Remesher.cpp

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#include "Remesher.hpp"
 
#include <polyfem/mesh/remesh/L2Projection.hpp>
 
#include <polyfem/assembler/Mass.hpp>
#include <polyfem/mesh/mesh2D/CMesh2D.hpp>
#include <polyfem/mesh/mesh3D/CMesh3D.hpp>
#include <polyfem/basis/LagrangeBasis2d.hpp>
#include <polyfem/basis/LagrangeBasis3d.hpp>
#include <polyfem/time_integrator/ImplicitTimeIntegrator.hpp>
#include <polyfem/utils/GeometryUtils.hpp>
#include <polyfem/utils/StringUtils.hpp>
#include <polyfem/io/OBJWriter.hpp>
#include <paraviewo/VTUWriter.hpp>
 
#include <igl/boundary_facets.h>
#include <igl/edges.h>
 
namespace polyfem::mesh
{
    Remesher::Remesher(const State &state,
                       const Eigen::MatrixXd &obstacle_displacements,
                       const Eigen::MatrixXd &obstacle_quantities,
                       const double current_time,
                       const double starting_energy)
        : state(state),
          args(state.args["space"]["remesh"]),
          m_obstacle_displacements(obstacle_displacements),
          m_obstacle_quantities(obstacle_quantities),
          current_time(current_time),
          starting_energy(starting_energy)
    {
    }
 
    void Remesher::init(
        const Eigen::MatrixXd &rest_positions,
        const Eigen::MatrixXd &positions,
        const Eigen::MatrixXi &elements,
        const Eigen::MatrixXd &projection_quantities,
        const BoundaryMap<int> &boundary_to_id,
        const std::vector<int> &body_ids,
        const EdgeMap<double> &elastic_energy,
        const EdgeMap<double> &contact_energy)
    {
        assert(elements.size() > 0);
 
        // --------------------------------------------------------------------
        // Determine which vertices are on the boundary
 
        // Partition mesh by body_ids
        assert(body_ids.size() == elements.rows());
        std::unordered_map<int, std::vector<int>> body_elements;
        for (int i = 0; i < elements.rows(); ++i)
        {
            const int body_id = body_ids[i];
            if (body_elements.find(body_id) == body_elements.end())
                body_elements[body_id] = std::vector<int>();
            body_elements[body_id].push_back(i);
        }
 
        // Determine boundary vertices
        std::vector<bool> is_boundary_vertex(positions.rows(), false);
        for (const auto &[body_id, rows] : body_elements)
        {
            Eigen::MatrixXi boundary_facets;
            igl::boundary_facets(elements(rows, Eigen::all), boundary_facets);
 
            for (int i = 0; i < boundary_facets.rows(); ++i)
                for (int j = 0; j < boundary_facets.cols(); ++j)
                    is_boundary_vertex[boundary_facets(i, j)] = true;
        }
 
        // --------------------------------------------------------------------
 
        // Initialize the mesh atributes and connectivity
        init_attributes_and_connectivity(positions.rows(), elements);
 
        // Save the vertex position in the vertex attributes
        set_rest_positions(rest_positions);
        set_positions(positions);
        set_projection_quantities(projection_quantities);
        set_fixed(is_boundary_vertex);
        set_boundary_ids(boundary_to_id);
        set_body_ids(body_ids);
    }
 
    void Remesher::cache_before()
    {
        global_projection_cache.rest_positions = rest_positions();
        global_projection_cache.elements = elements();
        global_projection_cache.projection_quantities = projection_quantities();
    }
 
    void Remesher::project_quantities()
    {
        POLYFEM_REMESHER_SCOPED_TIMER("Project quantities");
 
        using namespace polyfem::assembler;
        using namespace polyfem::basis;
        using namespace polyfem::utils;
 
        const std::unique_ptr<Mesh> from_mesh = Mesh::create(
            global_projection_cache.rest_positions, global_projection_cache.elements);
        std::vector<ElementBases> from_bases;
        std::vector<LocalBoundary> _;
        Eigen::VectorXi from_vertex_to_basis;
        int n_from_basis = build_bases(*from_mesh, state.formulation(), from_bases, _, from_vertex_to_basis);
        assert(from_vertex_to_basis.size() == global_projection_cache.rest_positions.rows());
 
        // Old values of independent variables
        Eigen::MatrixXd from_projection_quantities = reorder_matrix(
            global_projection_cache.projection_quantities,
            from_vertex_to_basis, n_from_basis, dim());
        append_rows(from_projection_quantities, obstacle_quantities());
        n_from_basis += obstacle().n_vertices();
        assert(dim() * n_from_basis == from_projection_quantities.rows());
 
        // --------------------------------------------------------------------
 
        Eigen::MatrixXd rest_positions = this->rest_positions();
        Eigen::MatrixXi elements = this->elements();
 
        const std::unique_ptr<Mesh> to_mesh = Mesh::create(rest_positions, elements);
        std::vector<ElementBases> to_bases;
        Eigen::VectorXi to_vertex_to_basis;
        int n_to_basis = build_bases(*to_mesh, state.formulation(), to_bases, _, to_vertex_to_basis);
        assert(to_vertex_to_basis.size() == rest_positions.rows());
 
        rest_positions = reorder_matrix(rest_positions, to_vertex_to_basis, n_to_basis);
        elements = map_index_matrix(elements, to_vertex_to_basis);
 
        // Interpolated values of independent variables
        Eigen::MatrixXd to_projection_quantities = reorder_matrix(
            projection_quantities(), to_vertex_to_basis, n_to_basis, dim());
        append_rows(to_projection_quantities, obstacle_quantities());
        n_to_basis += obstacle().n_vertices();
        assert(dim() * n_to_basis == to_projection_quantities.rows());
 
        // --------------------------------------------------------------------
 
        // solve M x = A y for x where M is the mass matrix and A is the cross mass matrix.
        Eigen::SparseMatrix<double> M, A;
        {
            MassMatrixAssembler assembler;
            assembler::Mass mass_matrix_assembler;
            AssemblyValsCache cache;
 
            mass_matrix_assembler.assemble(
                is_volume(),
                n_to_basis, to_bases, to_bases,
                cache, 0, M, true);
            assert(M.rows() == to_projection_quantities.rows());
 
            // if (lump_mass_matrix)
            //  M = lump_matrix(M);
 
            assembler.assemble_cross(
                is_volume(), dim(),
                n_from_basis, from_bases, from_bases,
                n_to_basis, to_bases, to_bases,
                cache, A);
            assert(A.rows() == to_projection_quantities.rows());
            assert(A.cols() == from_projection_quantities.rows());
        }
 
        // --------------------------------------------------------------------
 
        ipc::CollisionMesh collision_mesh;
        {
            Eigen::MatrixXi boundary_edges, boundary_faces;
            if (dim() == 2)
            {
                igl::boundary_facets(elements, boundary_edges);
            }
            else
            {
                igl::boundary_facets(elements, boundary_faces);
                igl::edges(boundary_faces, boundary_edges);
            }
 
            if (obstacle().n_edges() > 0)
                utils::append_rows(boundary_edges, obstacle().e().array() + rest_positions.rows());
            if (obstacle().n_faces() > 0)
                utils::append_rows(boundary_faces, obstacle().f().array() + rest_positions.rows());
 
            utils::append_rows(rest_positions, obstacle().v());
            assert(rest_positions.size() == to_projection_quantities.rows());
 
            collision_mesh = ipc::CollisionMesh::build_from_full_mesh(
                rest_positions, boundary_edges, boundary_faces);
        }
 
        // --------------------------------------------------------------------
 
        Eigen::MatrixXd projected_quantities(to_projection_quantities.rows(), n_quantities());
        const int n_constrained_quantaties = n_quantities() / 3;
        const int n_unconstrained_quantaties = n_quantities() - n_constrained_quantaties;
 
        const std::vector<int> boundary_nodes = this->boundary_nodes(to_vertex_to_basis);
        for (int i = 0; i < n_constrained_quantaties; ++i)
        {
            projected_quantities.col(i) = constrained_L2_projection(
                state.make_nl_solver(/*for_al=*/false),
                // L2 projection form
                M, A, /*y=*/from_projection_quantities.col(i),
                // Inversion-free form
                rest_positions, elements, dim(),
                // Contact form
                collision_mesh, state.args["contact"]["dhat"],
                state.solve_data.contact_form
                    ? state.solve_data.contact_form->barrier_stiffness()
                    : 1.0,
                state.args["contact"]["use_convergent_formulation"],
                state.args["solver"]["contact"]["CCD"]["broad_phase"],
                state.args["solver"]["contact"]["CCD"]["tolerance"],
                state.args["solver"]["contact"]["CCD"]["max_iterations"],
                // Augmented lagrangian form
                boundary_nodes, obstacle().ndof(), to_projection_quantities.col(i),
                // Initial guess
                to_projection_quantities.col(i));
        }
 
        // Set entry for obstacle to identity
        // ┌     ┐ ┌     ┐   ┌     ┐
        // │M   0│ │x_fem│   |y_fem|
        // │     │ │     │ = |     | ⟹ x_obs = y_obs
        // │0   I│ │x_obs│   |y_obs|
        // └     ┘ └     ┘   └     ┘
 
        for (int i = 0; i < dim() * obstacle().n_vertices(); ++i)
        {
            const int row = M.rows() - i - 1; // fill from bottom
            M.coeffRef(row, row) = 1.0;
        }
 
        for (int i = 0; i < dim() * obstacle().n_vertices(); ++i)
        {
            const int row = A.rows() - i - 1; // fill from bottom
            const int col = A.cols() - i - 1; // fill from bottom
            A.coeffRef(row, col) = 1.0;
        }
 
        // NOTE: no need for to_projection_quantities.rightCols(n_unconstrained_quantaties)
        projected_quantities.rightCols(n_unconstrained_quantaties) = unconstrained_L2_projection(
            M, A, from_projection_quantities.rightCols(n_unconstrained_quantaties));
 
        // --------------------------------------------------------------------
 
        assert(projected_quantities.rows() == dim() * n_to_basis);
        set_projection_quantities(unreorder_matrix(
            projected_quantities, to_vertex_to_basis, to_vertex_to_basis.size(), dim()));
    }
 
    int Remesher::build_bases(
        const Mesh &mesh,
        const std::string &assembler_formulation,
        std::vector<polyfem::basis::ElementBases> &bases,
        std::vector<LocalBoundary> &local_boundary,
        Eigen::VectorXi &vertex_to_basis)
    {
        using namespace polyfem::basis;
 
        int n_bases;
        std::map<int, basis::InterfaceData> poly_edge_to_data;
        std::shared_ptr<mesh::MeshNodes> mesh_nodes;
        if (mesh.dimension() == 2)
        {
            n_bases = LagrangeBasis2d::build_bases(
                dynamic_cast<const Mesh2D &>(mesh),
                assembler_formulation, /*quadrature_order=*/1,
                /*mass_quadrature_order=*/2, /*discr_order=*/1,
                /*serendipity=*/false, /*has_polys=*/false,
                /*is_geom_bases=*/false, bases, local_boundary,
                poly_edge_to_data, mesh_nodes);
        }
        else
        {
            assert(mesh.dimension() == 3);
            n_bases = LagrangeBasis3d::build_bases(
                dynamic_cast<const Mesh3D &>(mesh),
                assembler_formulation, /*quadrature_order=*/1,
                /*mass_quadrature_order=*/2, /*discr_order=*/1,
                /*serendipity=*/false, /*has_polys=*/false,
                /*is_geom_bases=*/false, bases, local_boundary,
                poly_edge_to_data, mesh_nodes);
        }
 
        // TODO: use mesh_nodes to build vertex_to_basis
        vertex_to_basis.setConstant(mesh.n_vertices(), -1);
        for (const ElementBases &elm : bases)
        {
            for (const Basis &basis : elm.bases)
            {
                assert(basis.global().size() == 1);
                const int basis_id = basis.global()[0].index;
                const RowVectorNd v = basis.global()[0].node;
 
                for (int i = 0; i < mesh.n_vertices(); i++)
                {
                    if ((mesh.point(i).array() == v.array()).all())
                    {
                        if (vertex_to_basis[i] == -1)
                            vertex_to_basis[i] = basis_id;
                        assert(vertex_to_basis[i] == basis_id);
                        break;
                    }
                }
            }
        }
 
        return n_bases;
    }
 
    void Remesher::write_mesh(const std::string &path) const
    {
        assert(utils::StringUtils::endswith(path, ".vtu"));
 
        paraviewo::VTUWriter writer;
 
        Eigen::MatrixXd rest_positions = this->rest_positions();
        Eigen::MatrixXd displacements = this->displacements();
 
        const Eigen::MatrixXd projection_quantities = this->projection_quantities();
        std::vector<Eigen::MatrixXd> unflattened_projection_quantities;
        for (const auto &q : projection_quantities.colwise())
            unflattened_projection_quantities.push_back(utils::unflatten(q, dim()));
 
        Eigen::MatrixXi elements = this->elements();
        std::vector<std::vector<int>> all_elements(elements.rows(), std::vector<int>(elements.cols()));
        for (int i = 0; i < elements.rows(); i++)
            for (int j = 0; j < elements.cols(); j++)
                all_elements[i][j] = elements(i, j);
 
        const int offset = rest_positions.rows();
        if (obstacle().n_vertices() > 0)
        {
            utils::append_rows(rest_positions, obstacle().v());
            utils::append_rows(displacements, obstacle_displacements());
            for (int i = 0; i < unflattened_projection_quantities.size(); ++i)
                utils::append_rows(
                    unflattened_projection_quantities[i],
                    utils::unflatten(obstacle_quantities().col(i), dim()));
 
            if (obstacle().n_edges() > 0)
            {
                const Eigen::MatrixXi obstacle_edges = obstacle().e().array() + offset;
                all_elements.resize(all_elements.size() + obstacle_edges.rows());
                for (int i = 0; i < obstacle().n_edges(); i++)
                {
                    all_elements[i + elements.rows()] = std::vector<int>(obstacle_edges.cols());
                    for (int j = 0; j < obstacle_edges.cols(); j++)
                        all_elements[i + elements.rows()][j] = obstacle_edges(i, j);
                }
            }
 
            if (obstacle().n_faces() > 0)
            {
                const Eigen::MatrixXi obstacle_faces = obstacle().f().array() + offset;
                all_elements.resize(all_elements.size() + obstacle_faces.rows());
                for (int i = 0; i < obstacle().n_edges(); i++)
                {
                    all_elements[i + elements.rows()] = std::vector<int>(obstacle_faces.cols());
                    for (int j = 0; j < obstacle_faces.cols(); j++)
                        all_elements[i + elements.rows()][j] = obstacle_faces(i, j);
                }
            }
        }
 
        for (int i = 0; i < unflattened_projection_quantities.size(); ++i)
            writer.add_field(fmt::format("projection_quantity_{:d}", i), unflattened_projection_quantities[i]);
        writer.add_field("displacement", displacements);
        writer.write_mesh(path, rest_positions, all_elements, /*is_simplicial=*/true, /*has_poly=*/false);
    }
 
    Eigen::MatrixXd Remesher::combine_time_integrator_quantities(
        const std::shared_ptr<time_integrator::ImplicitTimeIntegrator> &time_integrator)
    {
        if (time_integrator == nullptr)
            return Eigen::MatrixXd();
 
        // not including current displacement as this will be handled as positions
        Eigen::MatrixXd projection_quantities(
            time_integrator->x_prev().size(), 3 * time_integrator->steps());
        int i = 0;
        for (const Eigen::VectorXd &x : time_integrator->x_prevs())
            projection_quantities.col(i++) = x;
        for (const Eigen::VectorXd &v : time_integrator->v_prevs())
            projection_quantities.col(i++) = v;
        for (const Eigen::VectorXd &a : time_integrator->a_prevs())
            projection_quantities.col(i++) = a;
        assert(i == projection_quantities.cols());
 
        return projection_quantities;
    }
 
    void Remesher::split_time_integrator_quantities(
        const Eigen::MatrixXd &quantities,
        const int dim,
        Eigen::MatrixXd &x_prevs,
        Eigen::MatrixXd &v_prevs,
        Eigen::MatrixXd &a_prevs)
    {
        if (quantities.size() == 0)
            return;
 
        assert(quantities.cols() % 3 == 0);
        const int n_steps = quantities.cols() / 3;
 
        x_prevs = quantities.leftCols(n_steps);
        v_prevs = quantities.middleCols(n_steps, n_steps);
        a_prevs = quantities.rightCols(n_steps);
    }
 
    void Remesher::log_timings()
    {
        if (!logger().should_log(spdlog::level::debug) || timings.empty())
            return;
 
        std::cout << "--------------------------------------------------------------------------------" << std::endl;
 
        logger().debug("Total time: {:.3g}s", total_time);
        double sum = 0;
 
        // Copy key-value pair from Map to vector of pairs
        std::vector<std::pair<std::string, utils::Timing>> sorted_timings(timings.begin(), timings.end());
        // Sort timings by decreasing time
        std::sort(sorted_timings.begin(), sorted_timings.end(), [](const auto &a, const auto &b) { return a.second > b.second; });
        for (const auto &[name, time] : sorted_timings)
        {
            logger().debug("{:62s}: {:10.3g}s {:5.1f}% ({:6d} calls)", name, time, time / total_time * 100, time.count);
            sum += time;
        }
 
        // logger().debug("Miscellaneous: {:.3g}s {:.1f}%", total_time - sum, (total_time - sum) / total_time * 100);
        if (num_solves > 0)
            logger().debug("Avg. # DOF per solve: {}", total_ndofs / double(num_solves));
 
        std::cout << "--------------------------------------------------------------------------------" << std::endl;
    }
 
    // Static members must be initialized in the source file:
    decltype(Remesher::timings) Remesher::timings;
    double Remesher::total_time = 0;
    size_t Remesher::num_solves = 0;
    size_t Remesher::total_ndofs = 0;
 
} // namespace polyfem::mesh