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1 | // SPDX-FileCopyrightText: 2022-2023 Dennis Gläser <dennis.glaeser@iws.uni-stuttgart.de> | ||
2 | // SPDX-License-Identifier: MIT | ||
3 | /*! | ||
4 | * \file | ||
5 | * \ingroup VTK | ||
6 | * \brief Writer for the VTK HDF file format for unstructured grids. | ||
7 | */ | ||
8 | #ifndef GRIDFORMAT_VTK_HDF_UNSTRUCTURED_GRID_WRITER_HPP_ | ||
9 | #define GRIDFORMAT_VTK_HDF_UNSTRUCTURED_GRID_WRITER_HPP_ | ||
10 | #if GRIDFORMAT_HAVE_HIGH_FIVE | ||
11 | |||
12 | #include <type_traits> | ||
13 | #include <ostream> | ||
14 | |||
15 | #include <gridformat/common/exceptions.hpp> | ||
16 | #include <gridformat/common/md_layout.hpp> | ||
17 | #include <gridformat/common/concepts.hpp> | ||
18 | #include <gridformat/common/lvalue_reference.hpp> | ||
19 | |||
20 | #include <gridformat/parallel/communication.hpp> | ||
21 | #include <gridformat/parallel/concepts.hpp> | ||
22 | |||
23 | #include <gridformat/grid/concepts.hpp> | ||
24 | #include <gridformat/grid/writer.hpp> | ||
25 | |||
26 | #include <gridformat/vtk/common.hpp> | ||
27 | #include <gridformat/vtk/hdf_common.hpp> | ||
28 | |||
29 | namespace GridFormat { | ||
30 | |||
31 | template<bool is_transient, | ||
32 | Concepts::UnstructuredGrid G, | ||
33 | Concepts::Communicator Communicator = NullCommunicator> | ||
34 | class VTKHDFUnstructuredGridWriterImpl : public GridDetail::WriterBase<is_transient, G>::type { | ||
35 | static constexpr int root_rank = 0; | ||
36 | static constexpr std::size_t vtk_space_dim = 3; | ||
37 | |||
38 | using CT = CoordinateType<G>; | ||
39 | template<typename T> using Vector = std::array<T, vtk_space_dim>; | ||
40 | template<typename T> using Tensor = std::array<T, vtk_space_dim*vtk_space_dim>; | ||
41 | |||
42 | using IOContext = VTKHDF::IOContext; | ||
43 | using HDF5File = HDF5::File<Communicator>; | ||
44 | |||
45 | static constexpr WriterOptions writer_opts{ | ||
46 | .use_structured_grid_ordering = false, | ||
47 | .append_null_terminator_to_strings = true | ||
48 | }; | ||
49 | |||
50 | struct TimeSeriesOffsets { | ||
51 | std::size_t cell_offset; | ||
52 | std::size_t connectivity_offset; | ||
53 | std::size_t point_offset; | ||
54 | }; | ||
55 | |||
56 | public: | ||
57 | using Grid = G; | ||
58 | |||
59 | 11 | explicit VTKHDFUnstructuredGridWriterImpl(LValueReferenceOf<const Grid> grid) | |
60 | requires(!is_transient && std::is_same_v<Communicator, NullCommunicator>) | ||
61 |
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55 | : GridWriter<Grid>(grid.get(), ".hdf", writer_opts) |
62 | 11 | {} | |
63 | |||
64 | 41 | explicit VTKHDFUnstructuredGridWriterImpl(LValueReferenceOf<const Grid> grid, const Communicator& comm) | |
65 | requires(!is_transient && std::is_copy_constructible_v<Communicator>) | ||
66 | : GridWriter<Grid>(grid.get(), ".hdf", writer_opts) | ||
67 |
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205 | , _comm{comm} |
68 | 41 | {} | |
69 | |||
70 | 12 | explicit VTKHDFUnstructuredGridWriterImpl(LValueReferenceOf<const Grid> grid, | |
71 | std::string filename_without_extension, | ||
72 | VTK::HDFTransientOptions opts = {}) | ||
73 | requires(is_transient && std::is_same_v<Communicator, NullCommunicator>) | ||
74 | : TimeSeriesGridWriter<Grid>(grid.get(), writer_opts) | ||
75 | , _comm{} | ||
76 |
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12 | , _timeseries_filename{std::move(filename_without_extension) + ".hdf"} |
77 |
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24 | , _transient_opts{std::move(opts)} |
78 | 12 | {} | |
79 | |||
80 | 21 | explicit VTKHDFUnstructuredGridWriterImpl(LValueReferenceOf<const Grid> grid, | |
81 | const Communicator& comm, | ||
82 | std::string filename_without_extension, | ||
83 | VTK::HDFTransientOptions opts = {}) | ||
84 | requires(is_transient && std::is_copy_constructible_v<Communicator>) | ||
85 | : TimeSeriesGridWriter<Grid>(grid.get(), writer_opts) | ||
86 | 20 | , _comm{comm} | |
87 |
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21 | , _timeseries_filename{std::move(filename_without_extension) + ".hdf"} |
88 |
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42 | , _transient_opts{std::move(opts)} |
89 | 21 | {} | |
90 | |||
91 | const Communicator& communicator() const { | ||
92 | return _comm; | ||
93 | } | ||
94 | |||
95 | private: | ||
96 | ✗ | void _write(std::ostream&) const { | |
97 | ✗ | throw InvalidState("VTKHDFUnstructuredGridWriter does not support export into stream"); | |
98 | } | ||
99 | |||
100 | 61 | void _write(const std::string& filename_with_ext) const { | |
101 | if constexpr (is_transient) | ||
102 | throw InvalidState("This overload only works for non-transient output"); | ||
103 |
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61 | HDF5File file{filename_with_ext, _comm, HDF5File::overwrite}; |
104 |
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61 | _write_to(file); |
105 | 61 | } | |
106 | |||
107 | 141 | std::string _write(double t) { | |
108 | if constexpr (!is_transient) | ||
109 | throw InvalidState("This overload only works for transient output"); | ||
110 | |||
111 |
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141 | if (this->_step_count == 0) |
112 |
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33 | HDF5File::clear(_timeseries_filename, _comm); |
113 | |||
114 |
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141 | HDF5File file{_timeseries_filename, _comm, HDF5File::append}; |
115 |
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141 | const auto offsets = _write_to(file); |
116 | |||
117 |
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141 | file.write_attribute(this->_step_count+1, "/VTKHDF/Steps/NSteps"); |
118 |
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423 | file.write(std::array{t}, "VTKHDF/Steps/Values"); |
119 |
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705 | file.write(std::vector{offsets.point_offset}, "VTKHDF/Steps/PointOffsets"); |
120 |
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705 | file.write(std::vector{std::array{offsets.cell_offset}}, "/VTKHDF/Steps/CellOffsets"); |
121 |
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705 | file.write(std::vector{std::array{offsets.connectivity_offset}}, "VTKHDF/Steps/ConnectivityIdOffsets"); |
122 | |||
123 |
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705 | file.write(std::vector{Parallel::size(_comm)}, "/VTKHDF/Steps/NumberOfParts"); |
124 |
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141 | if (this->_step_count > 0 && _transient_opts.static_grid) { |
125 |
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16 | file.write( |
126 |
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12 | std::vector{_get_last_step_data(file, "PartOffsets")}, |
127 | "/VTKHDF/Steps/PartOffsets" | ||
128 | ); | ||
129 | } else { | ||
130 | 274 | const std::size_t offset = this->_step_count == 0 | |
131 |
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137 | ? 0 |
132 |
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137 | : _get_last_step_data(file, "PartOffsets") + Parallel::size(_comm); |
133 |
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685 | file.write(std::vector{offset}, "/VTKHDF/Steps/PartOffsets"); |
134 | } | ||
135 | |||
136 |
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282 | return _timeseries_filename; |
137 | 141 | } | |
138 | |||
139 | 292 | TimeSeriesOffsets _write_to(HDF5File& file) const { | |
140 |
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584 | file.write_attribute(std::array<std::size_t, 2>{(is_transient ? 2 : 1), 0}, "/VTKHDF/Version"); |
141 |
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292 | file.write_attribute("UnstructuredGrid", "/VTKHDF/Type"); |
142 | |||
143 | TimeSeriesOffsets offsets; | ||
144 |
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292 | const auto context = IOContext::from(this->grid(), _comm, root_rank); |
145 |
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292 | _write_num_cells_and_points(file, context); |
146 |
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292 | offsets.point_offset = _write_coordinates(file, context); |
147 |
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292 | offsets.connectivity_offset = _write_connectivity(file, context); |
148 |
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292 | offsets.cell_offset = _write_types(file, context); |
149 |
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292 | _write_offsets(file, context); |
150 |
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292 | _write_meta_data(file); |
151 |
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292 | _write_point_fields(file, context); |
152 |
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292 | _write_cell_fields(file, context); |
153 | |||
154 | 584 | return offsets; | |
155 | 292 | } | |
156 | |||
157 | 292 | void _write_num_cells_and_points(HDF5File& file, const IOContext& context) const { | |
158 |
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1168 | _write_values(file, "/VTKHDF/NumberOfPoints", std::vector{number_of_points(this->grid())}, context); |
159 |
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1168 | _write_values(file, "/VTKHDF/NumberOfCells", std::vector{number_of_cells(this->grid())}, context); |
160 | 292 | } | |
161 | |||
162 | 292 | std::size_t _write_coordinates(HDF5File& file, const IOContext& context) const { | |
163 | if constexpr (is_transient) { | ||
164 |
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216 | if (this->_step_count > 0 && _transient_opts.static_grid) |
165 |
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8 | return _get_last_step_data(file, "PointOffsets"); |
166 | } | ||
167 |
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288 | const auto coords_field = VTK::make_coordinates_field<CT>(this->grid(), false); |
168 |
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288 | const auto offset = _get_current_offset(file, "/VTKHDF/Points"); |
169 |
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576 | _write_point_field(file, "/VTKHDF/Points", *coords_field, context); |
170 | 288 | return offset; | |
171 | 288 | } | |
172 | |||
173 | 292 | std::size_t _write_connectivity(HDF5File& file, const IOContext& context) const { | |
174 | if constexpr (is_transient) { | ||
175 |
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216 | if (this->_step_count > 0 && _transient_opts.static_grid) |
176 |
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8 | return _get_last_step_data(file, "ConnectivityIdOffsets"); |
177 | } | ||
178 |
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288 | const auto point_id_map = make_point_id_map(this->grid()); |
179 |
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288 | const auto connectivity_field = VTK::make_connectivity_field(this->grid(), point_id_map); |
180 |
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288 | const auto num_entries = connectivity_field->layout().number_of_entries(); |
181 |
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864 | const auto my_num_ids = std::vector{static_cast<long>(num_entries)}; |
182 |
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288 | std::vector<long> connectivity(num_entries); |
183 |
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288 | connectivity_field->export_to(connectivity); |
184 |
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576 | const auto offset = _get_current_offset(file, "/VTKHDF/Connectivity"); |
185 |
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576 | _write_values(file, "/VTKHDF/Connectivity", connectivity, context); |
186 |
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288 | _write_values(file, "/VTKHDF/NumberOfConnectivityIds", my_num_ids, context); |
187 | 288 | return offset; | |
188 | 288 | } | |
189 | |||
190 | 292 | std::size_t _write_types(HDF5File& file, const IOContext& context) const { | |
191 | if constexpr (is_transient) { | ||
192 |
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216 | if (this->_step_count > 0 && _transient_opts.static_grid) |
193 |
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8 | return _get_last_step_data(file, "CellOffsets"); |
194 | } | ||
195 |
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288 | const auto types_field = VTK::make_cell_types_field(this->grid()); |
196 |
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288 | std::vector<std::uint8_t> types(types_field->layout().number_of_entries()); |
197 |
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288 | types_field->export_to(types); |
198 |
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576 | const auto offset = _get_current_offset(file, "VTKHDF/Types"); |
199 |
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288 | _write_values(file, "VTKHDF/Types", types, context); |
200 | 288 | return offset; | |
201 | 288 | } | |
202 | |||
203 | 292 | std::size_t _write_offsets(HDF5File& file, const IOContext& context) const { | |
204 | if constexpr (is_transient) { | ||
205 |
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216 | if (this->_step_count > 0 && _transient_opts.static_grid) |
206 |
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8 | return _get_last_step_data(file, "CellOffsets"); |
207 | } | ||
208 |
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288 | const auto offsets_field = VTK::make_offsets_field(this->grid()); |
209 |
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288 | const auto num_offset_entries = offsets_field->layout().number_of_entries() + 1; |
210 |
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288 | std::vector<long> offsets(num_offset_entries); |
211 |
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576 | offsets_field->export_to(std::ranges::subrange(std::next(offsets.begin()), offsets.end())); |
212 | 288 | offsets[0] = long{0}; | |
213 |
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576 | const auto offset = _get_current_offset(file, "/VTKHDF/Offsets"); |
214 |
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288 | _write_values(file, "/VTKHDF/Offsets", offsets, context); |
215 | 288 | return offset; | |
216 | 288 | } | |
217 | |||
218 | 292 | void _write_meta_data(HDF5File& file) const { | |
219 |
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691 | std::ranges::for_each(this->_meta_data_field_names(), [&] (const std::string& name) { |
220 | if constexpr (is_transient) { | ||
221 |
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423 | if (this->_step_count > 0 && _transient_opts.static_meta_data) { |
222 |
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312 | file.write(std::array{0}, "/VTKHDF/Steps/FieldDataOffsets/" + name); |
223 | 312 | return; | |
224 | } else { | ||
225 |
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111 | file.write(std::array{this->_step_count}, "/VTKHDF/Steps/FieldDataOffsets/" + name); |
226 | } | ||
227 | // For transient data, prepend a dimension indicating the step count | ||
228 |
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111 | TransformedField sub{this->_get_meta_data_field_ptr(name), FieldTransformation::as_sub_field}; |
229 |
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111 | file.write(sub, "/VTKHDF/FieldData/" + name); |
230 | 111 | } else { | |
231 |
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102 | file.write(*this->_get_meta_data_field_ptr(name), "/VTKHDF/FieldData/" + name); |
232 | } | ||
233 | }); | ||
234 | 292 | } | |
235 | |||
236 | 292 | void _write_point_fields(HDF5File& file, const IOContext& context) const { | |
237 |
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1149 | std::ranges::for_each(this->_point_field_names(), [&] (const std::string& name) { |
238 | if constexpr (is_transient) | ||
239 |
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666 | _write_step_offset( |
240 | file, | ||
241 |
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1332 | _get_current_offset(file, "/VTKHDF/PointData/" + name), |
242 |
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1332 | "/VTKHDF/Steps/PointDataOffsets/" + name |
243 | ); | ||
244 |
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857 | auto reshaped = _reshape(VTK::make_vtk_field(this->_get_point_field_ptr(name))); |
245 |
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857 | _write_point_field(file, "/VTKHDF/PointData/" + name, *reshaped, context); |
246 | 857 | }); | |
247 | 292 | } | |
248 | |||
249 | 292 | void _write_cell_fields(HDF5File& file, const IOContext& context) const { | |
250 |
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1137 | std::ranges::for_each(this->_cell_field_names(), [&] (const std::string& name) { |
251 | if constexpr (is_transient) | ||
252 |
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666 | _write_step_offset( |
253 | file, | ||
254 |
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1332 | _get_current_offset(file, "VTKHDF/CellData/" + name), |
255 |
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1332 | "/VTKHDF/Steps/CellDataOffsets/" + name |
256 | ); | ||
257 |
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845 | auto reshaped = _reshape(VTK::make_vtk_field(this->_get_cell_field_ptr(name))); |
258 |
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845 | _write_cell_field(file, "/VTKHDF/CellData/" + name, *reshaped, context); |
259 | 845 | }); | |
260 | 292 | } | |
261 | |||
262 | 2956 | FieldPtr _reshape(FieldPtr field_ptr) const { | |
263 | // VTK requires tensors to be written as flat fields | ||
264 |
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2956 | const auto layout = field_ptr->layout(); |
265 |
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2956 | if (layout.dimension() > 2) |
266 |
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2496 | return make_field_ptr(ReshapedField{ |
267 | field_ptr, | ||
268 |
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1248 | MDLayout{{layout.extent(0), layout.number_of_entries(1)}} |
269 |
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624 | }); |
270 | 2332 | return field_ptr; | |
271 | 2956 | } | |
272 | |||
273 | template<Concepts::Scalar T> | ||
274 | 2152 | void _write_values(HDF5File& file, | |
275 | const std::string& path, | ||
276 | const std::vector<T>& values, | ||
277 | const IOContext& context) const { | ||
278 |
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2152 | if (context.is_parallel) { |
279 | 1368 | const auto num_values = values.size(); | |
280 |
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1368 | const auto total_num_values = Parallel::sum(_comm, num_values, root_rank); |
281 |
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1368 | const auto my_total_num_values = Parallel::broadcast(_comm, total_num_values, root_rank); |
282 |
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1368 | const auto my_offset = _accumulate_rank_offset(num_values); |
283 |
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6840 | HDF5::Slice slice{ |
284 | .offset = std::vector{my_offset}, | ||
285 | .count = std::vector{num_values}, | ||
286 | .total_size = std::vector{my_total_num_values} | ||
287 | }; | ||
288 |
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1368 | file.write(values, path, slice); |
289 | 1368 | } else { | |
290 |
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784 | file.write(values, path); |
291 | } | ||
292 | 2152 | } | |
293 | |||
294 | 1775 | void _write_point_field(HDF5File& file, | |
295 | const std::string& path, | ||
296 | const Field& field, | ||
297 | const IOContext& context) const { | ||
298 | 1775 | _write_field(file, path, field, context.is_parallel, context.my_point_offset, context.num_points_total); | |
299 | 1775 | } | |
300 | |||
301 | 1469 | void _write_cell_field(HDF5File& file, | |
302 | const std::string& path, | ||
303 | const Field& field, | ||
304 | const IOContext& context) const { | ||
305 | 1469 | _write_field(file, path, field, context.is_parallel, context.my_cell_offset, context.num_cells_total); | |
306 | 1469 | } | |
307 | |||
308 | 3244 | void _write_field(HDF5File& file, | |
309 | const std::string& path, | ||
310 | const Field& field, | ||
311 | bool is_parallel, | ||
312 | std::size_t main_offset, | ||
313 | std::size_t main_size) const { | ||
314 |
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3244 | if (is_parallel) { |
315 |
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2102 | const auto layout = field.layout(); |
316 |
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2102 | std::vector<std::size_t> count(layout.dimension()); |
317 |
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2102 | layout.export_to(count); |
318 | |||
319 |
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2102 | std::vector<std::size_t> size = count; |
320 |
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2102 | std::vector<std::size_t> offset(layout.dimension(), 0); |
321 |
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2102 | offset.at(0) = main_offset; |
322 |
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2102 | size.at(0) = main_size; |
323 | |||
324 |
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2102 | file.write(field, path, HDF5::Slice{ |
325 | 2102 | .offset = std::move(offset), | |
326 | 2102 | .count = std::move(count), | |
327 | 2102 | .total_size = std::move(size) | |
328 | }); | ||
329 | 2102 | } else { | |
330 |
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1142 | file.write(field, path); |
331 | } | ||
332 |
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5346 | } |
333 | |||
334 | 1140 | std::size_t _accumulate_rank_offset(std::size_t my_size) const { | |
335 |
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1140 | auto all_offsets = Parallel::gather(_comm, my_size, root_rank); |
336 |
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1140 | if (Parallel::rank(_comm) == root_rank) { |
337 | 1092 | std::partial_sum(all_offsets.begin(), std::prev(all_offsets.end()), all_offsets.begin()); | |
338 |
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1092 | std::copy(std::next(all_offsets.rbegin()), all_offsets.rend(), all_offsets.rbegin()); |
339 | 546 | all_offsets[0] = 0; | |
340 | } | ||
341 |
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1140 | const auto my_offset = Parallel::scatter(_comm, all_offsets, root_rank); |
342 |
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1140 | if (my_offset.size() != 1) |
343 | ✗ | throw ValueError("Unexpected scatter result"); | |
344 | 2280 | return my_offset[0]; | |
345 | 1140 | } | |
346 | |||
347 | 1332 | void _write_step_offset(HDF5File& file, | |
348 | const std::size_t offset, | ||
349 | const std::string& path) const { | ||
350 |
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1332 | file.write(std::array{offset}, path); |
351 | 1332 | } | |
352 | |||
353 | 3384 | std::size_t _get_current_offset(HDF5File& file, const std::string& path) const { | |
354 |
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3384 | const auto cur_dimensions = file.get_dimensions(path); |
355 |
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6768 | return cur_dimensions ? (*cur_dimensions)[0] : 0; |
356 | 3384 | } | |
357 | |||
358 | 124 | std::size_t _get_last_step_data(const HDF5File& file, const std::string& sub_path) const { | |
359 |
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124 | if (this->_step_count == 0) |
360 | ✗ | throw ValueError("Last step data can only be read after at least one write"); | |
361 |
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124 | const std::string path ="VTKHDF/Steps/" + sub_path; |
362 | |||
363 |
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124 | auto step_dimensions = file.get_dimensions(path).value(); |
364 |
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124 | std::ranges::fill(step_dimensions, std::size_t{1}); |
365 | |||
366 |
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124 | auto access_offset = step_dimensions; |
367 |
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124 | std::ranges::fill(access_offset, std::size_t{0}); |
368 |
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124 | access_offset.at(0) = this->_step_count - 1; |
369 | |||
370 |
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248 | return file.template read_dataset_to<std::size_t>(path, HDF5::Slice{ |
371 | 124 | .offset = std::move(access_offset), | |
372 | 124 | .count = std::move(step_dimensions) | |
373 | 248 | }); | |
374 |
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248 | } |
375 | |||
376 | Communicator _comm; | ||
377 | std::string _timeseries_filename = ""; | ||
378 | VTK::HDFTransientOptions _transient_opts; | ||
379 | }; | ||
380 | |||
381 | /*! | ||
382 | * \ingroup VTK | ||
383 | * \brief Writer for the VTK HDF file format for unstructured grids. | ||
384 | */ | ||
385 | template<Concepts::UnstructuredGrid G, Concepts::Communicator C = NullCommunicator> | ||
386 | class VTKHDFUnstructuredGridWriter : public VTKHDFUnstructuredGridWriterImpl<false, G, C> { | ||
387 | using ParentType = VTKHDFUnstructuredGridWriterImpl<false, G, C>; | ||
388 | public: | ||
389 | using ParentType::ParentType; | ||
390 | }; | ||
391 | |||
392 | /*! | ||
393 | * \ingroup VTK | ||
394 | * \brief Writer for the transient VTK HDF file format for unstructured grids. | ||
395 | */ | ||
396 | template<Concepts::UnstructuredGrid G, Concepts::Communicator C = NullCommunicator> | ||
397 | class VTKHDFUnstructuredTimeSeriesWriter : public VTKHDFUnstructuredGridWriterImpl<true, G, C> { | ||
398 | using ParentType = VTKHDFUnstructuredGridWriterImpl<true, G, C>; | ||
399 | public: | ||
400 | using ParentType::ParentType; | ||
401 | }; | ||
402 | |||
403 | template<Concepts::UnstructuredGrid G> | ||
404 | VTKHDFUnstructuredGridWriter(const G&) -> VTKHDFUnstructuredGridWriter<G, NullCommunicator>; | ||
405 | template<Concepts::UnstructuredGrid G, Concepts::Communicator C> | ||
406 | VTKHDFUnstructuredGridWriter(const G&, const C&) -> VTKHDFUnstructuredGridWriter<G, C>; | ||
407 | |||
408 | template<Concepts::UnstructuredGrid G> | ||
409 | VTKHDFUnstructuredTimeSeriesWriter(const G&, std::string, VTK::HDFTransientOptions = {}) -> VTKHDFUnstructuredTimeSeriesWriter<G, NullCommunicator>; | ||
410 | template<Concepts::UnstructuredGrid G, Concepts::Communicator C> | ||
411 | VTKHDFUnstructuredTimeSeriesWriter(const G&, const C&, std::string, VTK::HDFTransientOptions = {}) -> VTKHDFUnstructuredTimeSeriesWriter<G, C>; | ||
412 | |||
413 | } // namespace GridFormat | ||
414 | |||
415 | #endif // GRIDFORMAT_HAVE_HIGH_FIVE | ||
416 | #endif // GRIDFORMAT_VTK_HDF_UNSTRUCTURED_GRID_WRITER_HPP_ | ||
417 |