in one long single vector to be gathered on the root processor
for (unsigned int map_num = 0; map_num < _maps_size; ++map_num)
_all_bubble_volumes.insert(_all_bubble_volumes.end(), bubble_volumes[map_num].begin(), bubble_volumes[map_num].end());
// do all the sums!
_communicator.sum(_all_bubble_volumes);
std::sort(_all_bubble_volumes.begin(), _all_bubble_volumes.end(), std::greater<Real>());
Moose::perf_log.pop("calculateBubbleVolume()", "FeatureFloodCount");
}
//-----------------------------------------------------------------
// Mesh refinement methods
bool MeshRefinement::limit_level_mismatch_at_node (const unsigned int max_mismatch)
{
// This function must be run on all processors at once
parallel_only();
bool flags_changed = false;
// Vector holding the maximum element level that touches a node.
std::vector<unsigned char> max_level_at_node (_mesh.n_nodes(), 0);
std::vector<unsigned char> max_p_level_at_node (_mesh.n_nodes(), 0);
// Loop over all the active elements & fill the vector
{
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 node
for (unsigned int n=0; n<elem->n_nodes(); n++)
{
const unsigned int node_number = elem->node(n);
libmesh_assert_less (node_number, max_level_at_node.size());
max_level_at_node[node_number] =
std::max (max_level_at_node[node_number], elem_level);
max_p_level_at_node[node_number] =
std::max (max_p_level_at_node[node_number], 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_nodes(); n++)
{
const unsigned int node_number = elem->node(n);
// Flag the element for refinement if it violates
// the requested level mismatch
if ( (elem_level + max_mismatch) < max_level_at_node[node_number]
&& elem->refinement_flag() != Elem::REFINE)
{
elem->set_refinement_flag (Elem::REFINE);
flags_changed = true;
}
if ( (elem_p_level + max_mismatch) < max_p_level_at_node[node_number]
&& 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 MeshBase::detect_interior_parents()
{
// This requires an inspection on every processor
parallel_object_only();
// Check if the mesh contains mixed dimensions. If so, then set interior parents, otherwise return.
if (this->elem_dimensions().size() == 1)
return;
//This map will be used to set interior parents
LIBMESH_BEST_UNORDERED_MAP<dof_id_type, std::vector<dof_id_type> > node_to_elem;
const_element_iterator el = this->active_elements_begin();
const_element_iterator end = this->active_elements_end();
for (; el!=end; ++el)
{
const Elem * elem = *el;
// Populating the node_to_elem map, same as MeshTools::build_nodes_to_elem_map
for (unsigned int n=0; n<elem->n_vertices(); n++)
{
libmesh_assert_less (elem->id(), this->max_elem_id());
node_to_elem[elem->node(n)].push_back(elem->id());
}
}
// Automatically set interior parents
el = this->elements_begin();
for (; el!=end; ++el)
{
Elem * element = *el;
// Ignore an 3D element or an element that already has an interior parent
if (element->dim()>=LIBMESH_DIM || element->interior_parent())
continue;
// Start by generating a SET of elements that are dim+1 to the current
// element at each vertex of the current element, thus ignoring interior nodes.
// If one of the SET of elements is empty, then we will not have an interior parent
// since an interior parent must be connected to all vertices of the current element
std::vector< std::set<dof_id_type> > neighbors( element->n_vertices() );
bool found_interior_parents = false;
for (dof_id_type n=0; n < element->n_vertices(); n++)
{
std::vector<dof_id_type> & element_ids = node_to_elem[element->node(n)];
for (std::vector<dof_id_type>::iterator e_it = element_ids.begin();
e_it != element_ids.end(); e_it++)
{
dof_id_type eid = *e_it;
if (this->elem(eid)->dim() == element->dim()+1)
neighbors[n].insert(eid);
}
if (neighbors[n].size()>0)
{
found_interior_parents = true;
}
else
{
// We have found an empty set, no reason to continue
// Ensure we set this flag to false before the break since it could have
// been set to true for previous vertex
found_interior_parents = false;
break;
}
}
// If we have successfully generated a set of elements for each vertex, we will compare
// the set for vertex 0 will the sets for the vertices until we find a id that exists in
// all sets. If found, this is our an interior parent id. The interior parent id found
// will be the lowest element id if there is potential for multiple interior parents.
if (found_interior_parents)
{
std::set<dof_id_type> & neighbors_0 = neighbors[0];
for (std::set<dof_id_type>::iterator e_it = neighbors_0.begin();
e_it != neighbors_0.end(); e_it++)
{
found_interior_parents=false;
dof_id_type interior_parent_id = *e_it;
for (dof_id_type n=1; n < element->n_vertices(); n++)
{
if (neighbors[n].find(interior_parent_id)!=neighbors[n].end())
{
found_interior_parents=true;
}
else
{
found_interior_parents=false;
break;
}
}
if (found_interior_parents)
{
element->set_interior_parent(this->elem(interior_parent_id));
break;
}
}
}
}
}
//-----------------------------------------------------------------
// Mesh refinement methods
bool MeshRefinement::limit_level_mismatch_at_node (const unsigned int max_mismatch)
{
// This function must be run on all processors at once
parallel_object_only();
bool flags_changed = false;
// Vector holding the maximum element level that touches a node.
std::vector<unsigned char> max_level_at_node (_mesh.n_nodes(), 0);
std::vector<unsigned char> max_p_level_at_node (_mesh.n_nodes(), 0);
// Loop over all the active elements & fill the vector
{
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 =
cast_int<unsigned char>(elem->level() +
((elem->refinement_flag() == Elem::REFINE) ? 1 : 0));
const unsigned char elem_p_level =
cast_int<unsigned char>(elem->p_level() +
((elem->p_refinement_flag() == Elem::REFINE) ? 1 : 0));
// Set the max_level at each node
for (unsigned int n=0; n<elem->n_nodes(); n++)
{
const dof_id_type node_number = elem->node(n);
libmesh_assert_less (node_number, max_level_at_node.size());
max_level_at_node[node_number] =
std::max (max_level_at_node[node_number], elem_level);
max_p_level_at_node[node_number] =
std::max (max_p_level_at_node[node_number], elem_p_level);
}
}
}
// Now loop over the active elements and flag the elements
// who violate the requested level mismatch. Alternatively, if
// _enforce_mismatch_limit_prior_to_refinement is true, swap refinement flags
// accordingly.
{
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
// unless we are enforcing mismatch prior to refienemnt and may need to
// remove the refinement flag(s)
if (elem->refinement_flag() == Elem::REFINE &&
elem->p_refinement_flag() == Elem::REFINE
&& !_enforce_mismatch_limit_prior_to_refinement)
continue;
// Loop over the nodes, check for possible mismatch
for (unsigned int n=0; n<elem->n_nodes(); n++)
{
const dof_id_type node_number = elem->node(n);
// Flag the element for refinement if it violates
// the requested level mismatch
if ((elem_level + max_mismatch) < max_level_at_node[node_number]
&& elem->refinement_flag() != Elem::REFINE)
{
elem->set_refinement_flag (Elem::REFINE);
flags_changed = true;
}
if ((elem_p_level + max_mismatch) < max_p_level_at_node[node_number]
&& elem->p_refinement_flag() != Elem::REFINE)
{
elem->set_p_refinement_flag (Elem::REFINE);
flags_changed = true;
}
// Possibly enforce limit mismatch prior to refinement
flags_changed |= this->enforce_mismatch_limit_prior_to_refinement(elem, POINT, max_mismatch);
}
}
}
// If flags changed on any processor then they changed globally
this->comm().max(flags_changed);
return flags_changed;
}