Functions
void	WriteParticleRealDataHDF5 (void *data, size_t size, hid_t fid) const
	Write a contiguous chunk of real particle data to an HDF5 file.

void	ReadParticleRealDataHDF5 (void *data, size_t size, hid_t fid)
	Read a contiguous chunk of real particle data from HDF5 file.

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.

void	CheckpointHDF5 (const std::string &dir, const std::string &name, bool is_checkpoint, const Vector< std::string > &real_comp_names=Vector< std::string >(), const Vector< std::string > &int_comp_names=Vector< std::string >(), const std::string &compression="None@0") const
	Writes a particle checkpoint to file, suitable for restarting.

template<class F >
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.

void	CheckpointPreHDF5 ()
	Prepare metadata used by deferred HDF5 checkpoint writes.

void	CheckpointPostHDF5 ()
	Finalize a checkpoint header handed off by CheckpointPreHDF5().

void	RestartHDF5 (const std::string &dir, const std::string &file)
	Restart from checkpoint.

void	RestartHDF5 (const std::string &dir, const std::string &file, bool is_checkpoint)
	Older version, for backwards compatibility.

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.

template<class F , std::enable_if_t<!std::is_same_v< F, Vector< std::string > > > * = nullptr>
void	WritePlotFileHDF5 (const std::string &dir, const std::string &name, const std::string &compression, F &&f) const
	This version of WritePlotFile writes all components and assigns component names.

void	WritePlotFileHDF5 (const std::string &dir, const std::string &name, const Vector< std::string > &real_comp_names, const Vector< std::string > &int_comp_names, const std::string &compression) const
	This version of WritePlotFile writes all components and allows the user to specify the names of the components.

template<class F >
void	WritePlotFileHDF5 (const std::string &dir, const std::string &name, const Vector< std::string > &real_comp_names, const Vector< std::string > &int_comp_names, const std::string &compression, F &&f) const
	This version of WritePlotFile writes all components and allows the user to specify the names of the components.

void	WritePlotFileHDF5 (const std::string &dir, const std::string &name, const Vector< std::string > &real_comp_names, const std::string &compression) const
	This version of WritePlotFile writes all components and allows the user to specify the names of the components.

template<class F , std::enable_if_t<!std::is_same_v< F, Vector< std::string > > > * = nullptr>
void	WritePlotFileHDF5 (const std::string &dir, const std::string &name, const Vector< std::string > &real_comp_names, const std::string &compression, F &&f) const
	This version of WritePlotFile writes all components and allows the user to specify the names of the components.

void	WritePlotFileHDF5 (const std::string &dir, const std::string &name, const Vector< int > &write_real_comp, const Vector< int > &write_int_comp, const std::string &compression) const
	This version of WritePlotFile assigns component names, but allows the user to pass in a vector of ints that toggle on / off the writing of specific components.

template<class F >
void	WritePlotFileHDF5 (const std::string &dir, const std::string &name, const Vector< int > &write_real_comp, const Vector< int > &write_int_comp, const std::string &compression, F &&f) const
	This version of WritePlotFile assigns component names, but allows the user to pass in a vector of ints that toggle on / off the writing of specific components.

void	WritePlotFileHDF5 (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) const
	This is the most general version of WritePlotFile, which takes component names and flags for whether to write each variable as components. Note that the user should pass in vectors containing names of all the components, whether they are written or not.

template<class F >
void	WritePlotFileHDF5 (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) const
	This is the most general version of WritePlotFile, which takes component names and flags for whether to write each variable as components. Note that the user should pass in vectors containing names of all the components, whether they are written or not.

void	WritePlotFilePreHDF5 ()
	Plotfile-friendly alias for CheckpointPreHDF5().

void	WritePlotFilePostHDF5 ()
	Plotfile-friendly alias for CheckpointPostHDF5().

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.

template<class RTYPE >
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.

Detailed Description

HDF5-specific ParticleContainer hooks (checkpointing, plotfile output, and supporting helpers shared by all particle types).

Function Documentation

◆ CheckpointHDF5() [1/2]

void CheckpointHDF5	(	const std::string &	dir,
		const std::string &	name,
		bool	is_checkpoint,
		const Vector< std::string > &	real_comp_names = `Vector< std::string >()`,
		const Vector< std::string > &	int_comp_names = `Vector< std::string >()`,
		const std::string &	compression = `"None@0"`
	)		const

Writes a particle checkpoint to file, suitable for restarting.

Parameters

dir	Directory that owns the per-type subdirectory.
name	Particle type subdirectory (e.g., "Tracer").
is_checkpoint	Reserved for parity with ASCII checkpoints (ignored because HDF5 always writes id/cpu).
real_comp_names	Optional labels for each real component.
int_comp_names	Optional labels for each integer component.
compression	Compression scheme, e.g., `"ZFP_ACCURACY@0.001"`.

◆ CheckpointHDF5() [2/2]

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.

Parameters

dir	The base directory into which to write (i.e. "plt00000")
name	The name of the sub-directory for this particle type (i.e. "Tracer")
compression	compression parameter (i.e. "ZFP_ACCURACY@0.001", "SZ@sz.config")

◆ CheckpointPostHDF5()

void CheckpointPostHDF5 ( )

Finalize a checkpoint header handed off by CheckpointPreHDF5().

Aggregates distributed offsets/counts, appends per-level bookkeeping, and removes empty per-file fragments when requested.

◆ CheckpointPreHDF5()

void CheckpointPreHDF5 ( )

Prepare metadata used by deferred HDF5 checkpoint writes.

Tallies particles/NextID values per level so CheckpointPostHDF5() can finish the header without revisiting particle data.

◆ ReadParticleRealDataHDF5()

void ReadParticleRealDataHDF5	(	void *	data,
		size_t	size,
		hid_t	fid
	)

Read a contiguous chunk of real particle data from HDF5 file.

Parameters

data	A pointer to the start of the buffer into which to read
size	The number of elements to read
fid	The istream from which to read the data

◆ ReadParticlesHDF5()

template<class RTYPE >

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
	)

protected

Read particle records from HDF5 datasets into a level/tile buffer.

Template Parameters

RTYPE Floating-point storage type stored in the file.

Parameters

offset	Starting element offset inside the dataset.
count	Number of entries to load.
grd	Grid index being populated.
lev	AMR level index being populated.
int_dset	HDF5 dataset handle for integer components.
real_dset	HDF5 dataset handle for real components.
finest_level_in_file	Finest level encoded in the file (for sanity checks).
convert_ids	True when reading `Version_Two_Dot_One` checkpoints whose 64-bit id/cpu pairs were split into two 32-bit words and must be reassembled.

◆ RestartHDF5() [1/2]

void RestartHDF5	(	const std::string &	dir,
		const std::string &	file
	)

Restart from checkpoint.

Parameters

dir	The base directory into which to write (i.e. "plt00000")
file	The name of the sub-directory for this particle type (i.e. "Tracer")

◆ RestartHDF5() [2/2]

void RestartHDF5	(	const std::string &	dir,
		const std::string &	file,
		bool	is_checkpoint
	)

Older version, for backwards compatibility.

Parameters

dir	The base directory into which to write (i.e. "plt00000")
file	The name of the sub-directory for this particle type (i.e. "Tracer")
is_checkpoint	Whether the particle id and cpu are included in the file.

◆ WriteHDF5ParticleData()

template<class F >

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.

Template Parameters

F	function type

Parameters

dir	The base directory into which to write (i.e. "plt00000")
name	The name of the sub-directory for this particle type (i.e. "Tracer")
write_real_comp	for each real component, whether or not we include that component in the file
write_int_comp	for each integer component, whether or not we include that component in the file
real_comp_names	for each real component, a name to label the data with
int_comp_names	for each integer component, a name to label the data with
f	callable that returns whether a given particle should be written or not
is_checkpoint	Whether the particle id and cpu are included in the file.
compression	compression parameter (i.e. "ZFP_ACCURACY@0.001", "SZ@sz.config")

◆ WriteParticleRealDataHDF5()

void WriteParticleRealDataHDF5	(	void *	data,
		size_t	size,
		hid_t	fid
	)		const

Write a contiguous chunk of real particle data to an HDF5 file.

Parameters

data	A pointer to the start of the buffer to write
size	The number of elements to write
fid	The HDF5 file ID

◆ 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.

Parameters

level	AMR level whose particles are written.
grp	Open HDF5 group corresponding to `level_d`.
which	Placeholder vector kept for API compatibility (unused by the HDF5 backend).
count	Per-grid particle counts updated in place.
where	Placeholder vector kept for API compatibility (unused by the HDF5 backend).
write_real_comp	Flags enabling each real component.
write_int_comp	Flags enabling each integer component.
compression	Compression string (`ZFP_*`, `SZ`, etc.).
particle_io_flags	Per-grid/tile masks returned by the filter functor.
is_checkpoint	Reserved; the HDF5 writer always preserves id/cpu regardless of this flag.

◆ WritePlotFileHDF5() [1/10]

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.

Parameters

dir	The base directory into which to write (i.e. "plt00000")
name	The name of the sub-directory for this particle type (i.e. "Tracer")
compression	compression parameter (i.e. "ZFP_ACCURACY@0.001", "SZ@sz.config")

◆ WritePlotFileHDF5() [2/10]

template<class F , std::enable_if_t<!std::is_same_v< F, Vector< std::string > > > * = nullptr>

void WritePlotFileHDF5	(	const std::string &	dir,
		const std::string &	name,
		const std::string &	compression,
		F &&	f
	)		const

This version of WritePlotFile writes all components and assigns component names.

This version also lets you pass in a functor to toggle whether each particle gets output.

Template Parameters

F	function type

Parameters

dir	The base directory into which to write (i.e. "plt00000")
name	The name of the sub-directory for this particle type (i.e. "Tracer")
compression	compression parameter (i.e. "ZFP_ACCURACY@0.001", "SZ@sz.config")
f	callable that returns whether or not to write each particle

◆ WritePlotFileHDF5() [3/10]

void WritePlotFileHDF5	(	const std::string &	dir,
		const std::string &	name,
		const Vector< int > &	write_real_comp,
		const Vector< int > &	write_int_comp,
		const std::string &	compression
	)		const

This version of WritePlotFile assigns component names, but allows the user to pass in a vector of ints that toggle on / off the writing of specific components.

Parameters

dir	The base directory into which to write (i.e. "plt00000")
name	The name of the sub-directory for this particle type (i.e. "Tracer")
write_real_comp	for each real component, whether to include that comp in the file
write_int_comp	for each integer component, whether to include that comp in the file
compression	compression parameter (i.e. "ZFP_ACCURACY@0.001", "SZ@sz.config")

◆ WritePlotFileHDF5() [4/10]

template<class F >

void WritePlotFileHDF5	(	const std::string &	dir,
		const std::string &	name,
		const Vector< int > &	write_real_comp,
		const Vector< int > &	write_int_comp,
		const std::string &	compression,
		F &&	f
	)		const

This version of WritePlotFile assigns component names, but allows the user to pass in a vector of ints that toggle on / off the writing of specific components.

This version also lets you pass in a functor to toggle whether each particle gets output.

Template Parameters

F	function type

Parameters

dir	The base directory into which to write (i.e. "plt00000")
name	The name of the sub-directory for this particle type (i.e. "Tracer")
write_real_comp	for each real component, whether to include that comp in the file
write_int_comp	for each integer component, whether to include that comp in the file
compression	compression parameter (i.e. "ZFP_ACCURACY@0.001", "SZ@sz.config")
f	callable that returns whether or not to write each particle

◆ WritePlotFileHDF5() [5/10]

void WritePlotFileHDF5	(	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
	)		const

This is the most general version of WritePlotFile, which takes component names and flags for whether to write each variable as components. Note that the user should pass in vectors containing names of all the components, whether they are written or not.

Parameters

dir	The base directory into which to write (i.e. "plt00000")
name	The name of the sub-directory for this particle type (i.e. "Tracer")
write_real_comp	for each real component, whether to include that comp in the file
write_int_comp	for each integer component, whether to include that comp in the file
real_comp_names	for each real component, a name to label the data with
int_comp_names	for each integer component, a name to label the data with
compression	compression parameter (i.e. "ZFP_ACCURACY@0.001", "SZ@sz.config")

◆ WritePlotFileHDF5() [6/10]

template<class F >

void WritePlotFileHDF5	(	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
	)		const

This is the most general version of WritePlotFile, which takes component names and flags for whether to write each variable as components. Note that the user should pass in vectors containing names of all the components, whether they are written or not.

This version also lets you pass in a functor to toggle whether each particle gets output.

Template Parameters

F	function type

Parameters

dir	The base directory into which to write (i.e. "plt00000")
name	The name of the sub-directory for this particle type (i.e. "Tracer")
write_real_comp	for each real component, whether to include that comp in the file
write_int_comp	for each integer component, whether to include that comp in the file
real_comp_names	for each real component, a name to label the data with
int_comp_names	for each integer component, a name to label the data with
compression	compression parameter (i.e. "ZFP_ACCURACY@0.001", "SZ@sz.config")
f	callable that returns whether or not to write each particle

◆ WritePlotFileHDF5() [7/10]

void WritePlotFileHDF5	(	const std::string &	dir,
		const std::string &	name,
		const Vector< std::string > &	real_comp_names,
		const std::string &	compression
	)		const

This version of WritePlotFile writes all components and allows the user to specify the names of the components.

Parameters

dir	The base directory into which to write (i.e. "plt00000")
name	The name of the sub-directory for this particle type (i.e. "Tracer")
real_comp_names	for each real component, a name to label the data with
compression	compression parameter (i.e. "ZFP_ACCURACY@0.001", "SZ@sz.config")

◆ WritePlotFileHDF5() [8/10]

template<class F , std::enable_if_t<!std::is_same_v< F, Vector< std::string > > > * = nullptr>

void WritePlotFileHDF5	(	const std::string &	dir,
		const std::string &	name,
		const Vector< std::string > &	real_comp_names,
		const std::string &	compression,
		F &&	f
	)		const

This version of WritePlotFile writes all components and allows the user to specify the names of the components.

This version also lets you pass in a functor to toggle whether each particle gets output.

Template Parameters

F	function type

Parameters

dir	The base directory into which to write (i.e. "plt00000")
name	The name of the sub-directory for this particle type (i.e. "Tracer")
real_comp_names	for each real component, a name to label the data with
compression	compression parameter (i.e. "ZFP_ACCURACY@0.001", "SZ@sz.config")
f	callable that returns whether or not to write each particle

◆ WritePlotFileHDF5() [9/10]

void WritePlotFileHDF5	(	const std::string &	dir,
		const std::string &	name,
		const Vector< std::string > &	real_comp_names,
		const Vector< std::string > &	int_comp_names,
		const std::string &	compression
	)		const

This version of WritePlotFile writes all components and allows the user to specify the names of the components.

Parameters

dir	The base directory into which to write (i.e. "plt00000")
name	The name of the sub-directory for this particle type (i.e. "Tracer")
real_comp_names	for each real component, a name to label the data with
int_comp_names	for each integer component, a name to label the data with
compression	compression parameter (i.e. "ZFP_ACCURACY@0.001", "SZ@sz.config")

◆ WritePlotFileHDF5() [10/10]

template<class F >

void WritePlotFileHDF5	(	const std::string &	dir,
		const std::string &	name,
		const Vector< std::string > &	real_comp_names,
		const Vector< std::string > &	int_comp_names,
		const std::string &	compression,
		F &&	f
	)		const

This version of WritePlotFile writes all components and allows the user to specify the names of the components.

This version also lets you pass in a functor to toggle whether each particle gets output.

Template Parameters

F	function type

Parameters

dir	The base directory into which to write (i.e. "plt00000")
name	The name of the sub-directory for this particle type (i.e. "Tracer")
real_comp_names	for each real component, a name to label the data with
int_comp_names	for each integer component, a name to label the data with
compression	compression parameter (i.e. "ZFP_ACCURACY@0.001", "SZ@sz.config")
f	callable that returns whether or not to write each particle

◆ WritePlotFilePostHDF5()

void WritePlotFilePostHDF5 ( )

Plotfile-friendly alias for CheckpointPostHDF5().

◆ WritePlotFilePreHDF5()

void WritePlotFilePreHDF5 ( )

Plotfile-friendly alias for CheckpointPreHDF5().

Functions

Detailed Description

Function Documentation

◆ CheckpointHDF5() [1/2]

◆ CheckpointHDF5() [2/2]

◆ CheckpointPostHDF5()

◆ CheckpointPreHDF5()

◆ ReadParticleRealDataHDF5()

◆ ReadParticlesHDF5()

◆ RestartHDF5() [1/2]

◆ RestartHDF5() [2/2]

◆ WriteHDF5ParticleData()

◆ WriteParticleRealDataHDF5()

◆ WriteParticlesHDF5()

◆ WritePlotFileHDF5() [1/10]

◆ WritePlotFileHDF5() [2/10]

◆ WritePlotFileHDF5() [3/10]

◆ WritePlotFileHDF5() [4/10]

◆ WritePlotFileHDF5() [5/10]

◆ WritePlotFileHDF5() [6/10]

◆ WritePlotFileHDF5() [7/10]

◆ WritePlotFileHDF5() [8/10]

◆ WritePlotFileHDF5() [9/10]

◆ WritePlotFileHDF5() [10/10]

◆ WritePlotFilePostHDF5()

◆ WritePlotFilePreHDF5()