DOLFINx 0.10.0.0
DOLFINx C++ interface
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Geometry.h
1// Copyright (C) 2006-2022 Anders Logg and Garth N. Wells
2//
3// This file is part of DOLFINx (https://www.fenicsproject.org)
4//
5// SPDX-License-Identifier: LGPL-3.0-or-later
6
7#pragma once
8
9#include "Topology.h"
10#include <algorithm>
11#include <basix/mdspan.hpp>
12#include <concepts>
13#include <cstdint>
14#include <dolfinx/common/IndexMap.h>
15#include <dolfinx/common/MPI.h>
16#include <dolfinx/common/sort.h>
17#include <dolfinx/fem/CoordinateElement.h>
18#include <dolfinx/fem/ElementDofLayout.h>
19#include <dolfinx/fem/dofmapbuilder.h>
20#include <dolfinx/graph/AdjacencyList.h>
21#include <dolfinx/graph/partition.h>
22#include <functional>
23#include <memory>
24#include <span>
25#include <utility>
26#include <vector>
27
28namespace dolfinx::mesh
29{
30
32template <std::floating_point T>
34{
35public:
37 using value_type = T;
38
62 template <typename U, typename V, typename W>
63 requires std::is_convertible_v<std::remove_cvref_t<U>,
64 std::vector<std::vector<std::int32_t>>>
65 and std::is_convertible_v<std::remove_cvref_t<V>,
66 std::vector<T>>
67 and std::is_convertible_v<std::remove_cvref_t<W>,
68 std::vector<std::int64_t>>
70 std::shared_ptr<const common::IndexMap> index_map, U&& dofmaps,
71 const std::vector<fem::CoordinateElement<
72 typename std::remove_reference_t<typename V::value_type>>>& elements,
73 V&& x, int dim, W&& input_global_indices)
74 : _dim(dim), _dofmaps(std::forward<U>(dofmaps)), _index_map(index_map),
75 _cmaps(elements), _x(std::forward<V>(x)),
76 _input_global_indices(std::forward<W>(input_global_indices))
77 {
78 assert(_x.size() % 3 == 0);
79 if (_x.size() / 3 != _input_global_indices.size())
80 throw std::runtime_error("Geometry size mismatch.");
81
82 if (_dofmaps.size() != _cmaps.size())
83 {
84 throw std::runtime_error("Geometry number of dofmaps not equal to the "
85 "number of coordinate elements.");
86 }
87
88 // TODO: check that elements dim == number of dofmap columns
89 }
90
92 Geometry(const Geometry&) = default;
93
95 Geometry(Geometry&&) = default;
96
98 ~Geometry() = default;
99
101 Geometry& operator=(const Geometry&) = delete;
102
105
107 int dim() const { return _dim; }
108
111 md::mdspan<const std::int32_t, md::dextents<std::size_t, 2>> dofmap() const
112 {
113 if (_dofmaps.size() != 1)
114 throw std::runtime_error("Multiple dofmaps");
115 return this->dofmap(0);
116 }
117
124 md::mdspan<const std::int32_t, md::dextents<std::size_t, 2>>
125 dofmap(std::size_t i) const
126 {
127 std::size_t ndofs = _cmaps.at(i).dim();
128 return md::mdspan<const std::int32_t, md::dextents<std::size_t, 2>>(
129 _dofmaps.at(i).data(), _dofmaps.at(i).size() / ndofs, ndofs);
130 }
131
134 std::shared_ptr<const common::IndexMap> index_map() const
135 {
136 return _index_map;
137 }
138
143 std::span<const value_type> x() const { return _x; }
144
150 std::span<value_type> x() { return _x; }
151
158 const std::vector<fem::CoordinateElement<value_type>>& cmaps() const
159 {
160 return _cmaps;
161 }
162
167 {
168 if (_cmaps.size() > 1)
169 throw std::runtime_error("Multiple cmaps.");
170 return _cmaps.front();
171 }
172
174 const std::vector<std::int64_t>& input_global_indices() const
175 {
176 return _input_global_indices;
177 }
178
179private:
180 // Geometric dimension
181 int _dim;
182
183 // Map per cell for extracting coordinate data for each cmap
184 std::vector<std::vector<std::int32_t>> _dofmaps;
185
186 // IndexMap for geometry 'dofmap'
187 std::shared_ptr<const common::IndexMap> _index_map;
188
189 // The coordinate elements
190 std::vector<fem::CoordinateElement<value_type>> _cmaps;
191
192 // Coordinates for all points stored as a contiguous array (row-major,
193 // column size = 3)
194 std::vector<value_type> _x;
195
196 // Global indices as provided on Geometry creation
197 std::vector<std::int64_t> _input_global_indices;
198};
199
202template <typename U, typename V, typename W>
203Geometry(std::shared_ptr<const common::IndexMap>, U&&,
204 const std::vector<fem::CoordinateElement<
205 typename std::remove_reference_t<typename V::value_type>>>&,
206 V&&, int, W&&)
207 -> Geometry<typename std::remove_cvref_t<typename V::value_type>>;
209
234template <typename U>
235Geometry<typename std::remove_reference_t<typename U::value_type>>
237 const Topology& topology,
238 const std::vector<fem::CoordinateElement<
239 std::remove_reference_t<typename U::value_type>>>& elements,
240 std::span<const std::int64_t> nodes, std::span<const std::int64_t> xdofs,
241 const U& x, int dim,
242 std::function<std::vector<int>(const graph::AdjacencyList<std::int32_t>&)>
243 reorder_fn
244 = nullptr)
245{
246 spdlog::info("Create Geometry (multiple)");
247
248 assert(std::ranges::is_sorted(nodes));
249 using T = typename std::remove_reference_t<typename U::value_type>;
250
251 // Check elements match cell types in topology
252 const int tdim = topology.dim();
253 const std::size_t num_cell_types = topology.entity_types(tdim).size();
254 if (elements.size() != num_cell_types)
255 throw std::runtime_error("Mismatch between topology and geometry.");
256
257 std::vector<fem::ElementDofLayout> dof_layouts;
258 for (const auto& el : elements)
259 dof_layouts.push_back(el.create_dof_layout());
260
261 spdlog::info("Got {} dof layouts", dof_layouts.size());
262
263 // Build 'geometry' dofmap on the topology
264 auto [_dof_index_map, bs, dofmaps]
265 = fem::build_dofmap_data(topology.index_maps(topology.dim())[0]->comm(),
266 topology, dof_layouts, reorder_fn);
267 auto dof_index_map
268 = std::make_shared<common::IndexMap>(std::move(_dof_index_map));
269
270 // If the mesh has higher order geometry, permute the dofmap
271 if (elements.front().needs_dof_permutations())
272 {
273 const std::int32_t num_cells
274 = topology.connectivity(topology.dim(), 0)->num_nodes();
275 const std::vector<std::uint32_t>& cell_info
276 = topology.get_cell_permutation_info();
277 int d = elements.front().dim();
278 for (std::int32_t cell = 0; cell < num_cells; ++cell)
279 {
280 std::span dofs(dofmaps.front().data() + cell * d, d);
281 elements.front().permute_inv(dofs, cell_info[cell]);
282 }
283 }
284
285 spdlog::info("Calling compute_local_to_global");
286 // Compute local-to-global map from local indices in dofmap to the
287 // corresponding global indices in cells, and pass to function to
288 // compute local (dof) to local (position in coords) map from (i)
289 // local-to-global for dofs and (ii) local-to-global for entries in
290 // coords
291
292 spdlog::info("xdofs.size = {}", xdofs.size());
293 std::vector<std::int32_t> all_dofmaps;
294 std::stringstream s;
295 for (auto q : dofmaps)
296 {
297 s << q.size() << " ";
298 all_dofmaps.insert(all_dofmaps.end(), q.begin(), q.end());
299 }
300 spdlog::info("dofmap sizes = {}", s.str());
301 spdlog::info("all_dofmaps.size = {}", all_dofmaps.size());
302 spdlog::info("nodes.size = {}", nodes.size());
303
304 const std::vector<std::int32_t> l2l = graph::build::compute_local_to_local(
305 graph::build::compute_local_to_global(xdofs, all_dofmaps), nodes);
306
307 // Allocate space for input global indices and copy data
308 std::vector<std::int64_t> igi(nodes.size());
309 std::ranges::transform(l2l, igi.begin(),
310 [&nodes](auto index) { return nodes[index]; });
311
312 // Build coordinate dof array, copying coordinates to correct position
313 assert(x.size() % dim == 0);
314 const std::size_t shape0 = x.size() / dim;
315 const std::size_t shape1 = dim;
316 std::vector<T> xg(3 * shape0, 0);
317 for (std::size_t i = 0; i < shape0; ++i)
318 {
319 std::copy_n(std::next(x.begin(), shape1 * l2l[i]), shape1,
320 std::next(xg.begin(), 3 * i));
321 }
322
323 spdlog::info("Creating geometry with {} dofmaps", dof_layouts.size());
324
325 return Geometry(dof_index_map, std::move(dofmaps), elements, std::move(xg),
326 dim, std::move(igi));
327}
328
329} // namespace dolfinx::mesh
Definition CoordinateElement.h:38
Definition AdjacencyList.h:27
Geometry stores the geometry imposed on a mesh.
Definition Geometry.h:34
~Geometry()=default
Destructor.
std::span< value_type > x()
Access geometry degrees-of-freedom data (non-const version).
Definition Geometry.h:150
Geometry(std::shared_ptr< const common::IndexMap > index_map, U &&dofmaps, const std::vector< fem::CoordinateElement< typename std::remove_reference_t< typename V::value_type > > > &elements, V &&x, int dim, W &&input_global_indices)
Constructor of object that holds mesh geometry data.
Definition Geometry.h:69
md::mdspan< const std::int32_t, md::dextents< std::size_t, 2 > > dofmap(std::size_t i) const
Degree-of-freedom map associated with the ith coordinate map element in the geometry.
Definition Geometry.h:125
std::shared_ptr< const common::IndexMap > index_map() const
Index map for the geometry 'degrees-of-freedom'.
Definition Geometry.h:134
Geometry(Geometry &&)=default
Move constructor.
Geometry(const Geometry &)=default
Copy constructor.
const fem::CoordinateElement< value_type > & cmap() const
The element that describes the geometry map.
Definition Geometry.h:166
int dim() const
Return dimension of the Euclidean coordinate system.
Definition Geometry.h:107
Geometry & operator=(Geometry &&)=default
Move assignment.
md::mdspan< const std::int32_t, md::dextents< std::size_t, 2 > > dofmap() const
DofMap for the geometry.
Definition Geometry.h:111
const std::vector< std::int64_t > & input_global_indices() const
Global user indices.
Definition Geometry.h:174
std::span< const value_type > x() const
Access geometry degrees-of-freedom data (const version).
Definition Geometry.h:143
Geometry & operator=(const Geometry &)=delete
Copy assignment.
const std::vector< fem::CoordinateElement< value_type > > & cmaps() const
The elements that describes the geometry map.
Definition Geometry.h:158
T value_type
Value type.
Definition Geometry.h:37
Topology stores the topology of a mesh, consisting of mesh entities and connectivity (incidence relat...
Definition Topology.h:46
const std::vector< std::uint32_t > & get_cell_permutation_info() const
Returns the permutation information.
Definition Topology.cpp:852
std::shared_ptr< const graph::AdjacencyList< std::int32_t > > connectivity(std::array< int, 2 > d0, std::array< int, 2 > d1) const
Get the connectivity from entities of topological dimension d0 to dimension d1.
Definition Topology.cpp:832
const std::vector< CellType > & entity_types(int dim) const
Entity types in the topology for a given dimension.
Definition Topology.cpp:790
int dim() const noexcept
Topological dimension of the mesh.
Definition Topology.cpp:785
std::vector< std::shared_ptr< const common::IndexMap > > index_maps(int dim) const
Get the index maps that described the parallel distribution of the mesh entities of a given topologic...
Definition Topology.cpp:811
std::tuple< common::IndexMap, int, std::vector< std::vector< std::int32_t > > > build_dofmap_data(MPI_Comm comm, const mesh::Topology &topology, const std::vector< ElementDofLayout > &element_dof_layouts, const std::function< std::vector< int >(const graph::AdjacencyList< std::int32_t > &)> &reorder_fn)
Definition dofmapbuilder.cpp:627
std::vector< std::int64_t > compute_local_to_global(std::span< const std::int64_t > global, std::span< const std::int32_t > local)
Definition partition.cpp:534
std::vector< std::int32_t > compute_local_to_local(std::span< const std::int64_t > local0_to_global, std::span< const std::int64_t > local1_to_global)
Compute a local0-to-local1 map from two local-to-global maps with common global indices.
Definition partition.cpp:556
Mesh data structures and algorithms on meshes.
Definition DofMap.h:32
Geometry< typename std::remove_reference_t< typename U::value_type > > create_geometry(const Topology &topology, const std::vector< fem::CoordinateElement< std::remove_reference_t< typename U::value_type > > > &elements, std::span< const std::int64_t > nodes, std::span< const std::int64_t > xdofs, const U &x, int dim, std::function< std::vector< int >(const graph::AdjacencyList< std::int32_t > &)> reorder_fn=nullptr)
Build Geometry from input data.
Definition Geometry.h:236