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 ElemCutter::cut_3D (const Elem & elem,
const std::vector<Real> & vertex_distance_func)
{
#ifndef LIBMESH_HAVE_TETGEN
// current implementation requires tetgen!
libMesh::err << "ERROR: current libMesh ElemCutter 3D implementation requires\n"
<< " the \"tetgen\" library!\n"
<< std::endl;
libmesh_not_implemented();
#else // OK, LIBMESH_HAVE_TETGEN
std::cout << "Inside cut cell element!\n";
libmesh_assert (_inside_mesh_3D.get() != nullptr);
libmesh_assert (_outside_mesh_3D.get() != nullptr);
_inside_mesh_3D->clear();
_outside_mesh_3D->clear();
for (unsigned int v=0; v<elem.n_vertices(); v++)
{
if (vertex_distance_func[v] >= 0.)
_outside_mesh_3D->add_point (elem.point(v));
if (vertex_distance_func[v] <= 0.)
_inside_mesh_3D->add_point (elem.point(v));
}
for (const auto & pt : _intersection_pts)
{
_inside_mesh_3D->add_point(pt);
_outside_mesh_3D->add_point(pt);
}
// Triangulate!
_tetgen_inside->triangulate_pointset();
//_inside_mesh_3D->print_info();
_tetgen_outside->triangulate_pointset();
//_outside_mesh_3D->print_info();
// (below generates some horribly expensive meshes,
// but seems immune to the 0 volume problem).
// _tetgen_inside->pointset_convexhull();
// _inside_mesh_3D->find_neighbors();
// _inside_mesh_3D->print_info();
// _tetgen_inside->triangulate_conformingDelaunayMesh (1.e3, 100.);
// _inside_mesh_3D->print_info();
// _tetgen_outside->pointset_convexhull();
// _outside_mesh_3D->find_neighbors();
// _outside_mesh_3D->print_info();
// _tetgen_outside->triangulate_conformingDelaunayMesh (1.e3, 100.);
// _outside_mesh_3D->print_info();
std::ostringstream name;
name << "cut_cell_"
<< cut_cntr++
<< ".dat";
_inside_mesh_3D->write ("in_" + name.str());
_outside_mesh_3D->write ("out_" + name.str());
// finally, add the elements to our lists.
_inside_elem.clear();
_outside_elem.clear();
for (const auto & elem : _inside_mesh_3D->element_ptr_range())
if (elem->volume() > std::numeric_limits<Real>::epsilon())
_inside_elem.push_back (elem);
for (const auto & elem : _outside_mesh_3D->element_ptr_range())
if (elem->volume() > std::numeric_limits<Real>::epsilon())
_outside_elem.push_back (elem);
#endif
}
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");
}