Mesh build_mesh(const std::vector<unsigned int>& cells, const std::vector<double>& vertices, int dim)
{
// vertices and cells are flattened
unsigned int vlen = vertices.size() / dim;
unsigned int clen = cells.size() / (dim + 1);
Mesh mesh;
MeshEditor editor;
editor.open(mesh, dim, dim);
editor.init_vertices(vlen);
editor.init_cells(clen);
if (dim==3)
{
for (int i=0; i<vlen; i++)
editor.add_vertex(i, vertices[3*i], vertices[3*i+1], vertices[3*i+2]);
for (int i=0; i<clen; i++)
editor.add_cell(i, cells[4*i], cells[4*i+1], cells[4*i+2], cells[4*i+3]);
}
else
{
for (int i=0; i<vlen; i++)
editor.add_vertex(i, vertices[2*i], vertices[2*i+1]);
for (int i=0; i<clen; i++)
editor.add_cell(i, cells[3*i], cells[3*i+1], cells[3*i+2]);
}
editor.close();
return mesh;
}
//-----------------------------------------------------------------------------
void dolfin::p_refine(Mesh& refined_mesh, const Mesh& mesh)
{
MeshEditor editor;
if (mesh.geometry().degree() != 1)
{
dolfin_error("refine.cpp",
"increase polynomial degree of mesh",
"Currently only linear -> quadratic is supported");
}
const CellType::Type cell_type = mesh.type().cell_type();
if (cell_type != CellType::Type::triangle
and cell_type != CellType::Type::tetrahedron
and cell_type != CellType::Type::interval)
{
dolfin_error("refine.cpp",
"increase polynomial degree of mesh",
"Unsupported cell type");
}
const std::size_t tdim = mesh.topology().dim();
const std::size_t gdim = mesh.geometry().dim();
editor.open(refined_mesh, cell_type, tdim, gdim, 2);
// Copy over mesh
editor.init_vertices_global(mesh.num_entities(0), mesh.num_entities_global(0));
for (VertexIterator v(mesh); !v.end(); ++v)
editor.add_vertex(v->index(), v->point());
editor.init_cells_global(mesh.num_entities(tdim), mesh.num_entities_global(tdim));
std::vector<std::size_t> verts(tdim + 1);
for (CellIterator c(mesh); !c.end(); ++c)
{
std::copy(c->entities(0), c->entities(0) + tdim + 1, verts.begin());
editor.add_cell(c->index(), verts);
}
// Initialise edges
editor.init_entities();
// Add points at centres of edges
for (EdgeIterator e(refined_mesh); !e.end(); ++e)
editor.add_entity_point(1, 0, e->index(), e->midpoint());
editor.close();
}
//-----------------------------------------------------------------------------
void DynamicMeshEditor::close(bool order)
{
dolfin_assert(_mesh);
dolfin_assert(_cell_type);
// Open default mesh editor
MeshEditor editor;
editor.open(*_mesh, _cell_type->cell_type(), _tdim, _gdim);
// Set number of vertices
const std::size_t num_vertices = vertex_coordinates.size()/_gdim;
editor.init_vertices(num_vertices);
// Set number of cells
const std::size_t vertices_per_cell = _cell_type->num_vertices(_gdim);
const std::size_t num_cells = cell_vertices.size()/vertices_per_cell;
editor.init_cells(num_cells);
// Add vertices
std::vector<double> p(_gdim);
for (std::size_t v = 0; v < num_vertices; v++)
{
const std::size_t offset = v*_gdim;
for (std::size_t i = 0; i < _gdim; i++)
p[i] = vertex_coordinates[offset + i];
editor.add_vertex(v, p);
}
// Add cells
std::vector<std::size_t> vertices(vertices_per_cell);
for (std::size_t c = 0; c < num_cells; c++)
{
const std::size_t offset = c*vertices_per_cell;
for (std::size_t i = 0; i < vertices_per_cell; i++)
vertices[i] = cell_vertices[offset + i];
editor.add_cell(c, vertices);
}
// Close editor
editor.close(order);
// Clear data
clear();
}
//-----------------------------------------------------------------------------
UnitTriangleMesh::UnitTriangleMesh() : Mesh()
{
// Receive mesh according to parallel policy
if (MPI::is_receiver(this->mpi_comm()))
{
MeshPartitioning::build_distributed_mesh(*this);
return;
}
// Open mesh for editing
MeshEditor editor;
editor.open(*this, CellType::triangle, 2, 2);
// Create vertices
editor.init_vertices_global(3, 3);
std::vector<double> x(2);
x[0] = 0.0; x[1] = 0.0;
editor.add_vertex(0, x);
x[0] = 1.0; x[1] = 0.0;
editor.add_vertex(1, x);
x[0] = 0.0; x[1] = 1.0;
editor.add_vertex(2, x);
// Create cells
editor.init_cells_global(1, 1);
std::vector<std::size_t> cell_data(3);
cell_data[0] = 0; cell_data[1] = 1; cell_data[2] = 2;
editor.add_cell(0, cell_data);
// Close mesh editor
editor.close();
// Broadcast mesh according to parallel policy
if (MPI::is_broadcaster(this->mpi_comm()))
{
MeshPartitioning::build_distributed_mesh(*this);
return;
}
}
//-----------------------------------------------------------------------------
void ParallelRefinement::build_local(Mesh& new_mesh) const
{
MeshEditor ed;
const std::size_t tdim = _mesh.topology().dim();
const std::size_t gdim = _mesh.geometry().dim();
dolfin_assert(new_vertex_coordinates.size()%gdim == 0);
const std::size_t num_vertices = new_vertex_coordinates.size()/gdim;
const std::size_t num_cell_vertices = tdim + 1;
dolfin_assert(new_cell_topology.size()%num_cell_vertices == 0);
const std::size_t num_cells = new_cell_topology.size()/num_cell_vertices;
ed.open(new_mesh, tdim, gdim);
ed.init_vertices(num_vertices);
std::size_t i = 0;
for (auto p = new_vertex_coordinates.begin();
p != new_vertex_coordinates.end(); p += gdim)
{
std::vector<double> vertex(p, p + gdim);
ed.add_vertex(i, vertex);
++i;
}
ed.init_cells(num_cells);
i = 0;
std::vector<std::size_t> cell(num_cell_vertices);
for (auto p = new_cell_topology.begin(); p != new_cell_topology.end();
p += num_cell_vertices)
{
std::copy(p, p + num_cell_vertices, cell.begin());
ed.add_cell(i, cell);
++i;
}
ed.close();
}
//-----------------------------------------------------------------------------
void IntervalMesh::build(std::size_t nx, double a, double b)
{
// Receive mesh according to parallel policy
if (MPI::is_receiver(this->mpi_comm()))
{
MeshPartitioning::build_distributed_mesh(*this);
return;
}
if (std::abs(a - b) < DOLFIN_EPS)
{
dolfin_error("Interval.cpp",
"create interval",
"Length of interval is zero. Consider checking your dimensions");
}
if (b < a)
{
dolfin_error("Interval.cpp",
"create interval",
"Length of interval is negative. Consider checking the order of your arguments");
}
if (nx < 1)
{
dolfin_error("Interval.cpp",
"create interval",
"Number of points on interval is (%d), it must be at least 1", nx);
}
rename("mesh", "Mesh of the interval (a, b)");
// Open mesh for editing
MeshEditor editor;
editor.open(*this, CellType::interval, 1, 1);
// Create vertices and cells:
editor.init_vertices_global((nx+1), (nx+1));
editor.init_cells_global(nx, nx);
// Create main vertices:
for (std::size_t ix = 0; ix <= nx; ix++)
{
const std::vector<double>
x(1, a + (static_cast<double>(ix)*(b - a)/static_cast<double>(nx)));
editor.add_vertex(ix, x);
}
// Create intervals
for (std::size_t ix = 0; ix < nx; ix++)
{
std::vector<std::size_t> cell(2);
cell[0] = ix; cell[1] = ix + 1;
editor.add_cell(ix, cell);
}
// Close mesh editor
editor.close();
// Broadcast mesh according to parallel policy
if (MPI::is_broadcaster(this->mpi_comm()))
{
std::cout << "Building mesh (dist 0a)" << std::endl;
MeshPartitioning::build_distributed_mesh(*this);
std::cout << "Building mesh (dist 1a)" << std::endl;
return;
}
}
//-----------------------------------------------------------------------------
UnitDiscMesh::UnitDiscMesh(MPI_Comm comm, std::size_t n,
std::size_t degree, std::size_t gdim)
: Mesh(comm)
{
dolfin_assert(n > 0);
dolfin_assert(gdim == 2 or gdim == 3);
dolfin_assert(degree == 1 or degree == 2);
MeshEditor editor;
editor.open(*this, 2, gdim, degree);
editor.init_vertices_global(1 + 3*n*(n + 1),
1 + 3*n*(n + 1));
std::size_t c = 0;
editor.add_vertex(c, Point(0,0,0));
++c;
for (std::size_t i = 1; i <= n; ++i)
for (std::size_t j = 0; j < 6*i; ++j)
{
double r = (double)i/(double)n;
double th = 2*M_PI*(double)j/(double)(6*i);
double x = r*cos(th);
double y = r*sin(th);
editor.add_vertex(c, Point(x, y, 0));
++c;
}
editor.init_cells(6*n*n);
c = 0;
std::size_t base_i = 0;
std::size_t row_i = 1;
for (std::size_t i = 1; i <= n; ++i)
{
std::size_t base_m = base_i;
base_i = 1 + 3*i*(i - 1);
std::size_t row_m = row_i;
row_i = 6*i;
for (std::size_t k = 0; k != 6; ++k)
for (std::size_t j = 0; j < (i*2 - 1); ++j)
{
std::size_t i0, i1, i2;
if (j%2 == 0)
{
i0 = base_i + (k*i + j/2)%row_i;
i1 = base_i + (k*i + j/2 + 1)%row_i;
i2 = base_m + (k*(i-1) + j/2)%row_m;
}
else
{
i0 = base_m + (k*(i-1) + j/2)%row_m;
i1 = base_m + (k*(i-1) + j/2 + 1)%row_m;
i2 = base_i + (k*i + j/2 + 1)%row_i;
}
editor.add_cell(c, i0, i1, i2);
++c;
}
}
// Initialise entities required for this degree polynomial mesh
// and allocate space for the point coordinate data
if (degree == 2)
{
editor.init_entities();
for (EdgeIterator e(*this); !e.end(); ++e)
{
Point v0 = Vertex(*this, e->entities(0)[0]).point();
Point v1 = Vertex(*this, e->entities(0)[1]).point();
Point pt = e->midpoint();
if (std::abs(v0.norm() - 1.0) < 1e-6 and
std::abs(v1.norm() - 1.0) < 1e-6)
pt *= v0.norm()/pt.norm();
// Add Edge-based point
editor.add_entity_point(1, 0, e->index(), pt);
}
}
editor.close();
}
//-----------------------------------------------------------------------------
void BoundaryComputation::compute_boundary(const Mesh& mesh,
const std::string type,
BoundaryMesh& boundary)
{
// We iterate over all facets in the mesh and check if they are on
// the boundary. A facet is on the boundary if it is connected to
// exactly one cell.
log(TRACE, "Computing boundary mesh.");
bool exterior = true;
bool interior = true;
if (type == "exterior")
interior = false;
else if (type == "interior")
exterior = false;
else if (type != "local")
{
dolfin_error("BoundaryComputation.cpp",
"determine boundary mesh type",
"Unknown boundary type (%d)", type.c_str());
}
// Get my MPI process rank and number of MPI processes
const std::size_t my_rank = MPI::rank(mesh.mpi_comm());
const std::size_t num_processes = MPI::size(mesh.mpi_comm());
// Open boundary mesh for editing
const std::size_t D = mesh.topology().dim();
MeshEditor editor;
editor.open(boundary, mesh.type().facet_type(), D - 1, mesh.geometry().dim());
// Generate facet - cell connectivity if not generated
mesh.init(D - 1, D);
// Temporary arrays for assignment of indices to vertices on the boundary
std::map<std::size_t, std::size_t> boundary_vertices;
// Map of index "owners" (process responsible for assigning global index)
std::map< std::size_t, std::size_t > global_index_owner;
// Shared vertices for full mesh
// FIXME: const_cast
const std::map<unsigned int, std::set<unsigned int>> &
shared_vertices = const_cast<Mesh&>(mesh).topology().shared_entities(0);
// Shared vertices for boundary mesh
std::map<unsigned int, std::set<unsigned int>> shared_boundary_vertices;
if (exterior)
{
// Extract shared vertices if vertex is identified as part of globally
// exterior facet.
std::vector<std::size_t> boundary_global_indices;
for (std::map<unsigned int, std::set<unsigned int>>::const_iterator
sv_it=shared_vertices.begin(); sv_it != shared_vertices.end(); ++sv_it)
{
std::size_t local_mesh_index = sv_it->first;
Vertex v(mesh, local_mesh_index);
for (FacetIterator f(v); !f.end(); ++f)
{
if (f->num_global_entities(D) == 1)
{
const std::size_t global_mesh_index
= mesh.topology().global_indices(0)[local_mesh_index];
shared_boundary_vertices[local_mesh_index] = sv_it->second;
boundary_global_indices.push_back(global_mesh_index);
break;
}
}
}
// Distribute all shared boundary vertices
std::vector<std::vector<std::size_t>> boundary_global_indices_all;
MPI::all_gather(mesh.mpi_comm(), boundary_global_indices,
boundary_global_indices_all);
// Identify and clean up discrepancies between shared vertices of full mesh
// and shared vertices of boundary mesh
for (auto sbv_it = shared_boundary_vertices.begin();
sbv_it != shared_boundary_vertices.end(); )
{
std::size_t local_mesh_index = sbv_it->first;
const std::size_t global_mesh_index
= mesh.topology().global_indices(0)[local_mesh_index];
// Check if this vertex is identified as boundary vertex on
// other processes sharing this vertex
std::set<unsigned int> &other_processes = sbv_it->second;
for (auto op_it=other_processes.begin();
op_it != other_processes.end(); )
{
// Check if vertex is identified as boundary vertex on process *op_it
bool is_boundary_vertex
= (std::find(boundary_global_indices_all[*op_it].begin(),
boundary_global_indices_all[*op_it].end(),
global_mesh_index)
!= boundary_global_indices_all[*op_it].end());
// Erase item if this is not identified as a boundary vertex
// on process *op_it, and increment iterator
if (!is_boundary_vertex)
{
// Erase item while carefully avoiding invalidating the
// iterator: First increment it to get the next, valid
// iterator, and then erase what it pointed to from
// other_processes
other_processes.erase(op_it++);
}
else
++op_it;
}
// Erase item from map if no other processes identify this
// vertex as a boundary vertex, and increment iterator
if (other_processes.size() == 0)
{
// Erase carefully as above
shared_boundary_vertices.erase(sbv_it++);
}
else
++sbv_it;
}
}
else
{
// If interior boundary, shared vertices are the same
shared_boundary_vertices = shared_vertices;
}
// Determine boundary facet, count boundary vertices and facets, and
// assign vertex indices
std::size_t num_boundary_vertices = 0;
std::size_t num_owned_vertices = 0;
std::size_t num_boundary_cells = 0;
MeshFunction<bool> boundary_facet(reference_to_no_delete_pointer(mesh),
D - 1, false);
for (FacetIterator f(mesh); !f.end(); ++f)
{
// Boundary facets are connected to exactly one cell
if (f->num_entities(D) == 1)
{
const bool global_exterior_facet = (f->num_global_entities(D) == 1);
if (global_exterior_facet && exterior)
boundary_facet[*f] = true;
else if (!global_exterior_facet && interior)
boundary_facet[*f] = true;
if (boundary_facet[*f])
{
// Count boundary vertices and assign indices
for (VertexIterator v(*f); !v.end(); ++v)
{
const std::size_t local_mesh_index = v->index();
if (boundary_vertices.find(local_mesh_index)
== boundary_vertices.end())
{
const std::size_t local_boundary_index = num_boundary_vertices;
boundary_vertices[local_mesh_index] = local_boundary_index;
// Determine "owner" of global_mesh_index
std::size_t owner = my_rank;
std::map<unsigned int, std::set<unsigned int>>::const_iterator
other_processes_it
= shared_boundary_vertices.find(local_mesh_index);
if (other_processes_it != shared_boundary_vertices.end() && D > 1)
{
const std::set<unsigned int>& other_processes
= other_processes_it->second;
const std::size_t min_process
= *std::min_element(other_processes.begin(),
other_processes.end());
boundary.topology().shared_entities(0)[local_boundary_index]
= other_processes;
// FIXME: More sophisticated ownership determination
if (min_process < owner)
owner = min_process;
}
const std::size_t global_mesh_index
= mesh.topology().global_indices(0)[local_mesh_index];
global_index_owner[global_mesh_index] = owner;
// Update counts
if (owner == my_rank)
num_owned_vertices++;
num_boundary_vertices++;
}
}
// Count boundary cells (facets of the mesh)
num_boundary_cells++;
}
}
}
// Initiate boundary topology
/*
boundary.topology().init(0, num_boundary_vertices,
MPI::sum(mesh.mpi_comm(), num_owned_vertices));
boundary.topology().init(D - 1, num_boundary_cells,
MPI::sum(mesh.mpi_comm(), num_boundary_cells));
*/
// Specify number of vertices and cells
editor.init_vertices_global(num_boundary_vertices,
MPI::sum(mesh.mpi_comm(), num_owned_vertices));
editor.init_cells_global(num_boundary_cells, MPI::sum(mesh.mpi_comm(),
num_boundary_cells));
// Write vertex map
MeshFunction<std::size_t>& vertex_map = boundary.entity_map(0);
if (num_boundary_vertices > 0)
{
vertex_map.init(reference_to_no_delete_pointer(boundary), 0,
num_boundary_vertices);
}
std::map<std::size_t, std::size_t>::const_iterator it;
for (it = boundary_vertices.begin(); it != boundary_vertices.end(); ++it)
vertex_map[it->second] = it->first;
// Get vertex ownership distribution, and find index to start global
// numbering from
std::vector<std::size_t> ownership_distribution(num_processes);
MPI::all_gather(mesh.mpi_comm(), num_owned_vertices, ownership_distribution);
std::size_t start_index = 0;
for (std::size_t j = 0; j < my_rank; j++)
start_index += ownership_distribution[j];
// Set global indices of owned vertices, request global indices for
// vertices owned elsewhere
std::map<std::size_t, std::size_t> global_indices;
std::vector<std::vector<std::size_t>> request_global_indices(num_processes);
std::size_t current_index = start_index;
for (std::size_t local_boundary_index = 0;
local_boundary_index<num_boundary_vertices; local_boundary_index++)
{
const std::size_t local_mesh_index = vertex_map[local_boundary_index];
const std::size_t global_mesh_index
= mesh.topology().global_indices(0)[local_mesh_index];
const std::size_t owner = global_index_owner[global_mesh_index];
if (owner != my_rank)
request_global_indices[owner].push_back(global_mesh_index);
else
global_indices[global_mesh_index] = current_index++;
}
// Send and receive requests from other processes
std::vector<std::vector<std::size_t>> global_index_requests(num_processes);
MPI::all_to_all(mesh.mpi_comm(), request_global_indices,
global_index_requests);
// Find response to requests of global indices
std::vector<std::vector<std::size_t>> respond_global_indices(num_processes);
for (std::size_t i = 0; i < num_processes; i++)
{
const std::size_t N = global_index_requests[i].size();
respond_global_indices[i].resize(N);
for (std::size_t j = 0; j < N; j++)
respond_global_indices[i][j]
= global_indices[global_index_requests[i][j]];
}
// Scatter responses back to requesting processes
std::vector<std::vector<std::size_t>> global_index_responses(num_processes);
MPI::all_to_all(mesh.mpi_comm(), respond_global_indices,
global_index_responses);
// Update global_indices
for (std::size_t i = 0; i < num_processes; i++)
{
const std::size_t N = global_index_responses[i].size();
// Check that responses are the same size as the requests made
dolfin_assert(global_index_responses[i].size()
== request_global_indices[i].size());
for (std::size_t j = 0; j < N; j++)
{
const std::size_t global_mesh_index = request_global_indices[i][j];
const std::size_t global_boundary_index = global_index_responses[i][j];
global_indices[global_mesh_index] = global_boundary_index;
}
}
// Create vertices
for (std::size_t local_boundary_index = 0;
local_boundary_index < num_boundary_vertices; local_boundary_index++)
{
const std::size_t local_mesh_index = vertex_map[local_boundary_index];
const std::size_t global_mesh_index
= mesh.topology().global_indices(0)[local_mesh_index];
const std::size_t global_boundary_index = global_indices[global_mesh_index];
Vertex v(mesh, local_mesh_index);
editor.add_vertex_global(local_boundary_index, global_boundary_index,
v.point());
}
// Find global index to start cell numbering from for current process
std::vector<std::size_t> cell_distribution(num_processes);
MPI::all_gather(mesh.mpi_comm(), num_boundary_cells, cell_distribution);
std::size_t start_cell_index = 0;
for (std::size_t i = 0; i < my_rank; i++)
start_cell_index += cell_distribution[i];
// Create cells (facets) and map between boundary mesh cells and facets parent
MeshFunction<std::size_t>& cell_map = boundary.entity_map(D - 1);
if (num_boundary_cells > 0)
{
cell_map.init(reference_to_no_delete_pointer(boundary), D - 1,
num_boundary_cells);
}
std::vector<std::size_t>
cell(boundary.type().num_vertices(boundary.topology().dim()));
std::size_t current_cell = 0;
for (FacetIterator f(mesh); !f.end(); ++f)
{
if (boundary_facet[*f])
{
// Compute new vertex numbers for cell
const unsigned int* vertices = f->entities(0);
for (std::size_t i = 0; i < cell.size(); i++)
cell[i] = boundary_vertices[vertices[i]];
// Reorder vertices so facet is right-oriented w.r.t. facet
// normal
reorder(cell, *f);
// Create mapping from boundary cell to mesh facet if requested
if (!cell_map.empty())
cell_map[current_cell] = f->index();
// Add cell
editor.add_cell(current_cell, start_cell_index+current_cell, cell);
current_cell++;
}
}
// Close mesh editor. Note the argument order=false to prevent
// ordering from destroying the orientation of facets accomplished
// by calling reorder() below.
editor.close(false);
}
//-----------------------------------------------------------------------------
bool LocalMeshCoarsening::coarsen_cell(Mesh& mesh, Mesh& coarse_mesh,
int cellid,
std::vector<int>& old2new_vertex,
std::vector<int>& old2new_cell,
bool coarsen_boundary)
{
cout << "coarsen_cell: " << cellid << endl;
cout << "num_cells: " << mesh.num_cells() << endl;
const std::size_t num_vertices = mesh.size(0);
const std::size_t num_cells = mesh.size(mesh.topology().dim());
auto _mesh = reference_to_no_delete_pointer(mesh);
// Initialise forbidden vertices
MeshFunction<bool> vertex_forbidden(_mesh);
vertex_forbidden.init(0);
for (VertexIterator v(mesh); !v.end(); ++v)
vertex_forbidden[v->index()] = false;
// Initialise boundary vertices
MeshFunction<bool> vertex_boundary(_mesh);
vertex_boundary.init(0);
for (VertexIterator v(mesh); !v.end(); ++v)
vertex_boundary[v->index()] = false;
BoundaryMesh boundary(mesh, "exterior");
MeshFunction<std::size_t>& bnd_vertex_map = boundary.entity_map(0);
for (VertexIterator v(boundary); !v.end(); ++v)
vertex_boundary[bnd_vertex_map[v->index()]] = true;
// If coarsen boundary is forbidden
if (coarsen_boundary == false)
{
for (VertexIterator v(boundary); !v.end(); ++v)
vertex_forbidden[bnd_vertex_map[v->index()]] = true;
}
// Initialise data for finding which vertex to remove
bool _collapse_edge = false;
const unsigned int* edge_vertex;
std::size_t shortest_edge_index = 0;
double lmin, l;
std::size_t num_cells_to_remove = 0;
// Get cell type
const CellType& cell_type = mesh.type();
const Cell cell(mesh, cellid);
MeshEditor editor;
editor.open(coarse_mesh, cell_type.cell_type(),
mesh.topology().dim(), mesh.geometry().dim());
MeshFunction<bool> cell_to_remove(_mesh);
cell_to_remove.init(mesh.topology().dim());
for (CellIterator ci(mesh); !ci.end(); ++ci)
cell_to_remove[ci->index()] = false;
MeshFunction<bool> cell_to_regenerate(_mesh);
cell_to_regenerate.init(mesh.topology().dim());
for (CellIterator ci(mesh); !ci.end(); ++ci)
cell_to_regenerate[ci->index()] = false;
// Find shortest edge of cell c
_collapse_edge = false;
lmin = 1.0e10*cell.diameter();
for (EdgeIterator e(cell); !e.end(); ++e)
{
edge_vertex = e->entities(0);
if (!vertex_forbidden[edge_vertex[0]] || !vertex_forbidden[edge_vertex[1]])
{
l = e->length();
if ( lmin > l )
{
lmin = l;
shortest_edge_index = e->index();
_collapse_edge = true;
}
}
}
Edge shortest_edge(mesh, shortest_edge_index);
// Decide which vertex to remove
std::size_t vert2remove_idx = 0;
// If at least one vertex should be removed
if ( _collapse_edge == true )
{
edge_vertex = shortest_edge.entities(0);
if(vertex_forbidden[edge_vertex[0]] &&
vertex_forbidden[edge_vertex[1]])
{
// Both vertices are forbidden, cannot coarsen
cout << "both vertices forbidden" << endl;
editor.close();
return false;
}
if(vertex_forbidden[edge_vertex[0]] == true)
vert2remove_idx = edge_vertex[1];
else if(vertex_forbidden[edge_vertex[1]] == true)
vert2remove_idx = edge_vertex[0];
else if(vertex_boundary[edge_vertex[1]] == true && vertex_boundary[edge_vertex[0]] == false)
vert2remove_idx = edge_vertex[0];
else if(vertex_boundary[edge_vertex[0]] == true && vertex_boundary[edge_vertex[1]] == false)
vert2remove_idx = edge_vertex[1];
else if ( edge_vertex[0] > edge_vertex[1] )
vert2remove_idx = edge_vertex[0];
else
vert2remove_idx = edge_vertex[1];
}
else
{
// No vertices to remove, cannot coarsen
cout << "all vertices forbidden" << endl;
editor.close();
return false;
}
Vertex vertex_to_remove(mesh, vert2remove_idx);
// Remove cells around edge
num_cells_to_remove = 0;
for (CellIterator cn(shortest_edge); !cn.end(); ++cn)
{
cell_to_remove[cn->index()] = true;
num_cells_to_remove++;
// Update cell map
old2new_cell[cn->index()] = -1;
}
// Regenerate cells around vertex
for (CellIterator cn(vertex_to_remove); !cn.end(); ++cn)
{
cell_to_regenerate[cn->index()] = true;
// Update cell map (will be filled in with correct index)
old2new_cell[cn->index()] = -1;
}
// Specify number of vertices and cells
editor.init_vertices_global(num_vertices - 1, num_vertices - 1);
editor.init_cells_global(num_cells - num_cells_to_remove,
num_cells - num_cells_to_remove);
cout << "Number of cells in old mesh: " << num_cells << "; to remove: " <<
num_cells_to_remove << endl;
// Add old vertices
std::size_t vertex = 0;
for(VertexIterator v(mesh); !v.end(); ++v)
{
if(vertex_to_remove.index() == v->index())
old2new_vertex[v->index()] = -1;
else
{
//cout << "adding old vertex at: " << v->point() << endl;
old2new_vertex[v->index()] = vertex;
editor.add_vertex(vertex, v->point());
vertex++;
}
}
// Add old unrefined cells
std::size_t cv_idx;
std::size_t current_cell = 0;
std::vector<std::size_t> cell_vertices(cell_type.num_entities(0));
for (CellIterator c(mesh); !c.end(); ++c)
{
if (cell_to_remove[*c] == false && cell_to_regenerate[*c] == false)
{
cv_idx = 0;
for (VertexIterator v(*c); !v.end(); ++v)
cell_vertices[cv_idx++] = old2new_vertex[v->index()];
//cout << "adding old cell" << endl;
editor.add_cell(current_cell++, cell_vertices);
// Update cell maps
old2new_cell[c->index()] = current_cell - 1;
}
}
// Add new cells.
collapse_edge(mesh, shortest_edge, vertex_to_remove, cell_to_remove,
old2new_vertex, old2new_cell, editor, current_cell);
editor.close();
// Set volume tolerance. This parameter determines a quality criterion
// for the new mesh: higher value indicates a sharper criterion.
double vol_tol = 1.0e-3;
bool mesh_ok = true;
Cell removed_cell(mesh, cellid);
// Check mesh quality (volume)
for (CellIterator c(removed_cell); !c.end(); ++c)
{
std::size_t id = c->index();
int nid = old2new_cell[id];
if(nid != -1)
{
Cell cn(coarse_mesh, nid);
double qm = cn.volume() / cn.diameter();
if(qm < vol_tol)
{
warning("Cell quality too low");
cout << "qm: " << qm << endl;
mesh_ok = false;
return mesh_ok;
}
}
}
// Checking for inverted cells
for (CellIterator c(removed_cell); !c.end(); ++c)
{
std::size_t id = c->index();
int nid = old2new_cell[id];
if(nid != -1)
{
Cell cn(coarse_mesh, nid);
if(c->orientation() != cn.orientation())
{
cout << "cell orientation inverted" << endl;
mesh_ok = false;
return mesh_ok;
}
}
}
return mesh_ok;
}
//-----------------------------------------------------------------------------
void UniformMeshRefinement::refine(Mesh& refined_mesh,
const Mesh& mesh)
{
not_working_in_parallel("UniformMeshRefinement::refine");
log(TRACE, "Refining simplicial mesh uniformly.");
// Check that refined_mesh and mesh are not the same
if (&refined_mesh == &mesh)
{
dolfin_error("UniformMeshRefinement.cpp",
"refine mesh",
"Refined_mesh and mesh point to the same object");
}
// Generate cell - edge connectivity if not generated
mesh.init(mesh.topology().dim(), 1);
// Generate edge - vertex connectivity if not generated
mesh.init(1, 0);
// Mesh needs to be ordered (so we can pick right combination of vertices/edges)
if (!mesh.ordered())
dolfin_error("UniformMeshRefinement.cpp",
"refine mesh",
"Mesh is not ordered according to the UFC numbering convention, consider calling mesh.order()");
// Get cell type
const CellType& cell_type = mesh.type();
// Open new mesh for editing
MeshEditor editor;
editor.open(refined_mesh, cell_type.cell_type(),
mesh.topology().dim(), mesh.geometry().dim());
// Get size of mesh
const std::size_t num_vertices = mesh.size(0);
const std::size_t num_edges = mesh.size(1);
const std::size_t num_cells = mesh.size(mesh.topology().dim());
// Specify number of vertices and cells
editor.init_vertices_global(num_vertices + num_edges, num_vertices + num_edges);
editor.init_cells_global(ipow(2, mesh.topology().dim())*num_cells,
ipow(2, mesh.topology().dim())*num_cells);
// Add old vertices
std::size_t vertex = 0;
for (VertexIterator v(mesh); !v.end(); ++v)
{
editor.add_vertex(vertex, v->point());
vertex++;
}
// Add new vertices
for (EdgeIterator e(mesh); !e.end(); ++e)
{
editor.add_vertex(vertex, e->midpoint());
vertex++;
}
// Add cells
std::size_t current_cell = 0;
for (CellIterator c(mesh); !c.end(); ++c)
cell_type.refine_cell(*c, editor, current_cell);
// Close editor
editor.close();
// Make sure that mesh is ordered after refinement
//refined_mesh.order();
}
int main(int argc, char *argv[]) {
if (argc < 3 ) {
std::cout<< "Usage: ./extract <checkpoint> <num>" << std::endl;
return 0;
}
std::ostringstream _fname;
_fname << argv[1] << "_";
std::vector<std::string> chkp_files;
for (int i = 0; i < atoi(argv[2]); i++) {
std::ostringstream tmp;
tmp << _fname.str();
tmp << i << ".chkp";
chkp_files.push_back(tmp.str());
}
CellType::Type type;
double t;
unsigned int id, tdim, gdim, num_vertices, num_cells, num_entities;
std::ifstream in;
std::list<dVertex> vlist;
std::list<dCell> dmesh;
for(std::vector<std::string>::iterator it = chkp_files.begin();
it != chkp_files.end(); ++it) {
in.open(it->c_str(), std::ifstream::binary);
if(in.good()) {
in.read((char *)&id, sizeof(unsigned int));
in.read((char *)&t, sizeof(double));
in.read((char *)&type, sizeof(CellType::Type));
in.read((char *)&tdim, sizeof(unsigned int));
in.read((char *)&gdim, sizeof(unsigned int));
in.read((char *)&num_vertices, sizeof(unsigned int));
in.read((char *)&num_cells, sizeof(unsigned int));
in.read((char *)&num_entities, sizeof(unsigned int));
double *coords = new double[gdim *num_vertices];
in.read((char *)coords, (gdim * num_vertices) * sizeof(double));
std::list<dVertex> _vlist;
int vi = 0;
for(unsigned int i = 0; i < gdim * num_vertices; i += gdim) {
switch(gdim)
{
case 2:
_vlist.push_back(dVertex(vi++, Point(coords[i], coords[i+1]))); break;
case 3:
_vlist.push_back(dVertex(vi++, Point(coords[i], coords[i+1], coords[i+2]))); break;
}
}
delete[] coords;
unsigned int *cells = new unsigned int[num_entities * num_cells];
in.read((char *)cells, (num_entities * num_cells) * sizeof(unsigned int));
unsigned int *mapping = new unsigned int[_vlist.size()];
in.read((char *)mapping, _vlist.size() * sizeof(unsigned int));
unsigned int *mp = &mapping[0];
std::map<unsigned int, unsigned int> vmap;
for(std::list<dVertex>::iterator it = _vlist.begin();
it != _vlist.end(); ++it)
vmap[it->id] = *(mp++);
delete[] mapping;
Array<unsigned int> v;
for(unsigned int i = 0; i < num_entities * num_cells; i += num_entities) {
v.clear();
for(unsigned int j = 0; j < num_entities; j++)
v.push_back(vmap[cells[i+j]]);
dmesh.push_back(dCell(v));
}
delete[] cells;
unsigned int num_ghost;
in.read((char *)&num_ghost, sizeof(unsigned int));
unsigned int *ghosts = new unsigned int[2 * num_ghost];
in.read((char *)ghosts, 2*num_ghost * sizeof(unsigned int));
std::set<unsigned int> ghost_set;
for (unsigned int i = 0; i < 2 * num_ghost; i += 2)
ghost_set.insert(ghosts[i]);
delete[] ghosts;
for(std::list<dVertex>::iterator it = _vlist.begin();
it != _vlist.end(); ++it)
if(ghost_set.find(it->id) == ghost_set.end())
vlist.push_back(dVertex(vmap[it->id], it->p));
}
in.close();
}
Mesh mesh;
MeshEditor editor;
editor.open(mesh, type, tdim, gdim);
editor.initVertices(vlist.size());
editor.initCells(dmesh.size());
for(std::list<dVertex>::iterator it = vlist.begin(); it != vlist.end(); ++it)
editor.addVertex(it->id, it->p);
unsigned int ci = 0;
for(std::list<dCell>::iterator it = dmesh.begin(); it != dmesh.end(); ++it)
editor.addCell(ci++, it->vertices);
editor.close();
File mesh_file("mesh.xml");
mesh_file << mesh;
}
//-----------------------------------------------------------------------------
dolfin::Mesh MeshRenumbering::renumber_by_color(const Mesh& mesh,
const std::vector<std::size_t> coloring_type)
{
// Start timer
Timer timer("Renumber mesh by color");
// Get some some mesh
const std::size_t tdim = mesh.topology().dim();
const std::size_t gdim = mesh.geometry().dim();
const std::size_t num_vertices = mesh.num_vertices();
const std::size_t num_cells = mesh.num_cells();
// Check that requested coloring is a cell coloring
if (coloring_type[0] != tdim)
{
dolfin_error("MeshRenumbering.cpp",
"renumber mesh by color",
"Coloring is not a cell coloring: only cell colorings are supported");
}
// Compute renumbering
std::vector<double> new_coordinates;
std::vector<std::size_t> new_connections;
MeshRenumbering::compute_renumbering(mesh, coloring_type, new_coordinates,
new_connections);
// Create new mesh
Mesh new_mesh;
// Create mesh editor
MeshEditor editor;
editor.open(new_mesh, mesh.type().cell_type(), tdim, gdim);
editor.init_cells(num_cells);
editor.init_vertices(num_vertices);
// Add vertices
dolfin_assert(new_coordinates.size() == num_vertices*gdim);
for (std::size_t i = 0; i < num_vertices; ++i)
{
std::vector<double> x(gdim);
for (std::size_t j = 0; j < gdim; ++j)
x[j] = new_coordinates[i*gdim + j];
editor.add_vertex(i, x);
}
cout << "Done adding vertices" << endl;
// Add cells
dolfin_assert(new_coordinates.size() == num_vertices*gdim);
const std::size_t vertices_per_cell = mesh.type().num_entities(0);
for (std::size_t i = 0; i < num_cells; ++i)
{
std::vector<std::size_t> c(vertices_per_cell);
std::copy(new_connections.begin() + i*vertices_per_cell,
new_connections.begin() + i*vertices_per_cell + vertices_per_cell,
c.begin());
editor.add_cell(i, c);
}
editor.close();
cout << "Close editor" << endl;
// Initialise coloring data
typedef std::map<const std::vector<std::size_t>, std::pair<std::vector<std::size_t>,
std::vector<std::vector<std::size_t> > > >::const_iterator ConstMeshColoringData;
// Get old coloring
ConstMeshColoringData mesh_coloring
= mesh.topology().coloring.find(coloring_type);
if (mesh_coloring == mesh.topology().coloring.end())
{
dolfin_error("MeshRenumbering.cpp",
"renumber mesh by color",
"Requested mesh coloring has not been computed");
}
// Get old coloring data
const std::vector<std::size_t>& colors = mesh_coloring->second.first;
const std::vector<std::vector<std::size_t> >&
entities_of_color = mesh_coloring->second.second;
dolfin_assert(colors.size() == num_cells);
dolfin_assert(!entities_of_color.empty());
const std::size_t num_colors = entities_of_color.size();
// New coloring data
dolfin_assert(new_mesh.topology().coloring.empty());
std::vector<std::size_t> new_colors(colors.size());
std::vector<std::vector<std::size_t> > new_entities_of_color(num_colors);
std::size_t current_cell = 0;
for (std::size_t color = 0; color < num_colors; color++)
{
// Get the array of cell indices of current color
const std::vector<std::size_t>& colored_cells = entities_of_color[color];
std::vector<std::size_t>& new_colored_cells = new_entities_of_color[color];
// Update cell color data
for (std::size_t i = 0; i < colored_cells.size(); i++)
{
new_colored_cells.push_back(current_cell);
new_colors[current_cell] = color;
current_cell++;
}
}
// Set new coloring mesh data
std::pair<ConstMeshColoringData, bool> insert
= new_mesh.topology().coloring.insert(std::make_pair(coloring_type,
std::make_pair(new_colors, new_entities_of_color)));
dolfin_assert(insert.second);
cout << "Return new mesh" << endl;
return new_mesh;
}
//-----------------------------------------------------------------------------
void SubMesh::init(const Mesh& mesh,
const std::vector<std::size_t>& sub_domains,
std::size_t sub_domain)
{
// Open mesh for editing
MeshEditor editor;
const std::size_t D = mesh.topology().dim();
editor.open(*this, mesh.type().cell_type(), D,
mesh.geometry().dim());
// Build set of cells that are in sub-mesh
std::vector<bool> parent_cell_in_subdomain(mesh.num_cells(), false);
std::set<std::size_t> submesh_cells;
for (CellIterator cell(mesh); !cell.end(); ++cell)
{
if (sub_domains[cell->index()] == sub_domain)
{
parent_cell_in_subdomain[cell->index()] = true;
submesh_cells.insert(cell->index());
}
}
// Map from parent vertex index to submesh vertex index
std::map<std::size_t, std::size_t> parent_to_submesh_vertex_indices;
// Map from submesh cell to parent cell
std::vector<std::size_t> submesh_cell_parent_indices;
submesh_cell_parent_indices.reserve(submesh_cells.size());
// Vector from parent cell index to submesh cell index
std::vector<std::size_t> parent_to_submesh_cell_indices(mesh.num_cells(), 0);
// Add sub-mesh cells
editor.init_cells_global(submesh_cells.size(), submesh_cells.size());
std::size_t current_cell = 0;
std::size_t current_vertex = 0;
for (std::set<std::size_t>::iterator cell_it = submesh_cells.begin();
cell_it != submesh_cells.end(); ++cell_it)
{
// Data structure to hold new vertex indices for cell
std::vector<std::size_t> cell_vertices;
// Create cell
Cell cell(mesh, *cell_it);
// Iterate over cell vertices
for (VertexIterator vertex(cell); !vertex.end(); ++vertex)
{
const std::size_t parent_vertex_index = vertex->index();
// Look for parent vertex in map
std::map<std::size_t, std::size_t>::iterator vertex_it
= parent_to_submesh_vertex_indices.find(parent_vertex_index);
// If vertex has been inserted, get new index, otherwise
// increment and insert
std::size_t submesh_vertex_index = 0;
if (vertex_it != parent_to_submesh_vertex_indices.end())
submesh_vertex_index = vertex_it->second;
else
{
submesh_vertex_index = current_vertex++;
parent_to_submesh_vertex_indices[parent_vertex_index]
= submesh_vertex_index;
}
// Add vertex to list of cell vertices (new indexing)
cell_vertices.push_back(submesh_vertex_index);
}
// Add parent cell index to list
submesh_cell_parent_indices.push_back(cell.index());
// Store parent cell -> submesh cell indices
parent_to_submesh_cell_indices[cell.index()] = current_cell;
// Add cell to mesh
editor.add_cell(current_cell++, cell_vertices);
}
// Vector to hold submesh vertex -> parent vertex
std::vector<std::size_t> parent_vertex_indices;
parent_vertex_indices.resize(parent_to_submesh_vertex_indices.size());
// Initialise mesh editor
editor.init_vertices_global(parent_to_submesh_vertex_indices.size(),
parent_to_submesh_vertex_indices.size());
// Add vertices
for (std::map<std::size_t, std::size_t>::iterator it
= parent_to_submesh_vertex_indices.begin();
it != parent_to_submesh_vertex_indices.end(); ++it)
{
Vertex vertex(mesh, it->first);
if (MPI::size(mesh.mpi_comm()) > 1)
error("SubMesh::init not working in parallel");
// FIXME: Get global vertex index
editor.add_vertex(it->second, vertex.point());
parent_vertex_indices[it->second] = it->first;
}
// Close editor
editor.close();
// Build submesh-to-parent map for vertices
std::vector<std::size_t>& parent_vertex_indices_mf
= data().create_array("parent_vertex_indices", 0);
parent_vertex_indices_mf.resize(num_vertices());
for (std::map<std::size_t, std::size_t>::iterator it
= parent_to_submesh_vertex_indices.begin();
it != parent_to_submesh_vertex_indices.end(); ++it)
{
parent_vertex_indices_mf[it->second] = it->first;
}
// Build submesh-to-parent map for cells
std::vector<std::size_t>& parent_cell_indices
= data().create_array("parent_cell_indices", D);
parent_cell_indices.resize(num_cells());
current_cell = 0;
for (std::vector<std::size_t>::iterator it
= submesh_cell_parent_indices.begin();
it != submesh_cell_parent_indices.end(); ++it)
{
parent_cell_indices[current_cell++] = *it;
}
// Initialise present MeshDomain
const MeshDomains& parent_domains = mesh.domains();
this->domains().init(parent_domains.max_dim());
// Collect MeshValueCollections from parent mesh
for (std::size_t dim_t = 0; dim_t <= parent_domains.max_dim(); dim_t++)
{
// If parent mesh does not has a data for dim_t
if (parent_domains.num_marked(dim_t) == 0)
continue;
// Initialise connectivity
mesh.init(dim_t, D);
// FIXME: Can avoid building this map for cell and vertices
// Build map from submesh entity (parent vertex list) -> (submesh index)
mesh.init(dim_t);
std::map<std::vector<std::size_t>, std::size_t> entity_map;
for (MeshEntityIterator e(*this, dim_t); !e.end(); ++e)
{
// Build list of entity vertex indices and sort
std::vector<std::size_t> vertex_list;
for (VertexIterator v(*e); !v.end(); ++v)
vertex_list.push_back(parent_vertex_indices[v->index()]);
std::sort(vertex_list.begin(), vertex_list.end());
entity_map.insert(std::make_pair(vertex_list, e->index()));
}
// Get submesh marker map
std::map<std::size_t, std::size_t>& submesh_markers
= this->domains().markers(dim_t);
// Get values map from parent MeshValueCollection
const std::map<std::size_t, std::size_t>& parent_markers
= parent_domains.markers(dim_t);
// Iterate over all parents marker values
std::map<std::size_t, std::size_t>::const_iterator itt;
for (itt = parent_markers.begin(); itt != parent_markers.end(); itt++)
{
// Create parent entity
const MeshEntity parent_entity(mesh, dim_t, itt->first);
// FIXME: Need to check all attached cells
std::size_t parent_cell_index = std::numeric_limits<std::size_t>::max();
if (dim_t == D)
{
parent_cell_index = itt->first;
}
else
{
// Get first parent cell index attached to parent entity
for (std::size_t i = 0; i < parent_entity.num_entities(D); ++i)
{
if (sub_domains[parent_entity.entities(D)[i]] == sub_domain)
{
parent_cell_index = parent_entity.entities(D)[i];
break;
}
}
}
// Check if the cell is included in the submesh
if (sub_domains[parent_cell_index] == sub_domain)
{
// Map markers from parent mesh to submesh
if (dim_t == D)
{
// Get submesh cell index
const std::size_t submesh_cell_index
= parent_to_submesh_cell_indices[parent_cell_index];
submesh_markers[submesh_cell_index] = itt->second;
}
else
{
std::vector<std::size_t> parent_vertex_list;
for (VertexIterator v(parent_entity); !v.end(); ++v)
parent_vertex_list.push_back(v->index());
std::sort(parent_vertex_list.begin(), parent_vertex_list.end());
// Get submesh entity index
std::map<std::vector<std::size_t>, std::size_t>::const_iterator
submesh_it = entity_map.find(parent_vertex_list);
dolfin_assert(submesh_it != entity_map.end());
submesh_markers[submesh_it->second] = itt->second;
}
}
}
}
}
//-----------------------------------------------------------------------------
UnitHexMesh::UnitHexMesh(MPI_Comm comm, std::size_t nx, std::size_t ny,
std::size_t nz) : Mesh(comm)
{
// Receive mesh according to parallel policy
if (MPI::is_receiver(this->mpi_comm()))
{
MeshPartitioning::build_distributed_mesh(*this);
return;
}
MeshEditor editor;
editor.open(*this, CellType::hexahedron, 3, 3);
// Create vertices and cells:
editor.init_vertices_global((nx + 1)*(ny + 1)*(nz + 1),
(nx + 1)*(ny + 1)*(nz + 1));
editor.init_cells_global(nx*ny*nz, nx*ny*nz);
// Storage for vertices
std::vector<double> x(3);
const double a = 0.0;
const double b = 1.0;
const double c = 0.0;
const double d = 1.0;
const double e = 0.0;
const double f = 1.0;
// Create main vertices:
std::size_t vertex = 0;
for (std::size_t iz = 0; iz <= nz; iz++)
{
x[2] = e + ((static_cast<double>(iz))*(f - e)/static_cast<double>(nz));
for (std::size_t iy = 0; iy <= ny; iy++)
{
x[1] = c + ((static_cast<double>(iy))*(d - c)/static_cast<double>(ny));
for (std::size_t ix = 0; ix <= nx; ix++)
{
x[0] = a + ((static_cast<double>(ix))*(b - a)/static_cast<double>(nx));
editor.add_vertex(vertex, x);
vertex++;
}
}
}
// Create cuboids
std::size_t cell = 0;
std::vector<std::size_t> v(8);
for (std::size_t iz = 0; iz < nz; iz++)
for (std::size_t iy = 0; iy < ny; iy++)
for (std::size_t ix = 0; ix < nx; ix++)
{
v[0] = (iz*(ny + 1) + iy)*(nx + 1) + ix;
v[1] = v[0] + 1;
v[2] = v[0] + (nx + 1);
v[3] = v[1] + (nx + 1);
v[4] = v[0] + (nx + 1)*(ny + 1);
v[5] = v[1] + (nx + 1)*(ny + 1);
v[6] = v[2] + (nx + 1)*(ny + 1);
v[7] = v[3] + (nx + 1)*(ny + 1);
editor.add_cell(cell, v);
++cell;
}
// Close mesh editor
editor.close();
// Broadcast mesh according to parallel policy
if (MPI::is_broadcaster(this->mpi_comm()))
{
MeshPartitioning::build_distributed_mesh(*this);
return;
}
}
//-----------------------------------------------------------------------------
void RegularCutRefinement::refine_marked(Mesh& refined_mesh,
const Mesh& mesh,
const std::vector<int>& refinement_markers,
const IndexSet& marked_edges)
{
// Count the number of cells in refined mesh
std::size_t num_cells = 0;
// Data structure to hold a cell
std::vector<std::size_t> cell_data(3);
for (CellIterator cell(mesh); !cell.end(); ++cell)
{
const int marker = refinement_markers[cell->index()];
switch (marker)
{
case no_refinement:
num_cells += 1;
break;
case regular_refinement:
num_cells += 4;
break;
case backtrack_bisection:
num_cells += 2;
break;
case backtrack_bisection_refine:
num_cells += 3;
break;
default:
num_cells += 2;
}
}
// Initialize mesh editor
const std::size_t num_vertices = mesh.num_vertices() + marked_edges.size();
MeshEditor editor;
editor.open(refined_mesh, mesh.topology().dim(), mesh.geometry().dim());
editor.init_vertices(num_vertices);
editor.init_cells(num_cells);
// Set vertex coordinates
std::size_t current_vertex = 0;
for (VertexIterator vertex(mesh); !vertex.end(); ++vertex)
{
editor.add_vertex(current_vertex, vertex->point());
current_vertex++;
}
for (std::size_t i = 0; i < marked_edges.size(); i++)
{
Edge edge(mesh, marked_edges[i]);
editor.add_vertex(current_vertex, edge.midpoint());
current_vertex++;
}
// Get bisection data for old mesh
const std::size_t D = mesh.topology().dim();
const std::vector<std::size_t>* bisection_twins = NULL;
if (mesh.data().exists("bisection_twins", D))
bisection_twins = &(mesh.data().array("bisection_twins", D));
// Markers for bisected cells pointing to their bisection twins in
// refined mesh
std::vector<std::size_t>& refined_bisection_twins
= refined_mesh.data().create_array("bisection_twins", D);
refined_bisection_twins.resize(num_cells);
for (std::size_t i = 0; i < num_cells; i++)
refined_bisection_twins[i] = i;
// Mapping from old to new unrefined cells (-1 means refined or not
// yet processed)
std::vector<int> unrefined_cells(mesh.num_cells());
std::fill(unrefined_cells.begin(), unrefined_cells.end(), -1);
// Iterate over all cells and add new cells
std::size_t current_cell = 0;
std::vector<std::vector<std::size_t> > cells(4, std::vector<std::size_t>(3));
for (CellIterator cell(mesh); !cell.end(); ++cell)
{
// Get marker
const int marker = refinement_markers[cell->index()];
if (marker == no_refinement)
{
// No refinement: just copy cell to new mesh
std::vector<std::size_t> vertices;
for (VertexIterator vertex(*cell); !vertex.end(); ++vertex)
vertices.push_back(vertex->index());
editor.add_cell(current_cell++, vertices);
// Store mapping to new cell index
unrefined_cells[cell->index()] = current_cell - 1;
// Remember unrefined bisection twins
if (bisection_twins)
{
const std::size_t bisection_twin = (*bisection_twins)[cell->index()];
const int twin_marker = refinement_markers[bisection_twin];
dolfin_assert(twin_marker == no_refinement);
if (unrefined_cells[bisection_twin] >= 0)
{
const std::size_t i = current_cell - 1;
const std::size_t j = unrefined_cells[bisection_twin];
refined_bisection_twins[i] = j;
refined_bisection_twins[j] = i;
}
}
}
else if (marker == regular_refinement)
{
// Regular refinement: divide into subsimplicies
dolfin_assert(unrefined_cells[cell->index()] == -1);
// Get vertices and edges
const unsigned int* v = cell->entities(0);
const unsigned int* e = cell->entities(1);
dolfin_assert(v);
dolfin_assert(e);
// Get offset for new vertex indices
const std::size_t offset = mesh.num_vertices();
// Compute indices for the six new vertices
const std::size_t v0 = v[0];
const std::size_t v1 = v[1];
const std::size_t v2 = v[2];
const std::size_t e0 = offset + marked_edges.find(e[0]);
const std::size_t e1 = offset + marked_edges.find(e[1]);
const std::size_t e2 = offset + marked_edges.find(e[2]);
// Create four new cells
cells[0][0] = v0; cells[0][1] = e2; cells[0][2] = e1;
cells[1][0] = v1; cells[1][1] = e0; cells[1][2] = e2;
cells[2][0] = v2; cells[2][1] = e1; cells[2][2] = e0;
cells[3][0] = e0; cells[3][1] = e1; cells[3][2] = e2;
// Add cells
std::vector<std::vector<std::size_t> >::const_iterator _cell;
for (_cell = cells.begin(); _cell != cells.end(); ++_cell)
editor.add_cell(current_cell++, *_cell);
}
else if (marker == backtrack_bisection || marker == backtrack_bisection_refine)
{
// Special case: backtrack bisected cells
dolfin_assert(unrefined_cells[cell->index()] == -1);
// Get index for bisection twin
dolfin_assert(bisection_twins);
const std::size_t bisection_twin = (*bisection_twins)[cell->index()];
dolfin_assert(bisection_twin != cell->index());
// Let lowest number twin handle refinement
if (bisection_twin < cell->index())
continue;
// Get marker for twin
const int twin_marker = refinement_markers[bisection_twin];
// Find common edge(s) and bisected edge(s)
const std::pair<std::size_t, std::size_t> common_edges
= find_common_edges(*cell, mesh, bisection_twin);
const std::pair<std::size_t, std::size_t> bisection_edges
= find_bisection_edges(*cell, mesh, bisection_twin);
const std::pair<std::size_t, std::size_t> bisection_vertices
= find_bisection_vertices(*cell, mesh, bisection_twin, bisection_edges);
// Get list of vertices and edges for both cells
const Cell twin(mesh, bisection_twin);
const unsigned int* vertices_0 = cell->entities(0);
const unsigned int* vertices_1 = twin.entities(0);
const unsigned int* edges_0 = cell->entities(1);
const unsigned int* edges_1 = twin.entities(1);
dolfin_assert(vertices_0);
dolfin_assert(vertices_1);
dolfin_assert(edges_0);
dolfin_assert(edges_1);
// Get offset for new vertex indices
const std::size_t offset = mesh.num_vertices();
// Locate vertices such that v_i is the vertex opposite to
// the edge e_i on the parent triangle
const std::size_t v0 = vertices_0[common_edges.first];
const std::size_t v1 = vertices_1[common_edges.second];
const std::size_t v2 = vertices_0[bisection_edges.first];
const std::size_t e0 = offset + marked_edges.find(edges_1[bisection_vertices.second]);
const std::size_t e1 = offset + marked_edges.find(edges_0[bisection_vertices.first]);
const std::size_t e2 = vertices_0[bisection_vertices.first];
// Locate new vertices on bisected edge (if any)
std::size_t E0 = 0;
std::size_t E1 = 0;
if (marker == backtrack_bisection_refine)
E0 = offset + marked_edges.find(edges_0[bisection_edges.first]);
if (twin_marker == backtrack_bisection_refine)
E1 = offset + marked_edges.find(edges_1[bisection_edges.second]);
// Add middle two cells (always)
dolfin_assert(cell_data.size() == 3);
cell_data[0] = e0; cell_data[1] = e1; cell_data[2] = e2;
editor.add_cell(current_cell++, cell_data);
cell_data[0] = v2; cell_data[1] = e1; cell_data[2] = e0;
editor.add_cell(current_cell++, cell_data);
// Add one or two remaining cells in current cell (left)
if (marker == backtrack_bisection)
{
cell_data[0] = v0; cell_data[1] = e2; cell_data[2] = e1;
editor.add_cell(current_cell++, cell_data);
}
else
{
// Add the two cells
cell_data[0] = v0; cell_data[1] = E0; cell_data[2] = e1;
editor.add_cell(current_cell++, cell_data);
cell_data[0] = E0; cell_data[1] = e2; cell_data[2] = e1;
editor.add_cell(current_cell++, cell_data);
// Set bisection twins
refined_bisection_twins[current_cell - 2] = current_cell - 1;
refined_bisection_twins[current_cell - 1] = current_cell - 2;
}
// Add one or two remaining cells in twin cell (right)
if (twin_marker == backtrack_bisection)
{
cell_data[0] = v1; cell_data[1] = e0; cell_data[2] = e2;
editor.add_cell(current_cell++, cell_data);
}
else
{
// Add the two cells
cell_data[0] = v1; cell_data[1] = e0; cell_data[2] = E1;
editor.add_cell(current_cell++, cell_data);
cell_data[0] = e0; cell_data[1] = e2; cell_data[2] = E1;
editor.add_cell(current_cell++, cell_data);
// Set bisection twins
refined_bisection_twins[current_cell - 2] = current_cell - 1;
refined_bisection_twins[current_cell - 1] = current_cell - 2;
}
}
else
{
// One edge marked for refinement: do bisection
dolfin_assert(unrefined_cells[cell->index()] == -1);
// Get vertices and edges
const unsigned int* v = cell->entities(0);
const unsigned int* e = cell->entities(1);
dolfin_assert(v);
dolfin_assert(e);
// Get edge number (equal to marker)
dolfin_assert(marker >= 0);
const std::size_t local_edge_index = static_cast<std::size_t>(marker);
const std::size_t global_edge_index = e[local_edge_index];
const std::size_t ee = mesh.num_vertices() + marked_edges.find(global_edge_index);
// Add the two new cells
if (local_edge_index == 0)
{
cell_data[0] = v[0]; cell_data[1] = ee; cell_data[2] = v[1];
editor.add_cell(current_cell++, cell_data);
cell_data[0] = v[0]; cell_data[1] = ee; cell_data[2] = v[2];
editor.add_cell(current_cell++, cell_data);
}
else if (local_edge_index == 1)
{
cell_data[0] = v[1]; cell_data[1] = ee; cell_data[2] = v[0];
editor.add_cell(current_cell++, cell_data);
cell_data[0] = v[1]; cell_data[1] = ee; cell_data[2] = v[2];
editor.add_cell(current_cell++, cell_data);
}
else
{
cell_data[0] = v[2]; cell_data[1] = ee; cell_data[2] = v[0];
editor.add_cell(current_cell++, cell_data);
cell_data[0] = v[2]; cell_data[1] = ee; cell_data[2] = v[1];
editor.add_cell(current_cell++, cell_data);
}
// Set bisection twins
refined_bisection_twins[current_cell - 2] = current_cell - 1;
refined_bisection_twins[current_cell - 1] = current_cell - 2;
}
}
// Close mesh editor
dolfin_assert(num_cells == current_cell);
editor.close();
}
//-----------------------------------------------------------------------------
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);
}
}
}
//-----------------------------------------------------------------------------
void XMLMesh::read_mesh(Mesh& mesh, const pugi::xml_node mesh_node)
{
// Get cell type and geometric dimension
const std::string cell_type_str = mesh_node.attribute("celltype").value();
const std::size_t gdim = mesh_node.attribute("dim").as_uint();
// Get topological dimension
boost::scoped_ptr<CellType> cell_type(CellType::create(cell_type_str));
const std::size_t tdim = cell_type->dim();
// Create mesh for editing
MeshEditor editor;
editor.open(mesh, cell_type_str, tdim, gdim);
// Get vertices xml node
pugi::xml_node xml_vertices = mesh_node.child("vertices");
dolfin_assert(xml_vertices);
// Get number of vertices and init editor
const std::size_t num_vertices = xml_vertices.attribute("size").as_uint();
editor.init_vertices_global(num_vertices, num_vertices);
// Iterate over vertices and add to mesh
Point p;
for (pugi::xml_node_iterator it = xml_vertices.begin();
it != xml_vertices.end(); ++it)
{
const std::size_t index = it->attribute("index").as_uint();
p[0] = it->attribute("x").as_double();
p[1] = it->attribute("y").as_double();
p[2] = it->attribute("z").as_double();
editor.add_vertex(index, p);
}
// Get cells node
pugi::xml_node xml_cells = mesh_node.child("cells");
dolfin_assert(xml_cells);
// Get number of cells and init editor
const std::size_t num_cells = xml_cells.attribute("size").as_uint();
editor.init_cells_global(num_cells, num_cells);
// Create list of vertex index attribute names
const unsigned int num_vertices_per_cell = cell_type->num_vertices(tdim);
std::vector<std::string> v_str(num_vertices_per_cell);
for (std::size_t i = 0; i < num_vertices_per_cell; ++i)
v_str[i] = "v" + boost::lexical_cast<std::string, unsigned int>(i);
// Iterate over cells and add to mesh
std::vector<std::size_t> v(num_vertices_per_cell);
for (pugi::xml_node_iterator it = xml_cells.begin(); it != xml_cells.end();
++it)
{
const std::size_t index = it->attribute("index").as_uint();
for (unsigned int i = 0; i < num_vertices_per_cell; ++i)
v[i] = it->attribute(v_str[i].c_str()).as_uint();
editor.add_cell(index, v);
}
// Close mesh editor
editor.close();
}
//-----------------------------------------------------------------------------
void RectangleMesh::build(const Point& p0, const Point& p1,
std::size_t nx, std::size_t ny,
std::string diagonal)
{
// Receive mesh according to parallel policy
if (MPI::is_receiver(this->mpi_comm()))
{
MeshPartitioning::build_distributed_mesh(*this);
return;
}
// Check options
if (diagonal != "left" && diagonal != "right" && diagonal != "right/left"
&& diagonal != "left/right" && diagonal != "crossed")
{
dolfin_error("RectangleMesh.cpp",
"create rectangle",
"Unknown mesh diagonal definition: allowed options are \"left\", \"right\", \"left/right\", \"right/left\" and \"crossed\"");
}
// Extract minimum and maximum coordinates
const double x0 = std::min(p0.x(), p1.x());
const double x1 = std::max(p0.x(), p1.x());
const double y0 = std::min(p0.y(), p1.y());
const double y1 = std::max(p0.y(), p1.y());
const double a = x0;
const double b = x1;
const double c = y0;
const double d = y1;
if (std::abs(x0 - x1) < DOLFIN_EPS || std::abs(y0 - y1) < DOLFIN_EPS)
{
dolfin_error("Rectangle.cpp",
"create rectangle",
"Rectangle seems to have zero width, height or depth. Consider checking your dimensions");
}
if (nx < 1 || ny < 1)
{
dolfin_error("RectangleMesh.cpp",
"create rectangle",
"Rectangle has non-positive number of vertices in some dimension: number of vertices must be at least 1 in each dimension");
}
rename("mesh", "Mesh of the unit square (a,b) x (c,d)");
// Open mesh for editing
MeshEditor editor;
editor.open(*this, CellType::triangle, 2, 2);
// Create vertices and cells:
if (diagonal == "crossed")
{
editor.init_vertices_global((nx + 1)*(ny + 1) + nx*ny,
(nx + 1)*(ny + 1) + nx*ny);
editor.init_cells_global(4*nx*ny, 4*nx*ny);
}
else
{
editor.init_vertices_global((nx + 1)*(ny + 1), (nx + 1)*(ny + 1));
editor.init_cells_global(2*nx*ny, 2*nx*ny);
}
// Storage for vertices
std::vector<double> x(2);
// Create main vertices:
std::size_t vertex = 0;
for (std::size_t iy = 0; iy <= ny; iy++)
{
x[1] = c + ((static_cast<double>(iy))*(d - c)/static_cast<double>(ny));
for (std::size_t ix = 0; ix <= nx; ix++)
{
x[0] = a + ((static_cast<double>(ix))*(b - a)/static_cast<double>(nx));
editor.add_vertex(vertex, x);
vertex++;
}
}
// Create midpoint vertices if the mesh type is crossed
if (diagonal == "crossed")
{
for (std::size_t iy = 0; iy < ny; iy++)
{
x[1] = c +(static_cast<double>(iy) + 0.5)*(d - c)/static_cast<double>(ny);
for (std::size_t ix = 0; ix < nx; ix++)
{
x[0] = a + (static_cast<double>(ix) + 0.5)*(b - a)/static_cast<double>(nx);
editor.add_vertex(vertex, x);
vertex++;
}
}
}
// Create triangles
std::size_t cell = 0;
if (diagonal == "crossed")
{
boost::multi_array<std::size_t, 2> cells(boost::extents[4][3]);
for (std::size_t iy = 0; iy < ny; iy++)
{
for (std::size_t ix = 0; ix < nx; ix++)
{
const std::size_t v0 = iy*(nx + 1) + ix;
const std::size_t v1 = v0 + 1;
const std::size_t v2 = v0 + (nx + 1);
const std::size_t v3 = v1 + (nx + 1);
const std::size_t vmid = (nx + 1)*(ny + 1) + iy*nx + ix;
// Note that v0 < v1 < v2 < v3 < vmid.
cells[0][0] = v0; cells[0][1] = v1; cells[0][2] = vmid;
cells[1][0] = v0; cells[1][1] = v2; cells[1][2] = vmid;
cells[2][0] = v1; cells[2][1] = v3; cells[2][2] = vmid;
cells[3][0] = v2; cells[3][1] = v3; cells[3][2] = vmid;
// Add cells
for (auto _cell = cells.begin(); _cell != cells.end(); ++_cell)
editor.add_cell(cell++, *_cell);
}
}
}
else if (diagonal == "left" || diagonal == "right" || diagonal == "right/left" || diagonal == "left/right")
{
std::string local_diagonal = diagonal;
boost::multi_array<std::size_t, 2> cells(boost::extents[2][3]);
for (std::size_t iy = 0; iy < ny; iy++)
{
// Set up alternating diagonal
if (diagonal == "right/left")
{
if (iy % 2)
local_diagonal = "right";
else
local_diagonal = "left";
}
if (diagonal == "left/right")
{
if (iy % 2)
local_diagonal = "left";
else
local_diagonal = "right";
}
for (std::size_t ix = 0; ix < nx; ix++)
{
const std::size_t v0 = iy*(nx + 1) + ix;
const std::size_t v1 = v0 + 1;
const std::size_t v2 = v0 + (nx + 1);
const std::size_t v3 = v1 + (nx + 1);
std::vector<std::size_t> cell_data;
if(local_diagonal == "left")
{
cells[0][0] = v0; cells[0][1] = v1; cells[0][2] = v2;
cells[1][0] = v1; cells[1][1] = v2; cells[1][2] = v3;
if (diagonal == "right/left" || diagonal == "left/right")
local_diagonal = "right";
}
else
{
cells[0][0] = v0; cells[0][1] = v1; cells[0][2] = v3;
cells[1][0] = v0; cells[1][1] = v2; cells[1][2] = v3;
if (diagonal == "right/left" || diagonal == "left/right")
local_diagonal = "left";
}
editor.add_cell(cell++, cells[0]);
editor.add_cell(cell++, cells[1]);
}
}
}
// Close mesh editor
editor.close();
// Broadcast mesh according to parallel policy
if (MPI::is_broadcaster(this->mpi_comm()))
{
MeshPartitioning::build_distributed_mesh(*this);
return;
}
}