1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
|
// Copyright (C) 2012-2023 Chris N. Richardson and Garth N. Wells
//
// This file is part of DOLFINx (https://www.fenicsproject.org)
//
// SPDX-License-Identifier: LGPL-3.0-or-later
#include "xdmf_utils.h"
#include <array>
#include <boost/algorithm/string.hpp>
#include <boost/lexical_cast.hpp>
#include <map>
#include <pugixml.hpp>
#include <vector>
using namespace dolfinx;
using namespace dolfinx::io;
namespace
{
template <typename T, std::size_t ndim>
using mdspan_t = md::mdspan<T, md::dextents<std::size_t, ndim>>;
} // namespace
//----------------------------------------------------------------------------
std::pair<std::string, int>
xdmf_utils::get_cell_type(const pugi::xml_node& topology_node)
{
assert(topology_node);
pugi::xml_attribute type_attr = topology_node.attribute("TopologyType");
assert(type_attr);
const static std::map<std::string, std::pair<std::string, int>> xdmf_to_dolfin
= {{"polyvertex", {"point", 1}},
{"polyline", {"interval", 1}},
{"edge_3", {"interval", 2}},
{"triangle", {"triangle", 1}},
{"triangle_6", {"triangle", 2}},
{"tetrahedron", {"tetrahedron", 1}},
{"tetrahedron_10", {"tetrahedron", 2}},
{"quadrilateral", {"quadrilateral", 1}},
{"quadrilateral_8", {"quadrilateral", 2}},
{"quadrilateral_9", {"quadrilateral", 2}},
{"quadrilateral_16", {"quadrilateral", 3}},
{"hexahedron", {"hexahedron", 1}},
{"hexahedron_20", {"hexahedron", 2}},
{"wedge", {"prism", 1}},
{"hexahedron_27", {"hexahedron", 2}}};
// Convert XDMF cell type string to DOLFINx cell type string
std::string cell_type = type_attr.as_string();
std::ranges::transform(cell_type, cell_type.begin(),
[](auto c) { return std::tolower(c); });
auto it = xdmf_to_dolfin.find(cell_type);
if (it == xdmf_to_dolfin.end())
{
throw std::runtime_error("Cannot recognise cell type. Unknown value: "
+ cell_type);
}
return it->second;
}
//----------------------------------------------------------------------------
std::array<std::string, 2>
xdmf_utils::get_hdf5_paths(const pugi::xml_node& dataitem_node)
{
// Check that node is a DataItem node
assert(dataitem_node);
const std::string dataitem_str = "DataItem";
if (dataitem_node.name() != dataitem_str)
{
throw std::runtime_error("Node name is \""
+ std::string(dataitem_node.name())
+ R"(", expecting "DataItem")");
}
// Check that format is HDF
pugi::xml_attribute format_attr = dataitem_node.attribute("Format");
assert(format_attr);
const std::string format = format_attr.as_string();
if (format.compare("HDF") != 0)
{
throw std::runtime_error("DataItem format \"" + format
+ R"(" is not "HDF")");
}
// Get path data
pugi::xml_node path_node = dataitem_node.first_child();
assert(path_node);
// Create string from path and trim leading and trailing whitespace
std::string path = path_node.text().get();
boost::algorithm::trim(path);
// Split string into file path and HD5 internal path
std::vector<std::string> paths;
boost::split(paths, path, boost::is_any_of(":"));
assert(paths.size() == 2);
return {{paths[0], paths[1]}};
}
//-----------------------------------------------------------------------------
std::filesystem::path
xdmf_utils::get_hdf5_filename(const std::filesystem::path& xdmf_filename)
{
std::filesystem::path p = xdmf_filename;
p.replace_extension("h5");
if (p.string() == xdmf_filename)
{
throw std::runtime_error("Cannot deduce name of HDF5 file from XDMF "
"filename. Filename clash. Check XDMF filename");
}
return p;
}
//-----------------------------------------------------------------------------
std::vector<std::int64_t>
xdmf_utils::get_dataset_shape(const pugi::xml_node& dataset_node)
{
// Get Dimensions attribute string
assert(dataset_node);
pugi::xml_attribute dimensions_attr = dataset_node.attribute("Dimensions");
// Gets dimensions, if attribute is present
std::vector<std::int64_t> dims;
if (dimensions_attr)
{
// Split dimensions string
const std::string dims_str = dimensions_attr.as_string();
std::vector<std::string> dims_list;
boost::split(dims_list, dims_str, boost::is_any_of(" "));
// Cast dims to integers
for (const auto& d : dims_list)
dims.push_back(boost::lexical_cast<std::int64_t>(d));
}
return dims;
}
//----------------------------------------------------------------------------
std::int64_t xdmf_utils::get_num_cells(const pugi::xml_node& topology_node)
{
assert(topology_node);
// Get number of cells from topology
std::int64_t num_cells_topology = -1;
pugi::xml_attribute num_cells_attr
= topology_node.attribute("NumberOfElements");
if (num_cells_attr)
num_cells_topology = num_cells_attr.as_llong();
// Get number of cells from topology dataset
pugi::xml_node topology_dataset_node = topology_node.child("DataItem");
assert(topology_dataset_node);
const std::vector tdims = get_dataset_shape(topology_dataset_node);
// Check that number of cells can be determined
if (tdims.size() != 2 and num_cells_topology == -1)
throw std::runtime_error("Cannot determine number of cells in XDMF mesh");
// Check for consistency if number of cells appears in both the
// topology and DataItem nodes
if (num_cells_topology != -1 and tdims.size() == 2)
{
if (num_cells_topology != tdims[0])
throw std::runtime_error("Cannot determine number of cells in XDMF mesh");
}
return std::max(num_cells_topology, tdims[0]);
}
//----------------------------------------------------------------------------
std::string xdmf_utils::vtk_cell_type_str(mesh::CellType cell_type,
int num_nodes)
{
static const std::map<mesh::CellType, std::map<int, std::string>> vtk_map
= {{mesh::CellType::point, {{1, "PolyVertex"}}},
{mesh::CellType::interval, {{2, "PolyLine"}, {3, "Edge_3"}}},
{mesh::CellType::triangle,
{{3, "Triangle"}, {6, "Triangle_6"}, {10, "Triangle_10"}}},
{mesh::CellType::quadrilateral,
{{4, "Quadrilateral"},
{8, "Quadrilateral_8"},
{9, "Quadrilateral_9"},
{16, "Quadrilateral_16"}}},
{mesh::CellType::prism, {{6, "Wedge"}}},
{mesh::CellType::tetrahedron,
{{4, "Tetrahedron"}, {10, "Tetrahedron_10"}, {20, "Tetrahedron_20"}}},
{mesh::CellType::hexahedron,
{{8, "Hexahedron"}, {27, "Hexahedron_27"}, {20, "Hexahedron_20"}}}};
// Get cell family
auto cell = vtk_map.find(cell_type);
if (cell == vtk_map.end())
throw std::runtime_error("Could not find cell type.");
// Get cell string
auto cell_str = cell->second.find(num_nodes);
if (cell_str == cell->second.end())
throw std::runtime_error("Could not find VTK string for cell order.");
return cell_str->second;
}
//-----------------------------------------------------------------------------
|
