Block-Structured AMR Software Framework
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AMReX_ParticlesHDF5.H
Go to the documentation of this file.
1#ifndef AMREX_PARTICLES_HDF5_H_
2#define AMREX_PARTICLES_HDF5_H_
3
11public:
19 void WriteParticleRealDataHDF5 (void* data, size_t size, hid_t fid) const;
20
28 void ReadParticleRealDataHDF5 (void* data, size_t size, hid_t fid);
29
37 void CheckpointHDF5 (const std::string& dir, const std::string& name,
38 const std::string& compression = "None@0") const;
39
50 void CheckpointHDF5 (const std::string& dir, const std::string& name, bool is_checkpoint,
51 const Vector<std::string>& real_comp_names = Vector<std::string>(),
52 const Vector<std::string>& int_comp_names = Vector<std::string>(),
53 const std::string& compression = "None@0") const;
54
70 template <class F>
71 void WriteHDF5ParticleData (const std::string& dir,
72 const std::string& name,
73 const Vector<int>& write_real_comp,
74 const Vector<int>& write_int_comp,
75 const Vector<std::string>& real_comp_names,
76 const Vector<std::string>& int_comp_names,
77 const std::string& compression,
78 F&& f, bool is_checkpoint=false) const;
79
80
87 void CheckpointPreHDF5 ();
88
95 void CheckpointPostHDF5 ();
96
103 void RestartHDF5 (const std::string& dir, const std::string& file);
104
112 void RestartHDF5 (const std::string& dir, const std::string& file, bool is_checkpoint);
113
121 void WritePlotFileHDF5 (const std::string& dir, const std::string& name, const std::string& compression) const;
122
135 template <class F>
136 requires (!std::same_as<F, Vector<std::string>>)
137 void WritePlotFileHDF5 (const std::string& dir, const std::string& name, const std::string& compression, F&& f) const;
138
148 void WritePlotFileHDF5 (const std::string& dir, const std::string& name,
149 const Vector<std::string>& real_comp_names,
150 const Vector<std::string>& int_comp_names,
151 const std::string& compression) const;
152
167 template <class F>
168 void WritePlotFileHDF5 (const std::string& dir, const std::string& name,
169 const Vector<std::string>& real_comp_names,
170 const Vector<std::string>& int_comp_names,
171 const std::string& compression, F&& f) const;
172
182 void WritePlotFileHDF5 (const std::string& dir, const std::string& name,
183 const Vector<std::string>& real_comp_names,
184 const std::string& compression) const;
185
200 template <class F>
201 requires (!std::same_as<F, Vector<std::string>>)
202 void WritePlotFileHDF5 (const std::string& dir, const std::string& name,
203 const Vector<std::string>& real_comp_names,
204 const std::string& compression, F&& f) const;
205
216 void WritePlotFileHDF5 (const std::string& dir,
217 const std::string& name,
218 const Vector<int>& write_real_comp,
219 const Vector<int>& write_int_comp,
220 const std::string& compression) const;
221
237 template <class F>
238 void WritePlotFileHDF5 (const std::string& dir,
239 const std::string& name,
240 const Vector<int>& write_real_comp,
241 const Vector<int>& write_int_comp,
242 const std::string& compression, F&& f) const;
243
258 void WritePlotFileHDF5 (const std::string& dir,
259 const std::string& name,
260 const Vector<int>& write_real_comp,
261 const Vector<int>& write_int_comp,
262 const Vector<std::string>& real_comp_names,
263 const Vector<std::string>& int_comp_names,
264 const std::string& compression) const;
265
285 template <class F>
286 void WritePlotFileHDF5 (const std::string& dir,
287 const std::string& name,
288 const Vector<int>& write_real_comp,
289 const Vector<int>& write_int_comp,
290 const Vector<std::string>& real_comp_names,
291 const Vector<std::string>& int_comp_names,
292 const std::string& compression,
293 F&& f) const;
294
298 void WritePlotFilePreHDF5 ();
299
303 void WritePlotFilePostHDF5 ();
304
319 void
320 WriteParticlesHDF5 (int level, hid_t grp,
321 Vector<int>& which, Vector<int>& count, Vector<Long>& where,
322 const Vector<int>& write_real_comp, const Vector<int>& write_int_comp,
323 const std::string& compression,
324 const Vector<std::map<std::pair<int, int>,IntVector>>& particle_io_flags, bool is_checkpoint) const;
325
326protected:
327
341template <class RTYPE>
342void ReadParticlesHDF5 (hsize_t offset, hsize_t count, int grd, int lev, hid_t int_dset, hid_t real_dset, int finest_level_in_file, bool convert_ids);
343
344#endif
offset
Array4< int const > offset
Definition AMReX_HypreMLABecLap.cpp:1139
CheckpointHDF5
void CheckpointHDF5(const std::string &dir, const std::string &name, const std::string &compression="None@0") const
Writes a particle checkpoint to file, suitable for restarting.
WritePlotFilePreHDF5
void WritePlotFilePreHDF5()
Plotfile-friendly alias for CheckpointPreHDF5().
CheckpointPreHDF5
void CheckpointPreHDF5()
Prepare metadata used by deferred HDF5 checkpoint writes.
WritePlotFilePostHDF5
void WritePlotFilePostHDF5()
Plotfile-friendly alias for CheckpointPostHDF5().
ReadParticleRealDataHDF5
void ReadParticleRealDataHDF5(void *data, size_t size, hid_t fid)
Read a contiguous chunk of real particle data from HDF5 file.
ReadParticlesHDF5
void ReadParticlesHDF5(hsize_t offset, hsize_t count, int grd, int lev, hid_t int_dset, hid_t real_dset, int finest_level_in_file, bool convert_ids)
Read particle records from HDF5 datasets into a level/tile buffer.
WriteParticlesHDF5
void WriteParticlesHDF5(int level, hid_t grp, Vector< int > &which, Vector< int > &count, Vector< Long > &where, const Vector< int > &write_real_comp, const Vector< int > &write_int_comp, const std::string &compression, const Vector< std::map< std::pair< int, int >, IntVector > > &particle_io_flags, bool is_checkpoint) const
Write all particles from one AMR level into the given HDF5 group.
WritePlotFileHDF5
void WritePlotFileHDF5(const std::string &dir, const std::string &name, const std::string &compression) const
This version of WritePlotFile writes all components and assigns component names.
RestartHDF5
void RestartHDF5(const std::string &dir, const std::string &file)
Restart from checkpoint.
WriteHDF5ParticleData
void WriteHDF5ParticleData(const std::string &dir, const std::string &name, const Vector< int > &write_real_comp, const Vector< int > &write_int_comp, const Vector< std::string > &real_comp_names, const Vector< std::string > &int_comp_names, const std::string &compression, F &&f, bool is_checkpoint=false) const
Writes particle data to disk in the HDF5 format.
CheckpointPostHDF5
void CheckpointPostHDF5()
Finalize a checkpoint header handed off by CheckpointPreHDF5().
WriteParticleRealDataHDF5
void WriteParticleRealDataHDF5(void *data, size_t size, hid_t fid) const
Write a contiguous chunk of real particle data to an HDF5 file.