//------------------------------------------------------------------------------
void LocalAssembler::assemble_interior_facet(Eigen::MatrixXd& A,
UFC& ufc,
const std::vector<double>& vertex_coordinates,
const ufc::cell& ufc_cell,
const Cell& cell,
const Facet& facet,
const std::size_t local_facet,
const MeshFunction<std::size_t>* domains)
{
// Skip if there are no interior facet integrals
if (!ufc.form.has_interior_facet_integrals())
return;
// Extract default interior facet integral
ufc::interior_facet_integral* integral
= ufc.default_interior_facet_integral.get();
// Get integral for sub domain (if any)
if (domains && !domains->empty())
integral = ufc.get_interior_facet_integral((*domains)[facet]);
// Skip integral if zero
if (!integral)
return;
// Update to current pair of cells and facets
ufc.update(cell, vertex_coordinates, ufc_cell,
cell, vertex_coordinates, ufc_cell,
integral->enabled_coefficients());
// Tabulate interior facet tensor on macro element
integral->tabulate_tensor(ufc.macro_A.data(), ufc.macro_w(),
vertex_coordinates.data(),
vertex_coordinates.data(),
local_facet, local_facet,
ufc_cell.orientation,
ufc_cell.orientation);
// Stuff upper left quadrant (corresponding to this cell) into A
const std::size_t M = A.rows();
const std::size_t N = A.cols();
if (N == 1)
{
for (std::size_t i = 0; i < M; i++)
A(i, 0) = ufc.macro_A[i];
}
else
{
for (std::size_t i = 0; i < M; i++)
for (std::size_t j = 0; j < N; j++)
A(i, j) += ufc.macro_A[2*N*i + j];
}
}
//-----------------------------------------------------------------------------
void PointIntegralSolver::_compute_jacobian(std::vector<double>& jac,
const std::vector<double>& u,
unsigned int local_vert,
UFC& loc_ufc, const Cell& cell,
const ufc::cell& ufc_cell,
int coefficient_index,
const std::vector<double>& coordinate_dofs)
{
const ufc::vertex_integral& J_integral = *loc_ufc.default_vertex_integral;
// TODO: Pass suitable bool vector here to avoid tabulating all
// coefficient dofs:
loc_ufc.update(cell, coordinate_dofs, ufc_cell);
//J_integral.enabled_coefficients());
// If there is a solution coefficient in the Jacobian form
if (coefficient_index > 0)
{
// Put solution back into restricted coefficients before tabulate
// new jacobian
for (unsigned int row = 0; row < _system_size; row++)
loc_ufc.w()[coefficient_index][_local_to_local_dofs[row]] = u[row];
}
// Tabulate Jacobian
J_integral.tabulate_tensor(loc_ufc.A.data(), loc_ufc.w(),
coordinate_dofs.data(),
local_vert,
ufc_cell.orientation);
// Extract vertex dofs from tabulated tensor
for (unsigned int row = 0; row < _system_size; row++)
{
for (unsigned int col = 0; col < _system_size; col++)
{
jac[row*_system_size + col]
= loc_ufc.A[_local_to_local_dofs[row]*_dof_offset*_system_size
+ _local_to_local_dofs[col]];
}
}
// LU factorize Jacobian
_lu_factorize(jac);
_num_jacobian_computations += 1;
}
//------------------------------------------------------------------------------
void LocalAssembler::assemble_exterior_facet(Eigen::MatrixXd& A,
UFC& ufc,
const std::vector<double>& vertex_coordinates,
const ufc::cell& ufc_cell,
const Cell& cell,
const Facet& facet,
const std::size_t local_facet,
const MeshFunction<std::size_t>* domains)
{
// Skip if there are no exterior facet integrals
if (!ufc.form.has_exterior_facet_integrals())
return;
// Extract default exterior facet integral
ufc::exterior_facet_integral* integral
= ufc.default_exterior_facet_integral.get();
// Get integral for sub domain (if any)
if (domains && !domains->empty())
integral = ufc.get_exterior_facet_integral((*domains)[facet]);
// Skip integral if zero
if (!integral)
return;
// Update to current cell
ufc.update(cell, vertex_coordinates, ufc_cell,
integral->enabled_coefficients());
// Tabulate exterior facet tensor
integral->tabulate_tensor(ufc.A.data(),
ufc.w(),
vertex_coordinates.data(),
local_facet,
ufc_cell.orientation);
// Stuff a_ufc.A into A
const std::size_t M = A.rows();
const std::size_t N = A.cols();
for (std::size_t i = 0; i < M; i++)
for (std::size_t j = 0; j < N; j++)
A(i, j) += ufc.A[N*i + j];
}
//-----------------------------------------------------------------------------
void Assembler::assemble_vertices(
GenericTensor& A,
const Form& a,
UFC& ufc,
std::shared_ptr<const MeshFunction<std::size_t>> domains)
{
// Skip assembly if there are no point integrals
if (!ufc.form.has_vertex_integrals())
return;
// Set timer
Timer timer("Assemble vertices");
// Extract mesh
const Mesh& mesh = a.mesh();
// Compute cell and vertex - cell connectivity if not already
// computed
const std::size_t D = mesh.topology().dim();
mesh.init(0);
mesh.init(0, D);
dolfin_assert(mesh.ordered());
// Logics for shared vertices
const bool has_shared_vertices = mesh.topology().have_shared_entities(0);
const std::map<unsigned int, std::set<unsigned int>>&
shared_vertices = mesh.topology().shared_entities(0);
// Form rank
const std::size_t form_rank = ufc.form.rank();
// Collect pointers to dof maps
std::vector<const GenericDofMap*> dofmaps(form_rank);
// Create a vector for storying local to local map for vertex entity
// dofs
std::vector<std::vector<std::size_t>> local_to_local_dofs(form_rank);
// Create a values vector to be used to fan out local tabulated
// values to the global tensor
std::vector<double> local_values(1);
// Vector to hold local dof map for a vertex
std::vector<std::vector<dolfin::la_index>> global_dofs(form_rank);
std::vector<ArrayView<const dolfin::la_index>> global_dofs_p(form_rank);
std::vector<dolfin::la_index> local_dof_size(form_rank);
for (std::size_t i = 0; i < form_rank; ++i)
{
dofmaps[i] = a.function_space(i)->dofmap().get();
// Check that the test and trial space as dofs on the vertices
if (dofmaps[i]->num_entity_dofs(0) == 0)
{
dolfin_error("Assembler.cpp",
"assemble form over vertices",
"Expecting test and trial spaces to have dofs on "\
"vertices for point integrals");
}
// Check that the test and trial spaces do not have dofs other
// than on vertices
for (std::size_t j = 1; j <= D; j++)
{
if (dofmaps[i]->num_entity_dofs(j)!=0)
{
dolfin_error("Assembler.cpp",
"assemble form over vertices",
"Expecting test and trial spaces to only have dofs on " \
"vertices for point integrals");
}
}
// Resize local values so it can hold dofs on one vertex
local_values.resize(local_values.size()*dofmaps[i]->num_entity_dofs(0));
// Resize local to local map according to the number of vertex
// entities dofs
local_to_local_dofs[i].resize(dofmaps[i]->num_entity_dofs(0));
// Resize local dof map vector
global_dofs[i].resize(dofmaps[i]->num_entity_dofs(0));
// Get size of local dofs
local_dof_size[i] = dofmaps[i]->ownership_range().second
- dofmaps[i]->ownership_range().first;
// Get pointer to global dofs
global_dofs_p[i].set(global_dofs[i]);
}
// Vector to hold dof map for a cell
std::vector<ArrayView<const dolfin::la_index>> dofs(form_rank);
// Exterior point integral
const ufc::vertex_integral* integral
= ufc.default_vertex_integral.get();
// Check whether integral is domain-dependent
bool use_domains = domains && !domains->empty();
// MPI rank
const unsigned int my_mpi_rank = MPI::rank(mesh.mpi_comm());
// Assemble over vertices
ufc::cell ufc_cell;
std::vector<double> coordinate_dofs;
Progress p(AssemblerBase::progress_message(A.rank(), "vertices"),
mesh.num_vertices());
for (VertexIterator vert(mesh); !vert.end(); ++vert)
{
// Get integral for sub domain (if any)
if (use_domains)
integral = ufc.get_vertex_integral((*domains)[*vert]);
// Skip integral if zero
if (!integral)
continue;
// Check if assembling a scalar and a vertex is shared
if (form_rank == 0 && has_shared_vertices)
{
// Find shared processes for this global vertex
std::map<unsigned int, std::set<unsigned int>>::const_iterator e;
e = shared_vertices.find(vert->index());
// If vertex is shared and this rank is not the lowest do not
// include the contribution from this vertex to scalar sum
if (e != shared_vertices.end())
{
bool skip_vertex = false;
std::set<unsigned int>::const_iterator it;
for (it = e->second.begin(); it != e->second.end(); it++)
{
// Check if a shared vertex has a lower process rank
if (*it < my_mpi_rank)
{
skip_vertex = true;
break;
}
}
if (skip_vertex)
continue;
}
}
// Get mesh cell to which mesh vertex belongs (pick first)
Cell mesh_cell(mesh, vert->entities(D)[0]);
// Check that cell is not a ghost
dolfin_assert(!mesh_cell.is_ghost());
// Get local index of vertex with respect to the cell
const std::size_t local_vertex = mesh_cell.index(*vert);
// Update UFC cell
mesh_cell.get_cell_data(ufc_cell);
mesh_cell.get_coordinate_dofs(coordinate_dofs);
// Update UFC object
ufc.update(mesh_cell, coordinate_dofs, ufc_cell,
integral->enabled_coefficients());
// Tabulate vertex tensor
integral->tabulate_tensor(ufc.A.data(),
ufc.w(),
coordinate_dofs.data(),
local_vertex,
ufc_cell.orientation);
// For rank 1 and 2 tensors we need to check if tabulated dofs for
// the test space is within the local range
bool owns_all_dofs = true;
for (std::size_t i = 0; i < form_rank; ++i)
{
// Get local-to-global dof maps for cell
dofs[i] = dofmaps[i]->cell_dofs(mesh_cell.index());
// Get local dofs of the local vertex
dofmaps[i]->tabulate_entity_dofs(local_to_local_dofs[i], 0, local_vertex);
// Copy cell dofs to local dofs and check owner ship range
for (std::size_t j = 0; j < local_to_local_dofs[i].size(); ++j)
{
global_dofs[i][j] = dofs[i][local_to_local_dofs[i][j]];
// It is the dofs for the test space that determines if a dof
// is owned by a process, therefore i==0
if (i == 0 && global_dofs[i][j] >= local_dof_size[i])
{
owns_all_dofs = false;
break;
}
}
}
// If not owning all dofs
if (!owns_all_dofs)
continue;
// Scalar
if (form_rank == 0)
{
// Add entries to global tensor
A.add_local(ufc.A.data(), dofs);
}
else if (form_rank == 1)
{
// Copy tabulated tensor to local value vector
for (std::size_t i = 0; i < local_to_local_dofs[0].size(); ++i)
local_values[i] = ufc.A[local_to_local_dofs[0][i]];
// Add local entries to global tensor
A.add_local(local_values.data(), global_dofs_p);
}
else
{
// Copy tabulated tensor to local value vector
const std::size_t num_cols = dofs[1].size();
for (std::size_t i = 0; i < local_to_local_dofs[0].size(); ++i)
{
for (std::size_t j = 0; j < local_to_local_dofs[1].size(); ++j)
{
local_values[i*local_to_local_dofs[1].size() + j]
= ufc.A[local_to_local_dofs[0][i]*num_cols
+ local_to_local_dofs[1][j]];
}
}
// Add local entries to global tensor
A.add_local(local_values.data(), global_dofs_p);
}
p++;
}
}
//-----------------------------------------------------------------------------
void Assembler::assemble_interior_facets(
GenericTensor& A,
const Form& a,
UFC& ufc,
std::shared_ptr<const MeshFunction<std::size_t>> domains,
std::shared_ptr<const MeshFunction<std::size_t>> cell_domains,
std::vector<double>* values)
{
// Skip assembly if there are no interior facet integrals
if (!ufc.form.has_interior_facet_integrals())
return;
// Set timer
Timer timer("Assemble interior facets");
// Extract mesh and coefficients
const Mesh& mesh = a.mesh();
// MPI rank
const int my_mpi_rank = MPI::rank(mesh.mpi_comm());
// Form rank
const std::size_t form_rank = ufc.form.rank();
// Collect pointers to dof maps
std::vector<const GenericDofMap*> dofmaps;
for (std::size_t i = 0; i < form_rank; ++i)
dofmaps.push_back(a.function_space(i)->dofmap().get());
// Vector to hold dofs for cells, and a vector holding pointers to same
std::vector<std::vector<dolfin::la_index>> macro_dofs(form_rank);
std::vector<ArrayView<const dolfin::la_index>> macro_dof_ptrs(form_rank);
// Interior facet integral
const ufc::interior_facet_integral* integral
= ufc.default_interior_facet_integral.get();
// Check whether integral is domain-dependent
bool use_domains = domains && !domains->empty();
bool use_cell_domains = cell_domains && !cell_domains->empty();
// Compute facets and facet - cell connectivity if not already computed
const std::size_t D = mesh.topology().dim();
mesh.init(D - 1);
mesh.init(D - 1, D);
dolfin_assert(mesh.ordered());
// Assemble over interior facets (the facets of the mesh)
ufc::cell ufc_cell[2];
std::vector<double> coordinate_dofs[2];
Progress p(AssemblerBase::progress_message(A.rank(), "interior facets"),
mesh.num_facets());
for (FacetIterator facet(mesh); !facet.end(); ++facet)
{
if (facet->num_entities(D) == 1)
continue;
// Check that facet is not a ghost
dolfin_assert(!facet->is_ghost());
// Get integral for sub domain (if any)
if (use_domains)
integral = ufc.get_interior_facet_integral((*domains)[*facet]);
// Skip integral if zero
if (!integral)
continue;
// Get cells incident with facet (which is 0 and 1 here is arbitrary)
dolfin_assert(facet->num_entities(D) == 2);
std::size_t cell_index_plus = facet->entities(D)[0];
std::size_t cell_index_minus = facet->entities(D)[1];
if (use_cell_domains && (*cell_domains)[cell_index_plus]
< (*cell_domains)[cell_index_minus])
{
std::swap(cell_index_plus, cell_index_minus);
}
// The convention '+' = 0, '-' = 1 is from ffc
const Cell cell0(mesh, cell_index_plus);
const Cell cell1(mesh, cell_index_minus);
// Get local index of facet with respect to each cell
std::size_t local_facet0 = cell0.index(*facet);
std::size_t local_facet1 = cell1.index(*facet);
// Update to current pair of cells
cell0.get_cell_data(ufc_cell[0], local_facet0);
cell0.get_coordinate_dofs(coordinate_dofs[0]);
cell1.get_cell_data(ufc_cell[1], local_facet1);
cell1.get_coordinate_dofs(coordinate_dofs[1]);
ufc.update(cell0, coordinate_dofs[0], ufc_cell[0],
cell1, coordinate_dofs[1], ufc_cell[1],
integral->enabled_coefficients());
// Tabulate dofs for each dimension on macro element
for (std::size_t i = 0; i < form_rank; i++)
{
// Get dofs for each cell
const ArrayView<const dolfin::la_index> cell_dofs0
= dofmaps[i]->cell_dofs(cell0.index());
const ArrayView<const dolfin::la_index> cell_dofs1
= dofmaps[i]->cell_dofs(cell1.index());
// Create space in macro dof vector
macro_dofs[i].resize(cell_dofs0.size() + cell_dofs1.size());
// Copy cell dofs into macro dof vector
std::copy(cell_dofs0.data(), cell_dofs0.data() + cell_dofs0.size(),
macro_dofs[i].begin());
std::copy(cell_dofs1.data(), cell_dofs1.data() + cell_dofs1.size(),
macro_dofs[i].begin() + cell_dofs0.size());
macro_dof_ptrs[i].set(macro_dofs[i]);
}
// Tabulate interior facet tensor on macro element
integral->tabulate_tensor(ufc.macro_A.data(),
ufc.macro_w(),
coordinate_dofs[0].data(),
coordinate_dofs[1].data(),
local_facet0,
local_facet1,
ufc_cell[0].orientation,
ufc_cell[1].orientation);
if (cell0.is_ghost() != cell1.is_ghost())
{
int ghost_rank = -1;
if (cell0.is_ghost())
ghost_rank = cell0.owner();
else
ghost_rank = cell1.owner();
dolfin_assert(my_mpi_rank != ghost_rank);
dolfin_assert(ghost_rank != -1);
if (ghost_rank < my_mpi_rank)
continue;
}
// Add entries to global tensor
A.add_local(ufc.macro_A.data(), macro_dof_ptrs);
p++;
}
}
//-----------------------------------------------------------------------------
void Assembler::assemble_exterior_facets(
GenericTensor& A,
const Form& a,
UFC& ufc,
std::shared_ptr<const MeshFunction<std::size_t>> domains,
std::vector<double>* values)
{
// Skip assembly if there are no exterior facet integrals
if (!ufc.form.has_exterior_facet_integrals())
return;
// Set timer
Timer timer("Assemble exterior facets");
// Extract mesh
const Mesh& mesh = a.mesh();
// Form rank
const std::size_t form_rank = ufc.form.rank();
// Collect pointers to dof maps
std::vector<const GenericDofMap*> 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);
// Exterior facet integral
const ufc::exterior_facet_integral* integral
= ufc.default_exterior_facet_integral.get();
// Check whether integral is domain-dependent
bool use_domains = domains && !domains->empty();
// Compute facets and facet - cell connectivity if not already computed
const std::size_t D = mesh.topology().dim();
mesh.init(D - 1);
mesh.init(D - 1, D);
dolfin_assert(mesh.ordered());
// Assemble over exterior facets (the cells of the boundary)
ufc::cell ufc_cell;
std::vector<double> coordinate_dofs;
Progress p(AssemblerBase::progress_message(A.rank(), "exterior facets"),
mesh.num_facets());
for (FacetIterator facet(mesh); !facet.end(); ++facet)
{
// Only consider exterior facets
if (!facet->exterior())
{
p++;
continue;
}
// Get integral for sub domain (if any)
if (use_domains)
integral = ufc.get_exterior_facet_integral((*domains)[*facet]);
// Skip integral if zero
if (!integral)
continue;
// Get mesh cell to which mesh facet belongs (pick first, there is
// only one)
dolfin_assert(facet->num_entities(D) == 1);
Cell mesh_cell(mesh, facet->entities(D)[0]);
// Check that cell is not a ghost
dolfin_assert(!mesh_cell.is_ghost());
// Get local index of facet with respect to the cell
const std::size_t local_facet = mesh_cell.index(*facet);
// Update UFC cell
mesh_cell.get_cell_data(ufc_cell, local_facet);
mesh_cell.get_coordinate_dofs(coordinate_dofs);
// Update UFC object
ufc.update(mesh_cell, coordinate_dofs, ufc_cell,
integral->enabled_coefficients());
// Get local-to-global dof maps for cell
for (std::size_t i = 0; i < form_rank; ++i)
dofs[i] = dofmaps[i]->cell_dofs(mesh_cell.index());
// Tabulate exterior facet tensor
integral->tabulate_tensor(ufc.A.data(),
ufc.w(),
coordinate_dofs.data(),
local_facet,
ufc_cell.orientation);
// Add entries to global tensor
A.add_local(ufc.A.data(), dofs);
p++;
}
}
//-----------------------------------------------------------------------------
void Assembler::assemble_cells(
GenericTensor& A,
const Form& a,
UFC& ufc,
std::shared_ptr<const MeshFunction<std::size_t>> domains,
std::vector<double>* values)
{
// Skip assembly if there are no cell integrals
if (!ufc.form.has_cell_integrals())
return;
// Set timer
Timer timer("Assemble cells");
// Extract mesh
const Mesh& mesh = a.mesh();
// Form rank
const std::size_t form_rank = ufc.form.rank();
// Check if form is a functional
const bool is_cell_functional = (values && form_rank == 0) ? true : false;
// Collect pointers to dof maps
std::vector<const GenericDofMap*> 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);
// Cell integral
ufc::cell_integral* integral = ufc.default_cell_integral.get();
// Check whether integral is domain-dependent
bool use_domains = domains && !domains->empty();
// Assemble over cells
ufc::cell ufc_cell;
std::vector<double> coordinate_dofs;
Progress p(AssemblerBase::progress_message(A.rank(), "cells"),
mesh.num_cells());
for (CellIterator cell(mesh); !cell.end(); ++cell)
{
// Get integral for sub domain (if any)
if (use_domains)
integral = ufc.get_cell_integral((*domains)[*cell]);
// Skip if no integral on current domain
if (!integral)
continue;
// Check that cell is not a ghost
dolfin_assert(!cell->is_ghost());
// Update to current cell
cell->get_cell_data(ufc_cell);
cell->get_coordinate_dofs(coordinate_dofs);
ufc.update(*cell, coordinate_dofs, ufc_cell,
integral->enabled_coefficients());
// Get local-to-global dof maps for cell
bool empty_dofmap = false;
for (std::size_t i = 0; i < form_rank; ++i)
{
dofs[i] = dofmaps[i]->cell_dofs(cell->index());
empty_dofmap = empty_dofmap || dofs[i].size() == 0;
}
// Skip if at least one dofmap is empty
if (empty_dofmap)
continue;
// Tabulate cell tensor
integral->tabulate_tensor(ufc.A.data(), ufc.w(),
coordinate_dofs.data(),
ufc_cell.orientation);
// Add entries to global tensor. Either store values cell-by-cell
// (currently only available for functionals)
if (is_cell_functional)
(*values)[cell->index()] = ufc.A[0];
else
A.add_local(ufc.A.data(), dofs);
p++;
}
}