//-----------------------------------------------------------------------------
void DofMap::tabulate_coordinates(boost::multi_array<double, 2>& coordinates,
const ufc::cell& ufc_cell) const
{
// FIXME: This is a hack because UFC wants a double pointer for coordinates
dolfin_assert(_ufc_dofmap);
// Check dimensions
if (coordinates.shape()[0] != cell_dimension(ufc_cell.index) ||
coordinates.shape()[1] != _ufc_dofmap->geometric_dimension())
{
boost::multi_array<double, 2>::extent_gen extents;
const std::size_t cell_dim = cell_dimension(ufc_cell.index);
coordinates.resize(extents[cell_dim][_ufc_dofmap->geometric_dimension()]);
}
// Set vertex coordinates
const std::size_t num_points = coordinates.size();
std::vector<double*> coords(num_points);
for (std::size_t i = 0; i < num_points; ++i)
coords[i] = &(coordinates[i][0]);
// Tabulate coordinates
_ufc_dofmap->tabulate_coordinates(coords.data(),
&ufc_cell.vertex_coordinates[0]);
}
XmlNode add_multi_array_in( Map & map, const std::string & name,
const boost::multi_array<Real, 2> & array,
const std::string & delimiter,
const std::vector<std::string> & labels )
{
cf_assert( map.content.is_valid() );
cf_assert( !name.empty())
cf_assert( !map.check_entry(name) );
cf_assert( !delimiter.empty() );
std::string labels_str = boost::algorithm::join(labels, delimiter);
XmlNode array_node = map.content.add_node( Protocol::Tags::node_array() );
array_node.add_node( Protocol::Tags::type<std::string>(), labels_str );
XmlNode data_node = array_node.add_node( Protocol::Tags::type<Real>() );
Uint nb_rows = array.size();
Uint nb_cols = 0;
std::string str;
std::string size;
if(nb_rows != 0)
nb_cols = array[0].size();
size = to_str(nb_rows) + ':' + to_str(nb_cols);
array_node.set_attribute( Protocol::Tags::attr_key(), name );
data_node.set_attribute( "dimensions", to_str((Uint)array.dimensionality) );
data_node.set_attribute( Protocol::Tags::attr_array_delimiter(), delimiter );
data_node.set_attribute( Protocol::Tags::attr_array_size(), size);
data_node.set_attribute( "merge_delimiter", to_str(true) ); // temporary
// build the value string (ideas are welcome to avoid multiple
// memory reallocations
for(Uint row = 0 ; row < nb_rows ; ++row)
{
for(Uint col = 0 ; col < nb_cols ; ++col)
str += to_str( array[row][col] ) + delimiter;
str += '\n'; // line break after each row
}
data_node.set_value(str.c_str());
return array_node;
}
object computeConvexDecomposition(const boost::multi_array<float, 2>& vertices, const boost::multi_array<int, 2>& indices,
NxF32 skinWidth=0, NxU32 decompositionDepth=8, NxU32 maxHullVertices=64, NxF32 concavityThresholdPercent=0.1f, NxF32 mergeThresholdPercent=30.0f, NxF32 volumeSplitThresholdPercent=0.1f, bool useInitialIslandGeneration=true, bool useIslandGeneration=false)
{
boost::shared_ptr<CONVEX_DECOMPOSITION::iConvexDecomposition> ic(CONVEX_DECOMPOSITION::createConvexDecomposition(),CONVEX_DECOMPOSITION::releaseConvexDecomposition);
if( indices.size() > 0 ) {
FOREACHC(it,indices)
ic->addTriangle(&vertices[(*it)[0]][0], &vertices[(*it)[1]][0], &vertices[(*it)[2]][0]);
}
else {
BOOST_ASSERT((vertices.size()%3)==0);
for(size_t i = 0; i < vertices.size(); i += 3)
ic->addTriangle(&vertices[i][0], &vertices[i+1][0], &vertices[i+2][0]);
}
ic->computeConvexDecomposition(skinWidth, decompositionDepth, maxHullVertices, concavityThresholdPercent, mergeThresholdPercent, volumeSplitThresholdPercent, useInitialIslandGeneration, useIslandGeneration, false);
NxU32 hullCount = ic->getHullCount();
boost::python::list hulls;
CONVEX_DECOMPOSITION::ConvexHullResult result;
for(NxU32 i = 0; i < hullCount; ++i) {
ic->getConvexHullResult(i,result);
npy_intp dims[] = { result.mVcount,3};
PyObject *pyvertices = PyArray_SimpleNew(2,dims, sizeof(result.mVertices[0])==8 ? PyArray_DOUBLE : PyArray_FLOAT);
std::copy(&result.mVertices[0],&result.mVertices[3*result.mVcount],(NxF32*)PyArray_DATA(pyvertices));
dims[0] = result.mTcount;
dims[1] = 3;
PyObject *pyindices = PyArray_SimpleNew(2,dims, PyArray_INT);
std::copy(&result.mIndices[0],&result.mIndices[3*result.mTcount],(int*)PyArray_DATA(pyindices));
hulls.append(boost::python::make_tuple(static_cast<numeric::array>(handle<>(pyvertices)), static_cast<numeric::array>(handle<>(pyindices))));
}
return hulls;
}
//-----------------------------------------------------------------------------
void MeshPartitioning::build_mesh(Mesh& mesh,
const std::vector<std::size_t>& global_cell_indices,
const boost::multi_array<std::size_t, 2>& cell_global_vertices,
const std::vector<std::size_t>& vertex_indices,
const boost::multi_array<double, 2>& vertex_coordinates,
const std::map<std::size_t, std::size_t>& vertex_global_to_local,
std::size_t tdim, std::size_t gdim, std::size_t num_global_cells,
std::size_t num_global_vertices)
{
Timer timer("PARALLEL 3: Build mesh (from local mesh data)");
// Get number of processes and process number
const std::size_t num_processes = MPI::num_processes();
const std::size_t process_number = MPI::process_number();
// Open mesh for editing
mesh.clear();
MeshEditor editor;
editor.open(mesh, tdim, gdim);
// Add vertices
editor.init_vertices(vertex_coordinates.size());
Point point(gdim);
dolfin_assert(vertex_indices.size() == vertex_coordinates.size());
for (std::size_t i = 0; i < vertex_coordinates.size(); ++i)
{
for (std::size_t j = 0; j < gdim; ++j)
point[j] = vertex_coordinates[i][j];
editor.add_vertex_global(i, vertex_indices[i], point);
}
// Add cells
editor.init_cells(cell_global_vertices.size());
const std::size_t num_cell_vertices = tdim + 1;
std::vector<std::size_t> cell(num_cell_vertices);
for (std::size_t i = 0; i < cell_global_vertices.size(); ++i)
{
for (std::size_t j = 0; j < num_cell_vertices; ++j)
{
// Get local cell vertex
std::map<std::size_t, std::size_t>::const_iterator iter
= vertex_global_to_local.find(cell_global_vertices[i][j]);
dolfin_assert(iter != vertex_global_to_local.end());
cell[j] = iter->second;
}
editor.add_cell(i, global_cell_indices[i], cell);
}
// Close mesh: Note that this must be done after creating the global
// vertex map or otherwise the ordering in mesh.close() will be wrong
// (based on local numbers).
editor.close();
// Set global number of cells and vertices
mesh.topology().init_global(0, num_global_vertices);
mesh.topology().init_global(tdim, num_global_cells);
// Construct boundary mesh
BoundaryMesh bmesh(mesh, "exterior");
const MeshFunction<std::size_t>& boundary_vertex_map = bmesh.entity_map(0);
const std::size_t boundary_size = boundary_vertex_map.size();
// Build sorted array of global boundary vertex indices (global
// numbering)
std::vector<std::size_t> global_vertex_send(boundary_size);
for (std::size_t i = 0; i < boundary_size; ++i)
global_vertex_send[i] = vertex_indices[boundary_vertex_map[i]];
std::sort(global_vertex_send.begin(), global_vertex_send.end());
// Receive buffer
std::vector<std::size_t> global_vertex_recv;
// Create shared_vertices data structure: mapping from shared vertices
// to list of neighboring processes
std::map<unsigned int, std::set<unsigned int> >& shared_vertices
= mesh.topology().shared_entities(0);
shared_vertices.clear();
// FIXME: Remove computation from inside communication loop
// Build shared vertex to sharing processes map
for (std::size_t i = 1; i < num_processes; ++i)
{
// We send data to process p - i (i steps to the left)
const int p = (process_number - i + num_processes) % num_processes;
// We receive data from process p + i (i steps to the right)
const int q = (process_number + i) % num_processes;
// Send and receive
MPI::send_recv(global_vertex_send, p, global_vertex_recv, q);
// Compute intersection of global indices
std::vector<std::size_t> intersection(std::min(global_vertex_send.size(),
global_vertex_recv.size()));
std::vector<std::size_t>::iterator intersection_end
= std::set_intersection(global_vertex_send.begin(),
global_vertex_send.end(),
global_vertex_recv.begin(),
global_vertex_recv.end(),
intersection.begin());
// Fill shared vertices information
std::vector<std::size_t>::const_iterator global_index;
for (global_index = intersection.begin(); global_index != intersection_end;
++global_index)
{
// Get local index
std::map<std::size_t, std::size_t>::const_iterator local_index;
local_index = vertex_global_to_local.find(*global_index);
dolfin_assert(local_index != vertex_global_to_local.end());
// Insert (local index, [proc])
shared_vertices[local_index->second].insert(q);
}
}
}