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Flatten integration entities in C++. (#91)
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* Flatten integration entities in C++.
Integration entities are unrolled in Python to be 1D (cell integrals), 2D (Exterior facet), 3D (Interior facet).

Preparing code for higher order function spaces. Currently does not work due to a bug in higher order submeshes, see: FEniCS/dolfinx#2233

* Various copy improvements
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@jorgensd
jorgensd authored Jun 15, 2022
1 parent 51dc322 commit 08704ad
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Showing 16 changed files with 526 additions and 570 deletions.
2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -65,3 +65,5 @@ core
*.png
**/CMakeFiles
CMakeCache.txt
*.txt
*.cache
2 changes: 1 addition & 1 deletion cpp/CMakeLists.txt
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Expand Up @@ -41,7 +41,7 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR})
find_package(DOLFINX 0.4.2.0 REQUIRED)
find_package(Basix 0.4.2.0 REQUIRED)
find_package(xtensor REQUIRED)
find_package(DOLFINX_CUAS 0.4.0 REQUIRED)
find_package(DOLFINX_CUAS 0.4.1 REQUIRED)

feature_summary(WHAT ALL)

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89 changes: 39 additions & 50 deletions cpp/Contact.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@
#include "error_handling.h"
#include "utils.h"
#include <dolfinx/common/log.h>
#include <dolfinx_cuas/utils.hpp>
using namespace dolfinx_contact;

namespace
Expand Down Expand Up @@ -87,15 +86,8 @@ dolfinx_contact::Contact::Contact(
{
std::vector<std::int32_t> facets = marker->find(links[i]);
int index = surfaces->offsets()[s] + int(i);
std::variant<
std::vector<std::int32_t>, std::vector<std::pair<std::int32_t, int>>,
std::vector<std::tuple<std::int32_t, int, std::int32_t, int>>>
pairs = dolfinx_cuas::compute_active_entities(
mesh, facets, dolfinx::fem::IntegralType::exterior_facet);

_cell_facet_pairs[index]
= std::get<std::vector<std::pair<std::int32_t, int>>>(pairs);

_cell_facet_pairs[index] = dolfinx_contact::compute_active_entities(
mesh, facets, dolfinx::fem::IntegralType::exterior_facet);
_submeshes[index]
= dolfinx_contact::SubMesh(mesh, _cell_facet_pairs[index]);
}
Expand Down Expand Up @@ -151,13 +143,13 @@ Mat dolfinx_contact::Contact::create_petsc_matrix(
= _submeshes[contact_pair[1]].facet_map();
const std::vector<std::int32_t>& parent_cells
= _submeshes[contact_pair[1]].parent_cells();
for (int i = 0; i < (int)_cell_facet_pairs[contact_pair[0]].size(); i++)
for (int i = 0; i < (int)_cell_facet_pairs[contact_pair[0]].size(); i += 2)
{
std::int32_t cell = _cell_facet_pairs[contact_pair[0]][i].first;
std::int32_t cell = _cell_facet_pairs[contact_pair[0]][i];
tcb::span<const int> cell_dofs = dofmap->cell_dofs(cell);

linked_dofs.clear();
for (auto link : _facet_maps[k]->links(i))
for (auto link : _facet_maps[k]->links(i / 2))
{
const int linked_sub_cell = facet_map->links(link)[0];
const std::int32_t linked_cell = parent_cells[linked_sub_cell];
Expand Down Expand Up @@ -185,12 +177,10 @@ void dolfinx_contact::Contact::create_distance_map(int pair)
{
// Get quadrature mesh info
int puppet_mt = _contact_pairs[pair][0];
const std::vector<std::pair<std::int32_t, int>>& puppet_facets
= _cell_facet_pairs[puppet_mt];
const std::vector<std::int32_t>& puppet_facets = _cell_facet_pairs[puppet_mt];
std::shared_ptr<const dolfinx::mesh::Mesh> puppet_mesh
= _submeshes[puppet_mt].mesh();
std::vector<std::pair<std::int32_t, int>> quadrature_facets(
puppet_facets.size());
std::vector<std::int32_t> quadrature_facets(puppet_facets.size());
{
const int tdim = puppet_mesh->topology().dim();
std::shared_ptr<const dolfinx::graph::AdjacencyList<int>> c_to_f
Expand All @@ -199,19 +189,18 @@ void dolfinx_contact::Contact::create_distance_map(int pair)
std::shared_ptr<const dolfinx::graph::AdjacencyList<int>> cell_map
= _submeshes[puppet_mt].cell_map();

for (std::size_t i = 0; i < puppet_facets.size(); ++i)
for (std::size_t i = 0; i < puppet_facets.size(); i += 2)
{
auto [f_cell, facet] = puppet_facets[i];
quadrature_facets[i] = {cell_map->links(f_cell)[0], facet};
auto sub_cells = cell_map->links(puppet_facets[i]);
assert(!sub_cells.empty());
quadrature_facets[i] = sub_cells.front();
quadrature_facets[i + 1] = puppet_facets[i + 1];
}
}

// Get candidate mesh information
int candidate_mt = _contact_pairs[pair][1];
const std::vector<std::pair<std::int32_t, int>>& candidate_facets
const std::vector<std::int32_t>& candidate_facets
= _cell_facet_pairs[candidate_mt];
std::vector<std::pair<std::int32_t, int>> submesh_facets(
candidate_facets.size());
std::vector<std::int32_t> submesh_facets(candidate_facets.size());
std::shared_ptr<const dolfinx::mesh::Mesh> candidate_mesh
= _submeshes[candidate_mt].mesh();
{
Expand All @@ -222,10 +211,12 @@ void dolfinx_contact::Contact::create_distance_map(int pair)
std::shared_ptr<const dolfinx::graph::AdjacencyList<int>> cell_map
= _submeshes[candidate_mt].cell_map();

for (std::size_t i = 0; i < candidate_facets.size(); ++i)
for (std::size_t i = 0; i < candidate_facets.size(); i += 2)
{
auto [f_cell, facet] = candidate_facets[i];
submesh_facets[i] = {cell_map->links(f_cell)[0], facet};
auto submesh_cell = cell_map->links(candidate_facets[i]);
assert(!submesh_cell.empty());
submesh_facets[i] = submesh_cell.front();
submesh_facets[i + 1] = candidate_facets[i + 1];
}
}

Expand Down Expand Up @@ -287,7 +278,7 @@ dolfinx_contact::Contact::pack_ny(int pair,
const std::vector<xt::xtensor<double, 2>>& qp_phys
= _qp_phys[contact_pair[0]];

const std::size_t num_facets = _cell_facet_pairs[contact_pair[0]].size();
const std::size_t num_facets = _cell_facet_pairs[contact_pair[0]].size() / 2;
const std::size_t num_q_points
= _quadrature_rule->offset()[1] - _quadrature_rule->offset()[0];

Expand Down Expand Up @@ -341,9 +332,8 @@ dolfinx_contact::Contact::pack_ny(int pair,
J, K, point, coordinate_dofs, linked_pair[1], cmap,
reference_normals);
// Copy normal into c
const std::size_t offset = i * cstride + q * gdim;
for (int l = 0; l < gdim; ++l)
normals[offset + l] = normal[l];
std::copy_n(normal.begin(), gdim,
std::next(normals.begin(), i * cstride + q * gdim));
}
}
return {std::move(normals), cstride};
Expand Down Expand Up @@ -388,7 +378,7 @@ void dolfinx_contact::Contact::assemble_matrix(
}

const std::array<int, 2>& contact_pair = _contact_pairs[pair];
const std::vector<std::pair<std::int32_t, int>>& active_facets
const std::vector<std::int32_t>& active_facets
= _cell_facet_pairs[contact_pair[0]];
std::shared_ptr<const dolfinx::graph::AdjacencyList<int>> map
= _facet_maps[pair];
Expand All @@ -402,11 +392,11 @@ void dolfinx_contact::Contact::assemble_matrix(
3 * max_links + 1,
std::vector<PetscScalar>(bs * ndofs_cell * bs * ndofs_cell));
std::vector<std::int32_t> linked_cells;
for (std::size_t i = 0; i < active_facets.size(); i++)
for (std::size_t i = 0; i < active_facets.size(); i += 2)
{
[[maybe_unused]] auto [cell, local_index] = active_facets[i];
// Get cell coordinates/geometry
const tcb::span<const int> x_dofs = x_dofmap.links(cell);
assert(active_facets[i] < x_dofmap.num_nodes());
const tcb::span<const int> x_dofs = x_dofmap.links(active_facets[i]);
for (std::size_t j = 0; j < x_dofs.size(); ++j)
{
std::copy_n(std::next(x_g.begin(), 3 * x_dofs[j]), gdim,
Expand All @@ -416,7 +406,7 @@ void dolfinx_contact::Contact::assemble_matrix(
if (max_links > 0)
{
// Compute the unique set of cells linked to the current facet
compute_linked_cells(linked_cells, map->links((int)i), facet_map,
compute_linked_cells(linked_cells, map->links((int)i / 2), facet_map,
parent_cells);
}
// Fill initial local element matrices with zeros prior to assembly
Expand All @@ -429,18 +419,18 @@ void dolfinx_contact::Contact::assemble_matrix(
std::fill(Aes[3 * j + 3].begin(), Aes[3 * j + 3].end(), 0);
}

kernel(Aes, coeffs.data() + i * cstride, constants.data(),
coordinate_dofs.data(), local_index, num_linked_cells);
kernel(Aes, coeffs.data() + i / 2 * cstride, constants.data(),
coordinate_dofs.data(), active_facets[i + 1], num_linked_cells);

// FIXME: We would have to handle possible Dirichlet conditions here, if we
// think that we can have a case with contact and Dirichlet
const tcb::span<const int> dmap_cell = dofmap->cell_dofs(cell);
auto dmap_cell = dofmap->cell_dofs(active_facets[i]);
mat_set(dmap_cell, dmap_cell, Aes[0]);

for (std::size_t j = 0; j < num_linked_cells; j++)
{
const tcb::span<const int> dmap_linked
= dofmap->cell_dofs(linked_cells[j]);
auto dmap_linked = dofmap->cell_dofs(linked_cells[j]);
assert(!dmap_linked.empty());
mat_set(dmap_cell, dmap_linked, Aes[3 * j + 1]);
mat_set(dmap_linked, dmap_cell, Aes[3 * j + 2]);
mat_set(dmap_linked, dmap_linked, Aes[3 * j + 3]);
Expand Down Expand Up @@ -484,7 +474,7 @@ void dolfinx_contact::Contact::assemble_vector(
// Select which side of the contact interface to loop from and get the
// correct map
const std::array<int, 2>& contact_pair = _contact_pairs[pair];
const std::vector<std::pair<std::int32_t, int>>& active_facets
const std::vector<std::int32_t>& active_facets
= _cell_facet_pairs[contact_pair[0]];
const dolfinx_contact::SubMesh& submesh = _submeshes[contact_pair[1]];
std::shared_ptr<const dolfinx::graph::AdjacencyList<int>> map
Expand All @@ -506,12 +496,11 @@ void dolfinx_contact::Contact::assemble_vector(

// Tempoary array to hold cell links
std::vector<std::int32_t> linked_cells;
for (std::size_t i = 0; i < active_facets.size(); i++)
for (std::size_t i = 0; i < active_facets.size(); i += 2)
{
[[maybe_unused]] auto [cell, local_index] = active_facets[i];

// Get cell coordinates/geometry
const tcb::span<const int> x_dofs = x_dofmap.links(cell);
const tcb::span<const int> x_dofs = x_dofmap.links(active_facets[i]);
for (std::size_t j = 0; j < x_dofs.size(); ++j)
{
std::copy_n(std::next(x_g.begin(), 3 * x_dofs[j]), gdim,
Expand All @@ -521,7 +510,7 @@ void dolfinx_contact::Contact::assemble_vector(
// Compute the unique set of cells linked to the current facet
if (max_links > 0)
{
compute_linked_cells(linked_cells, map->links((int)i), facet_map,
compute_linked_cells(linked_cells, map->links((int)i / 2), facet_map,
parent_cells);
}

Expand All @@ -530,11 +519,11 @@ void dolfinx_contact::Contact::assemble_vector(
std::fill(bes[0].begin(), bes[0].end(), 0);
for (std::size_t j = 0; j < num_linked_cells; j++)
std::fill(bes[j + 1].begin(), bes[j + 1].end(), 0);
kernel(bes, coeffs.data() + i * cstride, constants.data(),
coordinate_dofs.data(), local_index, num_linked_cells);
kernel(bes, coeffs.data() + i / 2 * cstride, constants.data(),
coordinate_dofs.data(), active_facets[i + 1], num_linked_cells);

// Add element vector to global vector
const tcb::span<const int> dofs_cell = dofmap->cell_dofs(cell);
const tcb::span<const int> dofs_cell = dofmap->cell_dofs(active_facets[i]);
for (std::size_t j = 0; j < ndofs_cell; ++j)
for (int k = 0; k < bs; ++k)
b[bs * dofs_cell[j] + k] += bes[0][bs * j + k];
Expand Down
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