vtk_utils.h

// Copyright (C) 2020-2022 Garth N. Wells and Jørgen S. Dokken
//
// This file is part of DOLFINx (https://www.fenicsproject.org)
//
// SPDX-License-Identifier:    LGPL-3.0-or-later
 
#pragma once
 
#include "cells.h"
#include "vtk_utils.h"
#include <array>
#include <basix/mdspan.hpp>
#include <concepts>
#include <cstdint>
#include <dolfinx/common/IndexMap.h>
#include <dolfinx/fem/DofMap.h>
#include <dolfinx/fem/FiniteElement.h>
#include <dolfinx/fem/FunctionSpace.h>
#include <dolfinx/mesh/Geometry.h>
#include <dolfinx/mesh/Mesh.h>
#include <dolfinx/mesh/Topology.h>
#include <span>
#include <tuple>
#include <vector>
 
namespace dolfinx
{
namespace fem
{
template <std::floating_point T>
class FunctionSpace;
}
 
namespace mesh
{
enum class CellType;
template <std::floating_point T>
class Geometry;
} // namespace mesh
 
namespace io
{
namespace impl
{
template <typename T>
std::tuple<std::vector<T>, std::array<std::size_t, 2>,
           std::vector<std::int64_t>, std::vector<std::uint8_t>>
tabulate_lagrange_dof_coordinates(const fem::FunctionSpace<T>& V)
{
  auto mesh = V.mesh();
  assert(mesh);
  auto topology = mesh->topology();
  assert(topology);
  const std::size_t gdim = mesh->geometry().dim();
  const int tdim = topology->dim();
 
  // Get dofmap data
  auto dofmap = V.dofmap();
  assert(dofmap);
  auto map_dofs = dofmap->index_map;
  assert(map_dofs);
  const int index_map_bs = dofmap->index_map_bs();
  const int dofmap_bs = dofmap->bs();
 
  // Get element data
  auto element = V.element();
  assert(element);
  const int e_bs = element->block_size();
  const std::size_t scalar_dofs = element->space_dimension() / e_bs;
  const std::size_t num_nodes
      = index_map_bs * (map_dofs->size_local() + map_dofs->num_ghosts())
        / dofmap_bs;
 
  // Get the dof coordinates on the reference element and the  mesh
  // coordinate map
  const auto [X, Xshape] = element->interpolation_points();
  const fem::CoordinateElement<T>& cmap = mesh->geometry().cmaps()[0];
 
  // Prepare cell geometry
  auto dofmap_x = mesh->geometry().dofmap();
  std::span<const T> x_g = mesh->geometry().x();
  const std::size_t num_dofs_g = cmap.dim();
 
  std::span<const std::uint32_t> cell_info;
  if (element->needs_dof_transformations())
  {
    mesh->topology_mutable()->create_entity_permutations();
    cell_info = std::span(mesh->topology()->get_cell_permutation_info());
  }
  auto apply_dof_transformation
      = element->template get_dof_transformation_function<T>();
 
  using mdspan2_t = MDSPAN_IMPL_STANDARD_NAMESPACE::mdspan<
      T, MDSPAN_IMPL_STANDARD_NAMESPACE::dextents<std::size_t, 2>>;
  using cmdspan4_t = MDSPAN_IMPL_STANDARD_NAMESPACE::mdspan<
      T, MDSPAN_IMPL_STANDARD_NAMESPACE::dextents<std::size_t, 4>>;
 
  // Tabulate basis functions at node reference coordinates
  const std::array<std::size_t, 4> phi_shape
      = cmap.tabulate_shape(0, Xshape[0]);
  std::vector<T> phi_b(
      std::reduce(phi_shape.begin(), phi_shape.end(), 1, std::multiplies{}));
  cmdspan4_t phi_full(phi_b.data(), phi_shape);
  cmap.tabulate(0, X, Xshape, phi_b);
  auto phi = MDSPAN_IMPL_STANDARD_NAMESPACE::MDSPAN_IMPL_PROPOSED_NAMESPACE::
      submdspan(phi_full, 0, MDSPAN_IMPL_STANDARD_NAMESPACE::full_extent,
                MDSPAN_IMPL_STANDARD_NAMESPACE::full_extent, 0);
 
  // Loop over cells and tabulate dofs
  auto map = topology->index_map(tdim);
  assert(map);
  const std::int32_t num_cells = map->size_local() + map->num_ghosts();
  std::vector<T> x_b(scalar_dofs * gdim);
  mdspan2_t x(x_b.data(), scalar_dofs, gdim);
  std::vector<T> coordinate_dofs_b(num_dofs_g * gdim);
  mdspan2_t coordinate_dofs(coordinate_dofs_b.data(), num_dofs_g, gdim);
 
  std::vector<T> coords(num_nodes * 3, 0.0);
  std::array<std::size_t, 2> cshape = {num_nodes, 3};
  for (std::int32_t c = 0; c < num_cells; ++c)
  {
    // Extract cell geometry
    for (std::size_t i = 0; i < dofmap_x.extent(1); ++i)
      for (std::size_t j = 0; j < gdim; ++j)
        coordinate_dofs(i, j) = x_g[3 * dofmap_x(c, i) + j];
 
    // Tabulate dof coordinates on cell
    cmap.push_forward(x, coordinate_dofs, phi);
    apply_dof_transformation(x_b, std::span(cell_info.data(), cell_info.size()),
                             c, x.extent(1));
 
    // Copy dof coordinates into vector
    auto dofs = dofmap->cell_dofs(c);
    for (std::size_t i = 0; i < dofs.size(); ++i)
    {
      std::int32_t dof = dofs[i];
      for (std::size_t j = 0; j < gdim; ++j)
        coords[3 * dof + j] = x(i, j);
    }
  }
 
  // Original point IDs
  std::vector<std::int64_t> x_id(num_nodes);
  std::array<std::int64_t, 2> range = map_dofs->local_range();
  std::int32_t size_local = range[1] - range[0];
  std::iota(x_id.begin(), std::next(x_id.begin(), size_local), range[0]);
  const std::vector<std::int64_t>& ghosts = map_dofs->ghosts();
  std::copy(ghosts.begin(), ghosts.end(), std::next(x_id.begin(), size_local));
 
  // Ghosts
  std::vector<std::uint8_t> id_ghost(num_nodes, 0);
  std::fill(std::next(id_ghost.begin(), size_local), id_ghost.end(), 1);
 
  return {std::move(coords), cshape, std::move(x_id), std::move(id_ghost)};
}
 
} // namespace impl
 
template <typename T>
std::tuple<std::vector<T>, std::array<std::size_t, 2>,
           std::vector<std::int64_t>, std::vector<std::uint8_t>,
           std::vector<std::int64_t>, std::array<std::size_t, 2>>
vtk_mesh_from_space(const fem::FunctionSpace<T>& V)
{
  auto mesh = V.mesh();
  assert(mesh);
  auto topology = mesh->topology();
  assert(topology);
  const int tdim = topology->dim();
 
  assert(V.element());
  if (V.element()->is_mixed())
    throw std::runtime_error("Can't create VTK mesh from a mixed element");
 
  const auto [x, xshape, x_id, x_ghost]
      = impl::tabulate_lagrange_dof_coordinates(V);
  auto map = topology->index_map(tdim);
  const std::size_t num_cells = map->size_local() + map->num_ghosts();
 
  // Create permutation from DOLFINx dof ordering to VTK
  auto dofmap = V.dofmap();
  assert(dofmap);
  const int element_block_size = V.element()->block_size();
  const std::uint32_t num_nodes
      = V.element()->space_dimension() / element_block_size;
  const std::vector<std::uint8_t> vtkmap = io::cells::transpose(
      io::cells::perm_vtk(topology->cell_types()[0], num_nodes));
 
  // Extract topology for all local cells as
  // [v0_0, ...., v0_N0, v1_0, ...., v1_N1, ....]
  std::array<std::size_t, 2> shape = {num_cells, num_nodes};
  std::vector<std::int64_t> vtk_topology(shape[0] * shape[1]);
  for (std::size_t c = 0; c < shape[0]; ++c)
  {
    auto dofs = dofmap->cell_dofs(c);
    for (std::size_t i = 0; i < dofs.size(); ++i)
      vtk_topology[c * shape[1] + i] = dofs[vtkmap[i]];
  }
 
  return {std::move(x),
          xshape,
          std::move(x_id),
          std::move(x_ghost),
          std::move(vtk_topology),
          shape};
}
 
std::pair<std::vector<std::int64_t>, std::array<std::size_t, 2>>
extract_vtk_connectivity(
    MDSPAN_IMPL_STANDARD_NAMESPACE::mdspan<
        const std::int32_t,
        MDSPAN_IMPL_STANDARD_NAMESPACE::dextents<std::size_t, 2>>
        dofmap_x,
    mesh::CellType cell_type);
} // namespace io
} // namespace dolfinx