DOLFINx
DOLFINx C++ interface
xdmf_meshtags.h
1 // Copyright (C) 2020 Michal Habera
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 "pugixml.hpp"
10 #include "xdmf_mesh.h"
11 #include "xdmf_utils.h"
12 #include <dolfinx/common/MPI.h>
13 #include <dolfinx/common/log.h>
14 #include <dolfinx/mesh/MeshTags.h>
15 #include <hdf5.h>
16 #include <string>
17 #include <vector>
18 #include <xtl/xspan.hpp>
19 
20 namespace dolfinx
21 {
22 namespace io
23 {
24 namespace xdmf_meshtags
25 {
26 
28 template <typename T>
29 void add_meshtags(MPI_Comm comm, const mesh::MeshTags<T>& meshtags,
30  pugi::xml_node& xml_node, const hid_t h5_id,
31  const std::string name)
32 {
33  LOG(INFO) << "XDMF: add meshtags (" << name << ")";
34  // Get mesh
35  assert(meshtags.mesh());
36  std::shared_ptr<const mesh::Mesh> mesh = meshtags.mesh();
37  const int dim = meshtags.dim();
38 
39  const std::int32_t num_local_entities
40  = mesh->topology().index_map(dim)->size_local();
41 
42  // Find number of tagged entities in local range
43  auto it = std::lower_bound(meshtags.indices().begin(),
44  meshtags.indices().end(), num_local_entities);
45  const int num_active_entities = std::distance(meshtags.indices().begin(), it);
46 
47  const std::string path_prefix = "/MeshTags/" + name;
49  comm, xml_node, h5_id, path_prefix, mesh->topology(), mesh->geometry(),
50  dim,
51  xtl::span<const std::int32_t>(meshtags.indices().data(),
52  num_active_entities));
53 
54  // Add attribute node with values
55  pugi::xml_node attribute_node = xml_node.append_child("Attribute");
56  assert(attribute_node);
57  attribute_node.append_attribute("Name") = name.c_str();
58  attribute_node.append_attribute("AttributeType") = "Scalar";
59  attribute_node.append_attribute("Center") = "Cell";
60 
61  std::int64_t global_num_values = 0;
62  const std::int64_t local_num_values = num_active_entities;
63  MPI_Allreduce(&local_num_values, &global_num_values, 1, MPI_INT64_T, MPI_SUM,
64  comm);
65  const std::int64_t num_local = num_active_entities;
66  std::int64_t offset = 0;
67  MPI_Exscan(&num_local, &offset, 1, MPI_INT64_T, MPI_SUM, comm);
68  const bool use_mpi_io = (dolfinx::MPI::size(comm) > 1);
69  xdmf_utils::add_data_item(
70  attribute_node, h5_id, path_prefix + std::string("/Values"),
71  xtl::span<const T>(meshtags.values().data(), num_active_entities), offset,
72  {global_num_values, 1}, "", use_mpi_io);
73 }
74 
75 } // namespace xdmf_meshtags
76 } // namespace io
77 } // namespace dolfinx
int size(MPI_Comm comm)
Return size of the group (number of processes) associated with the communicator.
Definition: MPI.cpp:83
void add_topology_data(MPI_Comm comm, pugi::xml_node &xml_node, const hid_t h5_id, const std::string path_prefix, const mesh::Topology &topology, const mesh::Geometry &geometry, int cell_dim, const xtl::span< const std::int32_t > &entities)
Add Topology xml node.
Definition: xdmf_mesh.cpp:18