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Various fixes to contact #44

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Feb 16, 2022
Merged

Various fixes to contact #44

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9feca98
Various fixes to contact
jorgensd Feb 15, 2022
0b3b2ed
Activate sonarcloud
jorgensd Feb 15, 2022
ed51530
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jorgensd Feb 15, 2022
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10 changes: 5 additions & 5 deletions .github/workflows/sonarcloud.yml
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
name: Run sonarcloud analysis
on:
push:
branches-ignore:
- '**'
# branches:
# - main
# - dokken/*
# branches-ignore:
# - '**'
branches:
- main
- dokken/*
jorgensd marked this conversation as resolved.
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# pull_request:
# branches:
# - main
Expand Down
144 changes: 75 additions & 69 deletions cpp/Contact.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@
#include <dolfinx_contact/geometric_quantities.h>
#include <dolfinx_contact/utils.h>
#include <dolfinx_cuas/QuadratureRule.hpp>
#include <dolfinx_cuas/math.hpp>
#include <dolfinx_cuas/utils.hpp>
#include <iostream>
#include <xtensor/xindex_view.hpp>
Expand Down Expand Up @@ -53,7 +52,6 @@ class Contact
: _marker(marker), _surfaces(surfaces), _V(V)
{
auto mesh = _marker->mesh();
const int gdim = mesh->geometry().dim(); // geometrical dimension
const int tdim = mesh->topology().dim(); // topological dimension
const int fdim = tdim - 1; // topological dimension of facet
const dolfinx::mesh::Topology& topology = mesh->topology();
Expand Down Expand Up @@ -122,12 +120,9 @@ class Contact
= dolfinx::fem::create_sparsity_pattern(a);

// facet to cell connectivity
auto mesh = _marker->mesh();
auto dofmap = a.function_spaces().at(0)->dofmap();
const int gdim = mesh->geometry().dim(); // geometrical dimension
const int tdim = mesh->topology().dim(); // topological dimension
const int fdim = tdim - 1; // topological dimension of facet

// Temporary array to hold dofs for sparsity pattern
std::vector<std::int32_t> linked_dofs;
for (int s = 0; s < 2; ++s)
{
auto facet_map = _submeshes[_opposites[s]].facet_map();
Expand All @@ -136,20 +131,18 @@ class Contact
{
auto cell = _cell_facet_pairs[s][i].first;
auto cell_dofs = dofmap->cell_dofs(cell);
std::vector<std::int32_t> linked_dofs;
auto links = _facet_maps[s]->links(i);
for (std::int32_t j = 0; j < _facet_maps[s]->num_links(i); j++)

linked_dofs.clear();
for (auto link : _facet_maps[s]->links(i))
{
auto linked_sub_cell = facet_map->links(links[j])[0];
auto linked_sub_cell = facet_map->links(link)[0];
auto linked_cell = parent_cells[linked_sub_cell];
auto linked_cell_dofs = dofmap->cell_dofs(linked_cell);
for (std::int32_t k = 0; k < linked_cell_dofs.size(); k++)
{
linked_dofs.push_back(linked_cell_dofs[k]);
}
for (auto dof : linked_cell_dofs)
linked_dofs.push_back(dof);
}
// Remove duplicates
std::sort(linked_dofs.begin(), linked_dofs.end());
dolfinx::radix_sort(xtl::span(linked_dofs));
linked_dofs.erase(std::unique(linked_dofs.begin(), linked_dofs.end()),
linked_dofs.end());

Expand All @@ -175,9 +168,9 @@ class Contact
/// @param[in] cstride Number of coefficients per facet
/// @param[in] constants used in the variational form
void assemble_matrix(
const std::function<int(std::int32_t, const std::int32_t*, std::int32_t,
const std::int32_t*, const PetscScalar*)>&
mat_set,
const std::function<int(const xtl::span<const std::int32_t>&,
const xtl::span<const std::int32_t>&,
const xtl::span<const PetscScalar>&)>& mat_set,
const std::vector<
std::shared_ptr<const dolfinx::fem::DirichletBC<PetscScalar>>>& bcs,
int origin_meshtag, contact_kernel_fn& kernel,
Expand All @@ -186,11 +179,9 @@ class Contact
{
auto mesh = _marker->mesh();
const int gdim = mesh->geometry().dim(); // geometrical dimension
const int tdim = mesh->topology().dim(); // topological dimension
const int fdim = tdim - 1; // topological dimension of facet

// Prepare cell geometry
const graph::AdjacencyList<std::int32_t>& x_dofmap
const dolfinx::graph::AdjacencyList<std::int32_t>& x_dofmap
= mesh->geometry().dofmap();

// FIXME: Add proper interface for num coordinate dofs
Expand All @@ -215,27 +206,29 @@ class Contact
std::vector<std::vector<PetscScalar>> Ae_vec(
3 * max_links + 1,
std::vector<PetscScalar>(bs * ndofs_cell * bs * ndofs_cell));
std::vector<std::int32_t> linked_cells;
for (int i = 0; i < active_facets.size(); i++)
{
auto cell = active_facets[i].first;
auto [cell, local_index] = active_facets[i];
// Get cell coordinates/geometry
auto x_dofs = x_dofmap.links(cell);
for (std::size_t i = 0; i < x_dofs.size(); ++i)
{
std::copy_n(std::next(x_g.begin(), 3 * x_dofs[i]), gdim,
std::next(coordinate_dofs.begin(), i * gdim));
}
std::int32_t local_index = active_facets[i].second;
std::vector<std::int32_t> linked_cells;
auto links = map->links(i);
for (auto link : links)
linked_cells.resize(links.size());
for (int i = 0; i < (int)links.size(); ++i)
{
auto facet_pair = facet_map->links(link);
linked_cells.push_back(parent_cells[facet_pair[0]]);
// Extract (cell, facet) pair from submesh
auto facet_pair = facet_map->links((int)links[i]);
assert(facet_pair.size() == 2);
linked_cells[i] = parent_cells[facet_pair[0]];
}

// Remove duplicates
std::sort(linked_cells.begin(), linked_cells.end());
dolfinx::radix_sort(xtl::span(linked_cells));
linked_cells.erase(std::unique(linked_cells.begin(), linked_cells.end()),
linked_cells.end());
const int num_linked_cells = linked_cells.size();
Expand All @@ -255,18 +248,14 @@ class Contact
// Ae_vec at this stage This is not need for the function spaces we
// currently consider
auto dmap_cell = dofmap->cell_dofs(cell);
mat_set(dmap_cell.size(), dmap_cell.data(), dmap_cell.size(),
dmap_cell.data(), Ae_vec[0].data());
mat_set(dmap_cell, dmap_cell, Ae_vec[0]);

for (std::int32_t j = 0; j < num_linked_cells; j++)
{
auto dmap_linked = dofmap->cell_dofs(linked_cells[j]);
mat_set(dmap_cell.size(), dmap_cell.data(), dmap_linked.size(),
dmap_linked.data(), Ae_vec[3 * j + 1].data());
mat_set(dmap_linked.size(), dmap_linked.data(), dmap_cell.size(),
dmap_cell.data(), Ae_vec[3 * j + 2].data());
mat_set(dmap_linked.size(), dmap_linked.data(), dmap_linked.size(),
dmap_linked.data(), Ae_vec[3 * j + 3].data());
mat_set(dmap_cell, dmap_linked, Ae_vec[3 * j + 1]);
mat_set(dmap_linked, dmap_cell, Ae_vec[3 * j + 2]);
mat_set(dmap_linked, dmap_linked, Ae_vec[3 * j + 3]);
}
}
}
Expand All @@ -279,11 +268,9 @@ class Contact
// Extract mesh
auto mesh = _marker->mesh();
const int gdim = mesh->geometry().dim(); // geometrical dimension
const int tdim = mesh->topology().dim(); // topological dimension
const int fdim = tdim - 1; // topological dimension of facet

// Prepare cell geometry
const graph::AdjacencyList<std::int32_t>& x_dofmap
const dolfinx::graph::AdjacencyList<std::int32_t>& x_dofmap
= mesh->geometry().dofmap();

// FIXME: Add proper interface for num coordinate dofs
Expand All @@ -293,7 +280,6 @@ class Contact
// Extract function space data (assuming same test and trial space)
std::shared_ptr<const dolfinx::fem::DofMap> dofmap = _V->dofmap();
const std::int32_t ndofs_cell = dofmap->cell_dofs(0).size();
const dolfinx::graph::AdjacencyList<std::int32_t>& dofs = dofmap->list();
const int bs = dofmap->bs();

// FIXME: Need to reconsider facet permutations for jump integrals
Expand All @@ -310,34 +296,40 @@ class Contact
std::vector<std::vector<PetscScalar>> be_vec(
max_links + 1, std::vector<PetscScalar>(bs * ndofs_cell));

// Tempoary array to hold cell links
std::vector<std::int32_t> linked_cells;
for (std::size_t i = 0; i < active_facets.size(); i++)
{
auto cell = active_facets[i].first;
auto [cell, local_index] = active_facets[i];

// Get cell coordinates/geometry
auto x_dofs = x_dofmap.links(cell);
for (std::size_t j = 0; j < x_dofs.size(); ++j)
{
std::copy_n(std::next(x_g.begin(), 3 * x_dofs[j]), gdim,
std::next(coordinate_dofs.begin(), j * gdim));
}
std::int32_t local_index = active_facets[i].second;
std::vector<std::int32_t> linked_cells;

auto links = map->links(i);
for (auto link : links)
linked_cells.resize(links.size());
for (int i = 0; i < (int)links.size(); ++i)
{
auto facet_pair = facet_map->links(link);
linked_cells.push_back(parent_cells[facet_pair[0]]);
// Extract (cell, facet) pair from submesh
auto facet_pair = facet_map->links((int)links[i]);
assert(facet_pair.size() == 2);
linked_cells[i] = parent_cells[facet_pair[0]];
}

// Remove duplicates
std::sort(linked_cells.begin(), linked_cells.end());
dolfinx::radix_sort(xtl::span(linked_cells));
linked_cells.erase(std::unique(linked_cells.begin(), linked_cells.end()),
linked_cells.end());

// Using integer loop here to reduce number of zeroed vectors
const int num_linked_cells = linked_cells.size();
std::fill(be_vec[0].begin(), be_vec[0].end(), 0);
for (std::int32_t j = 0; j < num_linked_cells; j++)
{
std::fill(be_vec[j + 1].begin(), be_vec[j + 1].end(), 0);
}
kernel(be_vec, coeffs.data() + i * cstride, constants.data(),
coordinate_dofs.data(), &local_index, &perm, num_linked_cells);
// NOTE: Normally dof transform needs to be applied to the elements in
Expand Down Expand Up @@ -365,12 +357,13 @@ class Contact
auto mesh = _marker->mesh();
const std::size_t gdim = mesh->geometry().dim(); // geometrical dimension
const std::size_t tdim = mesh->topology().dim(); // topological dimension
const std::size_t fdim = tdim - 1;

// Extract function space data (assuming same test and trial space)
std::shared_ptr<const dolfinx::fem::DofMap> dofmap = _V->dofmap();
const std::size_t ndofs_cell = dofmap->cell_dofs(0).size();
const std::size_t bs = dofmap->bs();

// NOTE: Assuming same number of quadrature points on each cell
const std::size_t num_q_points = _qp_ref_facet[0].shape(0);
int max_links = std::max(_max_links[0], _max_links[1]);

Expand All @@ -391,24 +384,36 @@ class Contact
std::vector<xt ::xtensor<double, 3>> dphi_c;
dphi_c.reserve(num_facets);

// Temporary structures used in loop
xt::xtensor<double, 4> cell_tab({tdim + 1, num_q_points, ndofs_cell, bs});
xt::xtensor<double, 2> phi_i({num_q_points, ndofs_cell});
xt::xtensor<double, 3> dphi_i({tdim, num_q_points, ndofs_cell});
std::array<std::size_t, 4> tabulate_shape
= basix_element.tabulate_shape(1, num_q_points);
xt::xtensor<double, 4> c_tab(tabulate_shape);
xt::xtensor<double, 3> dphi_ci(
{tdim, tabulate_shape[1], tabulate_shape[2]});

// Tabulate basis functions and first order derivatives for each facet in
// the reference cell. This tabulation is done both for the finite element
// of the unknown and the coordinate element (which might differ)
for (std::size_t i = 0; i < num_facets; ++i)
{
// Push quadrature points forward
auto facet = facets[i];
const xt::xarray<double>& q_facet = _qp_ref_facet[i];

xt::xtensor<double, 4> cell_tab({tdim + 1, num_q_points, ndofs_cell, bs});
assert(q_facet.shape(0) == num_q_points);
element->tabulate(cell_tab, q_facet, 1);
xt::xtensor<double, 2> phi_i
= xt::view(cell_tab, 0, xt::all(), xt::all(), 0);

phi_i = xt::view(cell_tab, 0, xt::all(), xt::all(), 0);
phi.push_back(phi_i);
xt::xtensor<double, 3> dphi_i

dphi_i
= xt::view(cell_tab, xt::range(1, tdim + 1), xt::all(), xt::all(), 0);
dphi.push_back(dphi_i);

// Tabulate coordinate element of reference cell
auto c_tab = basix_element.tabulate(1, q_facet);
xt::xtensor<double, 3> dphi_ci
basix_element.tabulate(1, q_facet, c_tab);
dphi_ci
= xt::view(c_tab, xt::range(1, tdim + 1), xt::all(), xt::all(), 0);
dphi_c.push_back(dphi_ci);
}
Expand All @@ -434,11 +439,11 @@ class Contact
num_q_points * bs};
// As reference facet and reference cell are affine, we do not need to
// compute this per quadrature point
auto ref_jacobians
xt::xtensor<double, 3> ref_jacobians
= basix::cell::facet_jacobians(basix_element.cell_type());

// Get facet normals on reference cell
auto facet_normals
xt::xtensor<double, 2> facet_normals
= basix::cell::facet_outward_normals(basix_element.cell_type());

// right hand side kernel
Expand All @@ -455,10 +460,9 @@ class Contact

// Reshape coordinate dofs to two dimensional array
// NOTE: DOLFINx has 3D input coordinate dofs
std::array<std::size_t, 2> shape = {num_coordinate_dofs, 3};

// FIXME: These array should be views (when compute_jacobian doesn't use
// xtensor)
std::array<std::size_t, 2> shape = {num_coordinate_dofs, 3};
xt::xtensor<double, 2> coord = xt::adapt(
coordinate_dofs, num_coordinate_dofs * 3, xt::no_ownership(), shape);

Expand All @@ -473,8 +477,8 @@ class Contact
xt::xtensor<double, 2> J = xt::zeros<double>({gdim, tdim});
xt::xtensor<double, 2> K = xt::zeros<double>({tdim, gdim});
auto c_view = xt::view(coord, xt::all(), xt::range(0, gdim));
dolfinx_cuas::math::compute_jacobian(dphi0_c, c_view, J);
dolfinx_cuas::math::compute_inv(J, K);
dolfinx::fem::CoordinateElement::compute_jacobian(dphi0_c, c_view, J);
dolfinx::fem::CoordinateElement::compute_jacobian_inverse(J, K);

// Compute normal of physical facet using a normalized covariant Piola
// transform n_phys = J^{-T} n_ref / ||J^{-T} n_ref|| See for instance
Expand All @@ -501,7 +505,8 @@ class Contact
xt::xtensor<double, 2> J_tot
= xt::zeros<double>({J.shape(0), J_f.shape(1)});
dolfinx::math::dot(J, J_f, J_tot);
double detJ = std::fabs(dolfinx_cuas::math::compute_determinant(J_tot));
double detJ = std::fabs(
dolfinx::fem::CoordinateElement::compute_jacobian_determinant(J_tot));

const xt::xtensor<double, 3>& dphi_f = dphi[facet_index];
const xt::xtensor<double, 2>& phi_f = phi[facet_index];
Expand Down Expand Up @@ -627,8 +632,8 @@ class Contact
xt::xtensor<double, 2> J = xt::zeros<double>({gdim, tdim});
xt::xtensor<double, 2> K = xt::zeros<double>({tdim, gdim});
auto c_view = xt::view(coord, xt::all(), xt::range(0, gdim));
dolfinx_cuas::math::compute_jacobian(dphi0_c, c_view, J);
dolfinx_cuas::math::compute_inv(J, K);
dolfinx::fem::CoordinateElement::compute_jacobian(dphi0_c, c_view, J);
dolfinx::fem::CoordinateElement::compute_jacobian_inverse(J, K);

// Compute normal of physical facet using a normalized covariant Piola
// transform n_phys = J^{-T} n_ref / ||J^{-T} n_ref|| See for instance
Expand Down Expand Up @@ -656,7 +661,8 @@ class Contact
xt::xtensor<double, 2> J_tot
= xt::zeros<double>({J.shape(0), J_f.shape(1)});
dolfinx::math::dot(J, J_f, J_tot);
double detJ = std::fabs(dolfinx_cuas::math::compute_determinant(J_tot));
double detJ = std::fabs(
dolfinx::fem::CoordinateElement::compute_jacobian_determinant(J_tot));

const xt::xtensor<double, 3>& dphi_f = dphi[facet_index];
const xt::xtensor<double, 2>& phi_f = phi[facet_index];
Expand Down
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