DOLFINx 0.10.0.0
DOLFINx C++ interface
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xdmf_mesh.h
1// Copyright (C) 2012-2018 Chris N. Richardson 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 "xdmf_utils.h"
10#include <array>
11#include <cstdint>
12#include <dolfinx/mesh/MeshTags.h>
13#include <hdf5.h>
14#include <mpi.h>
15#include <pugixml.hpp>
16#include <span>
17#include <string>
18#include <utility>
19#include <variant>
20#include <vector>
21
22namespace pugi
23{
24class xml_node;
25} // namespace pugi
26
27namespace dolfinx
28{
29
30namespace mesh
31{
32template <std::floating_point T>
33class Geometry;
34template <std::floating_point T>
35class Mesh;
36class Topology;
37} // namespace mesh
38
41{
42
47template <std::floating_point U>
48void add_mesh(MPI_Comm comm, pugi::xml_node& xml_node, hid_t h5_id,
49 const mesh::Mesh<U>& mesh, const std::string& path_prefix);
50
61template <std::floating_point U>
62void add_topology_data(MPI_Comm comm, pugi::xml_node& xml_node, hid_t h5_id,
63 std::string path_prefix, const mesh::Topology& topology,
64 const mesh::Geometry<U>& geometry, int cell_dim,
65 std::span<const std::int32_t> entities);
66
68template <std::floating_point U>
69void add_geometry_data(MPI_Comm comm, pugi::xml_node& xml_node, hid_t h5_id,
70 std::string path_prefix,
72
79std::pair<std::variant<std::vector<float>, std::vector<double>>,
80 std::array<std::size_t, 2>>
81read_geometry_data(MPI_Comm comm, hid_t h5_id, const pugi::xml_node& node);
82
89std::pair<std::vector<std::int64_t>, std::array<std::size_t, 2>>
90read_topology_data(MPI_Comm comm, hid_t h5_id, const pugi::xml_node& node);
91
93template <typename T, std::floating_point U>
94void add_meshtags(MPI_Comm comm, const mesh::MeshTags<T>& meshtags,
95 const mesh::Geometry<U>& geometry, pugi::xml_node& xml_node,
96 hid_t h5_id, const std::string& name)
97{
98 spdlog::info("XDMF: add meshtags ({})", name.c_str());
99 // Get mesh
100 const int dim = meshtags.dim();
101 std::shared_ptr<const common::IndexMap> entity_map
102 = meshtags.topology()->index_map(dim);
103 if (!entity_map)
104 {
105 throw std::runtime_error("Missing entities. Did you forget to call "
106 "dolfinx::mesh::Topology::create_entities?");
107 }
108 const std::int32_t num_local_entities = entity_map->size_local();
109
110 // Find number of tagged entities in local range
111 auto it = std::ranges::lower_bound(meshtags.indices(), num_local_entities);
112 const int num_active_entities = std::distance(meshtags.indices().begin(), it);
113
114 const std::string path_prefix = "/MeshTags/" + name;
116 comm, xml_node, h5_id, path_prefix, *meshtags.topology(), geometry, dim,
117 std::span<const std::int32_t>(meshtags.indices().data(),
118 num_active_entities));
119
120 // Add attribute node with values
121 pugi::xml_node attribute_node = xml_node.append_child("Attribute");
122 assert(attribute_node);
123 attribute_node.append_attribute("Name") = name.c_str();
124 attribute_node.append_attribute("AttributeType") = "Scalar";
125 attribute_node.append_attribute("Center") = "Cell";
126
127 std::int64_t global_num_values = 0;
128 const std::int64_t local_num_values = num_active_entities;
129 MPI_Allreduce(&local_num_values, &global_num_values, 1, MPI_INT64_T, MPI_SUM,
130 comm);
131 const std::int64_t num_local = num_active_entities;
132 std::int64_t offset = 0;
133 MPI_Exscan(&num_local, &offset, 1, MPI_INT64_T, MPI_SUM, comm);
134 const bool use_mpi_io = (dolfinx::MPI::size(comm) > 1);
135 xdmf_utils::add_data_item(
136 attribute_node, h5_id, path_prefix + std::string("/Values"),
137 std::span<const T>(meshtags.values().data(), num_active_entities), offset,
138 {global_num_values, 1}, "", use_mpi_io);
139}
140} // namespace io::xdmf_mesh
141} // namespace dolfinx
Geometry stores the geometry imposed on a mesh.
Definition Geometry.h:34
MeshTags associate values with mesh topology entities.
Definition MeshTags.h:33
std::span< const std::int32_t > indices() const
Definition MeshTags.h:101
std::span< const T > values() const
Values attached to topology entities.
Definition MeshTags.h:104
int dim() const
Return topological dimension of tagged entities.
Definition MeshTags.h:107
std::shared_ptr< const Topology > topology() const
Return topology.
Definition MeshTags.h:110
A Mesh consists of a set of connected and numbered mesh topological entities, and geometry data.
Definition Mesh.h:23
Topology stores the topology of a mesh, consisting of mesh entities and connectivity (incidence relat...
Definition Topology.h:46
int size(MPI_Comm comm)
Definition MPI.cpp:72
Geometry data structures and algorithms.
Definition BoundingBoxTree.h:22
Low-level methods for reading XDMF files.
Definition xdmf_mesh.h:41
std::pair< std::vector< std::int64_t >, std::array< std::size_t, 2 > > read_topology_data(MPI_Comm comm, hid_t h5_id, const pugi::xml_node &node)
Read topology (cell connectivity) data.
Definition xdmf_mesh.cpp:292
std::pair< std::variant< std::vector< float >, std::vector< double > >, std::array< std::size_t, 2 > > read_geometry_data(MPI_Comm comm, hid_t h5_id, const pugi::xml_node &node)
Read geometry (coordinate) data.
Definition xdmf_mesh.cpp:252
void add_meshtags(MPI_Comm comm, const mesh::MeshTags< T > &meshtags, const mesh::Geometry< U > &geometry, pugi::xml_node &xml_node, hid_t h5_id, const std::string &name)
Add mesh tags to XDMF file.
Definition xdmf_mesh.h:94
void add_geometry_data(MPI_Comm comm, pugi::xml_node &xml_node, hid_t h5_id, std::string path_prefix, const mesh::Geometry< U > &geometry)
Add Geometry xml node.
Definition xdmf_mesh.cpp:158
void add_mesh(MPI_Comm comm, pugi::xml_node &xml_node, hid_t h5_id, const mesh::Mesh< U > &mesh, const std::string &path_prefix)
Definition xdmf_mesh.cpp:212
void add_topology_data(MPI_Comm comm, pugi::xml_node &xml_node, hid_t h5_id, std::string path_prefix, const mesh::Topology &topology, const mesh::Geometry< U > &geometry, int cell_dim, std::span< const std::int32_t > entities)
Definition xdmf_mesh.cpp:23
Mesh data structures and algorithms on meshes.
Definition DofMap.h:32
Top-level namespace.
Definition defines.h:12