//-----------------------------------------------------------------------------
void SparsityPatternBuilder::build_multimesh_sparsity_pattern(
GenericSparsityPattern& sparsity_pattern,
const MultiMeshForm& form)
{
// Get global dimensions and local range
const std::size_t rank = form.rank();
std::vector<std::size_t> global_dimensions(rank);
std::vector<std::pair<std::size_t, std::size_t>> local_range(rank);
std::vector<ArrayView<const std::size_t>> local_to_global(rank);
std::vector<ArrayView<const int>> off_process_owner(rank);
for (std::size_t i = 0; i < rank; ++i)
{
global_dimensions[i] = form.function_space(i)->dofmap()->global_dimension();
local_range[i] = form.function_space(i)->dofmap()->ownership_range();
off_process_owner[i].set(form.function_space(i)->dofmap()->off_process_owner());
}
// Initialize sparsity pattern
const std::vector<std::size_t> block_sizes(rank, 1);
sparsity_pattern.init(form.function_space(0)->part(0)->mesh()->mpi_comm(),
global_dimensions,
local_range, local_to_global,
off_process_owner, block_sizes);
// Iterate over each part
for (std::size_t part = 0; part < form.num_parts(); part++)
{
// Get mesh on current part (assume it's the same for all arguments)
const Mesh& mesh = *form.function_space(0)->part(part)->mesh();
// Build list of dofmaps
std::vector<const GenericDofMap*> dofmaps;
for (std::size_t i = 0; i < form.rank(); i++)
dofmaps.push_back(&*form.function_space(i)->dofmap()->part(part));
log(PROGRESS, "Building intra-mesh sparsity pattern on part %d.", part);
// Build sparsity pattern for part by calling the regular dofmap
// builder. This builds the sparsity pattern for all interacting
// dofs on the current part.
build(sparsity_pattern, mesh, dofmaps,
true, false, false, true, false, false);
log(PROGRESS, "Building inter-mesh sparsity pattern on part %d.", part);
// Build sparsity pattern for interface. This builds the sparsity
// pattern for all dofs that may interact across the interface
// between cutting meshes.
_build_multimesh_sparsity_pattern_interface(sparsity_pattern, form, part);
}
log(PROGRESS, "Applying changes to sparsity pattern.");
// Finalize sparsity pattern
sparsity_pattern.apply();
}
//-----------------------------------------------------------------------------
void MultiMeshAssembler::_assemble_uncut_cells(GenericTensor& A,
const MultiMeshForm& a)
{
// Get form rank
const std::size_t form_rank = a.rank();
// Extract multimesh
std::shared_ptr<const MultiMesh> multimesh = a.multimesh();
// Collect pointers to dof maps
std::vector<const MultiMeshDofMap*> dofmaps;
for (std::size_t i = 0; i < form_rank; i++)
dofmaps.push_back(a.function_space(i)->dofmap().get());
// Vector to hold dof map for a cell
std::vector<ArrayView<const dolfin::la_index>> dofs(form_rank);
// Initialize variables that will be reused throughout assembly
ufc::cell ufc_cell;
std::vector<double> coordinate_dofs;
// Iterate over parts
for (std::size_t part = 0; part < a.num_parts(); part++)
{
log(PROGRESS, "Assembling multimesh form over uncut cells on part %d.", part);
// Get form for current part
const Form& a_part = *a.part(part);
// Create data structure for local assembly data
UFC ufc_part(a_part);
// Extract mesh
const Mesh& mesh_part = a_part.mesh();
// FIXME: Handle subdomains
// Get integral
ufc::cell_integral* integral = ufc_part.default_cell_integral.get();
// Skip if we don't have a cell integral
if (!integral) continue;
// Get uncut cells
const std::vector<unsigned int>& uncut_cells = multimesh->uncut_cells(part);
// Iterate over uncut cells
for (auto it = uncut_cells.begin(); it != uncut_cells.end(); ++it)
{
// Create cell
Cell cell(mesh_part, *it);
// Update to current cell
cell.get_cell_data(ufc_cell);
cell.get_coordinate_dofs(coordinate_dofs);
ufc_part.update(cell, coordinate_dofs, ufc_cell);
// Get local-to-global dof maps for cell
for (std::size_t i = 0; i < form_rank; ++i)
{
const auto dofmap = a.function_space(i)->dofmap()->part(part);
dofs[i] = dofmap->cell_dofs(cell.index());
}
// Tabulate cell tensor
integral->tabulate_tensor(ufc_part.A.data(),
ufc_part.w(),
coordinate_dofs.data(),
ufc_cell.orientation);
// Add entries to global tensor
A.add(ufc_part.A.data(), dofs);
}
}
}
//-----------------------------------------------------------------------------
void MultiMeshAssembler::_assemble_overlap(GenericTensor& A,
const MultiMeshForm& a)
{
// FIXME: This function and assemble_interface are very similar.
// FIXME: Refactor to improve code reuse.
// Extract multimesh
std::shared_ptr<const MultiMesh> multimesh = a.multimesh();
// Get form rank
const std::size_t form_rank = a.rank();
// Collect pointers to dof maps
std::vector<const MultiMeshDofMap*> dofmaps;
for (std::size_t i = 0; i < form_rank; i++)
dofmaps.push_back(a.function_space(i)->dofmap().get());
// Vector to hold dof map for a cell
std::vector<const std::vector<dolfin::la_index>* > dofs(form_rank);
// Initialize variables that will be reused throughout assembly
ufc::cell ufc_cell[2];
std::vector<double> coordinate_dofs[2];
std::vector<double> macro_coordinate_dofs;
// Vector to hold dofs for cells, and a vector holding pointers to same
std::vector<ArrayView<const dolfin::la_index>> macro_dof_ptrs(form_rank);
std::vector<std::vector<dolfin::la_index>> macro_dofs(form_rank);
// Iterate over parts
for (std::size_t part = 0; part < a.num_parts(); part++)
{
log(PROGRESS, "Assembling multimesh form over overlap on part %d.", part);
// Get form for current part
const Form& a_part = *a.part(part);
// Create data structure for local assembly data
UFC ufc_part(a_part);
// FIXME: Handle subdomains
// Get integral
ufc::overlap_integral* integral = ufc_part.default_overlap_integral.get();
// Skip if we don't have an overlap integral
if (!integral) continue;
// Get quadrature rules
const auto& quadrature_rules = multimesh->quadrature_rule_overlap(part);
// Get collision map
const auto& cmap = multimesh->collision_map_cut_cells(part);
// Iterate over all cut cells in collision map
for (auto it = cmap.begin(); it != cmap.end(); ++it)
{
// Get cut cell
const unsigned int cut_cell_index = it->first;
const Cell cut_cell(*multimesh->part(part), cut_cell_index);
// Iterate over cutting cells
const auto& cutting_cells = it->second;
for (auto jt = cutting_cells.begin(); jt != cutting_cells.end(); jt++)
{
// Get cutting part and cutting cell
const std::size_t cutting_part = jt->first;
const std::size_t cutting_cell_index = jt->second;
const Cell cutting_cell(*multimesh->part(cutting_part), cutting_cell_index);
// Get quadrature rule for interface part defined by
// intersection of the cut and cutting cells
const std::size_t k = jt - cutting_cells.begin();
dolfin_assert(k < quadrature_rules.at(cut_cell_index).size());
const auto& qr = quadrature_rules.at(cut_cell_index)[k];
// FIXME: There might be quite a few cases when we skip cutting
// FIXME: cells because there are no quadrature points. Perhaps
// FIXME: we can rewrite this inner loop to avoid unnecessary
// FIXME: iterations.
// Skip if there are no quadrature points
const std::size_t num_quadrature_points = qr.second.size();
if (num_quadrature_points == 0)
continue;
// Create aliases for cells to simplify notation
const Cell& cell_0 = cut_cell;
const Cell& cell_1 = cutting_cell;
// Update to current pair of cells
cell_0.get_cell_data(ufc_cell[0], 0);
cell_1.get_cell_data(ufc_cell[1], 0);
cell_0.get_coordinate_dofs(coordinate_dofs[0]);
cell_1.get_coordinate_dofs(coordinate_dofs[1]);
ufc_part.update(cell_0, coordinate_dofs[0], ufc_cell[0],
cell_1, coordinate_dofs[1], ufc_cell[1]);
// Collect vertex coordinates
macro_coordinate_dofs.resize(coordinate_dofs[0].size() +
coordinate_dofs[0].size());
std::copy(coordinate_dofs[0].begin(),
coordinate_dofs[0].end(),
macro_coordinate_dofs.begin());
std::copy(coordinate_dofs[1].begin(),
coordinate_dofs[1].end(),
macro_coordinate_dofs.begin() + coordinate_dofs[0].size());
// Tabulate dofs for each dimension on macro element
for (std::size_t i = 0; i < form_rank; i++)
{
// Get dofs for cut mesh
const auto dofmap_0 = a.function_space(i)->dofmap()->part(part);
const auto dofs_0 = dofmap_0->cell_dofs(cell_0.index());
// Get dofs for cutting mesh
const auto dofmap_1 = a.function_space(i)->dofmap()->part(cutting_part);
const auto dofs_1 = dofmap_1->cell_dofs(cell_1.index());
// Create space in macro dof vector
macro_dofs[i].resize(dofs_0.size() + dofs_1.size());
// Copy cell dofs into macro dof vector
std::copy(dofs_0.begin(), dofs_0.end(),
macro_dofs[i].begin());
std::copy(dofs_1.begin(), dofs_1.end(),
macro_dofs[i].begin() + dofs_0.size());
// Update array view
macro_dof_ptrs[i]
= ArrayView<const dolfin::la_index>(macro_dofs[i].size(),
macro_dofs[i].data());
}
// FIXME: Cell orientation not supported
const int cell_orientation = ufc_cell[0].orientation;
// Tabulate overlap tensor on macro element
integral->tabulate_tensor(ufc_part.macro_A.data(),
ufc_part.macro_w(),
macro_coordinate_dofs.data(),
num_quadrature_points,
qr.first.data(),
qr.second.data(),
cell_orientation);
// Add entries to global tensor
A.add(ufc_part.macro_A.data(), macro_dof_ptrs);
}
}
}
}
//-----------------------------------------------------------------------------
void MultiMeshAssembler::_assemble_cut_cells(GenericTensor& A,
const MultiMeshForm& a)
{
// Get form rank
const std::size_t form_rank = a.rank();
// Extract multimesh
std::shared_ptr<const MultiMesh> multimesh = a.multimesh();
// Collect pointers to dof maps
std::vector<const MultiMeshDofMap*> dofmaps;
for (std::size_t i = 0; i < form_rank; i++)
dofmaps.push_back(a.function_space(i)->dofmap().get());
// Vector to hold dof map for a cell
std::vector<ArrayView<const dolfin::la_index>> dofs(form_rank);
// Initialize variables that will be reused throughout assembly
ufc::cell ufc_cell;
std::vector<double> coordinate_dofs;
// Iterate over parts
for (std::size_t part = 0; part < a.num_parts(); part++)
{
log(PROGRESS, "Assembling multimesh form over cut cells on part %d.", part);
// Get form for current part
const Form& a_part = *a.part(part);
// Create data structure for local assembly data
UFC ufc_part(a_part);
// Extract mesh
const Mesh& mesh_part = a_part.mesh();
// FIXME: Handle subdomains
// Get integral
ufc::cutcell_integral* integral = ufc_part.default_cutcell_integral.get();
// Skip if we don't have a cutcell integral
if (!integral) continue;
// Get cut cells and quadrature rules
const std::vector<unsigned int>& cut_cells = multimesh->cut_cells(part);
const auto& quadrature_rules = multimesh->quadrature_rule_cut_cells(part);
// Iterate over cut cells
for (auto it = cut_cells.begin(); it != cut_cells.end(); ++it)
{
// Create cell
Cell cell(mesh_part, *it);
// Update to current cell
cell.get_cell_data(ufc_cell);
cell.get_coordinate_dofs(coordinate_dofs);
ufc_part.update(cell, coordinate_dofs, ufc_cell);
// Get local-to-global dof maps for cell
for (std::size_t i = 0; i < form_rank; ++i)
{
const auto dofmap = a.function_space(i)->dofmap()->part(part);
dofs[i] = dofmap->cell_dofs(cell.index());
}
// Get quadrature rule for cut cell
const auto& qr = quadrature_rules.at(*it);
// Skip if there are no quadrature points
std::size_t num_quadrature_points = qr.second.size();
if (num_quadrature_points == 0)
continue;
// FIXME: Handle this inside the quadrature point generation,
// FIXME: perhaps by storing three different sets of points,
// FIXME: including cut cell, overlap and the whole cell.
// Include only quadrature points with positive weight if
// integration should be extended on cut cells
std::pair<std::vector<double>, std::vector<double>> pr;
if (extend_cut_cell_integration)
{
const std::size_t gdim = mesh_part.geometry().dim();
for (std::size_t i = 0; i < num_quadrature_points; i++)
{
if (qr.second[i] > 0.0)
{
pr.second.push_back(qr.second[i]);
for (std::size_t j = i*gdim; j < (i + 1)*gdim; j++)
pr.first.push_back(qr.first[j]);
}
}
num_quadrature_points = pr.second.size();
}
else
{
pr = qr;
}
// Tabulate cell tensor
integral->tabulate_tensor(ufc_part.A.data(),
ufc_part.w(),
coordinate_dofs.data(),
num_quadrature_points,
pr.first.data(),
pr.second.data(),
ufc_cell.orientation);
// Add entries to global tensor
A.add(ufc_part.A.data(), dofs);
}
}
}
//-----------------------------------------------------------------------------
void MultiMeshAssembler::_assemble_interface(GenericTensor& A,
const MultiMeshForm& a)
{
// Extract multimesh
std::shared_ptr<const MultiMesh> multimesh = a.multimesh();
// Get form rank
const std::size_t form_rank = a.rank();
// Get multimesh coefficients
// These are updated in within this assembly loop
std::map<std::size_t, std::shared_ptr<const MultiMeshFunction> >
multimesh_coefficients = a.multimesh_coefficients();
// Identify the coefficents that are not MultiMeshFunction
// These will be updated by UFC
// It is assumed that the coefficents are the same for all parts
std::vector<bool> ufc_enabled_coefficients;
for (std::size_t i = 0; i < a.part(0)->coefficients().size(); i++)
{
bool ufc_update = multimesh_coefficients.find(i) == multimesh_coefficients.end();
ufc_enabled_coefficients.push_back(ufc_update);
}
// Collect pointers to dof maps
std::vector<const MultiMeshDofMap*> dofmaps;
for (std::size_t i = 0; i < form_rank; i++)
dofmaps.push_back(a.function_space(i)->dofmap().get());
// Vector to hold dof map for a cell
std::vector<const std::vector<dolfin::la_index>* > dofs(form_rank);
// Initialize variables that will be reused throughout assembly
ufc::cell ufc_cell[2];
std::vector<double> coordinate_dofs[2];
std::vector<double> macro_coordinate_dofs;
// Vector to hold dofs for cells, and a vector holding pointers to same
std::vector<ArrayView<const dolfin::la_index>> macro_dof_ptrs(form_rank);
std::vector<std::vector<dolfin::la_index>> macro_dofs(form_rank);
// Iterate over parts
for (std::size_t part = 0; part < a.num_parts(); part++)
{
log(PROGRESS, "Assembling multimesh form over interface on part %d.",
part);
// Get form for current part
const Form& a_part = *a.part(part);
// Create data structure for local assembly data
UFC ufc_part(a_part);
// FIXME: Handle subdomains
// Get integral
ufc::interface_integral* integral = ufc_part.default_interface_integral.get();
// Skip if we don't have an interface integral
if (!integral) continue;
// Get quadrature rules
const auto& quadrature_rules = multimesh->quadrature_rules_interface(part);
// Get collision map
const auto& cmap = multimesh->collision_map_cut_cells(part);
// Get facet normals
const auto& facet_normals = multimesh->facet_normals(part);
// Iterate over all cut cells in collision map
for (auto it = cmap.begin(); it != cmap.end(); ++it)
{
// Get cut cell
const unsigned int cut_cell_index = it->first;
const Cell cut_cell(*multimesh->part(part), cut_cell_index);
// Iterate over cutting cells
const auto& cutting_cells = it->second;
for (auto jt = cutting_cells.begin(); jt != cutting_cells.end(); jt++)
{
// Get cutting part and cutting cell
const std::size_t cutting_part = jt->first;
const std::size_t cutting_cell_index = jt->second;
const Cell cutting_cell(*multimesh->part(cutting_part),
cutting_cell_index);
// Get quadrature rule for interface part defined by
// intersection of the cut and cutting cells
const std::size_t k = jt - cutting_cells.begin();
dolfin_assert(k < quadrature_rules.at(cut_cell_index).size());
const auto& qr = quadrature_rules.at(cut_cell_index)[k];
// FIXME: There might be quite a few cases when we skip cutting
// FIXME: cells because there are no quadrature points. Perhaps
// FIXME: we can rewrite this inner loop to avoid unnecessary
// FIXME: iterations.
// Skip if there are no quadrature points
const std::size_t num_quadrature_points = qr.second.size();
if (num_quadrature_points == 0)
continue;
// Create aliases for cells to simplify notation
const std::size_t& part_1 = cutting_part;
const std::size_t& part_0 = part;
const Cell& cell_1 = cutting_cell;
const Cell& cell_0 = cut_cell;
// Update to current pair of cells
// Let UFC update the coefficients that are not MultiMeshFunction
cell_0.get_cell_data(ufc_cell[0], 0);
cell_1.get_cell_data(ufc_cell[1], 0);
cell_0.get_coordinate_dofs(coordinate_dofs[0]);
cell_1.get_coordinate_dofs(coordinate_dofs[1]);
ufc_part.update(cell_0, coordinate_dofs[0], ufc_cell[0],
cell_1, coordinate_dofs[1], ufc_cell[1],
ufc_enabled_coefficients);
// Manually update multimesh coefficients
for (auto it : multimesh_coefficients)
{
std::size_t coefficient_number = it.first;
std::shared_ptr<const MultiMeshFunction> coefficient = it.second;
double** macro_w = ufc_part.macro_w();
const FiniteElement& element = *coefficient->function_space()->part(part_0)->element();
std::size_t offset = element.space_dimension();
double * w_0 = macro_w[coefficient_number];
double * w_1 = macro_w[coefficient_number] + offset;
coefficient->restrict(w_0, element,
part_0, cell_0, coordinate_dofs[0].data(), ufc_cell[0]);
coefficient->restrict(w_1, element,
part_1, cell_1, coordinate_dofs[1].data(), ufc_cell[1]);
}
// Collect vertex coordinates
macro_coordinate_dofs.resize(coordinate_dofs[0].size() +
coordinate_dofs[1].size());
std::copy(coordinate_dofs[0].begin(), coordinate_dofs[0].end(),
macro_coordinate_dofs.begin());
std::copy(coordinate_dofs[1].begin(), coordinate_dofs[1].end(),
macro_coordinate_dofs.begin() + coordinate_dofs[0].size());
// Tabulate dofs for each dimension on macro element
for (std::size_t i = 0; i < form_rank; i++)
{
// Get dofs for cut mesh
const auto dofmap_0 = a.function_space(i)->dofmap()->part(part_0);
const auto dofs_0 = dofmap_0->cell_dofs(cell_0.index());
// Get dofs for cutting mesh
const auto dofmap_1 = a.function_space(i)->dofmap()->part(part_1);
const auto dofs_1 = dofmap_1->cell_dofs(cell_1.index());
// Create space in macro dof vector
macro_dofs[i].resize(dofs_0.size() + dofs_1.size());
// Copy cell dofs into macro dof vector
std::copy(dofs_0.data(), dofs_0.data() + dofs_0.size(),
macro_dofs[i].begin());
std::copy(dofs_1.data(), dofs_1.data() + dofs_1.size(),
macro_dofs[i].begin() + dofs_0.size());
// Update array view
macro_dof_ptrs[i]
= ArrayView<const dolfin::la_index>(macro_dofs[i].size(),
macro_dofs[i].data());
}
// Get facet normals
const auto& n = facet_normals.at(cut_cell_index)[k];
// FIXME: We would like to use this assertion (but it fails
// for 2 meshes)
dolfin_assert(n.size() == a_part.mesh()->geometry().dim()*num_quadrature_points);
// FIXME: For now, use this assertion (which fails for 3 meshes)
//dolfin_assert(n.size() > 0);
// FIXME: Cell orientation not supported
const int cell_orientation = ufc_cell[0].orientation;
// Tabulate interface tensor on macro element
integral->tabulate_tensor(ufc_part.macro_A.data(),
ufc_part.macro_w(),
macro_coordinate_dofs.data(),
num_quadrature_points,
qr.first.data(),
qr.second.data(),
n.data(),
cell_orientation);
// Add entries to global tensor
A.add(ufc_part.macro_A.data(), macro_dof_ptrs);
}
}
}
}