Interface to the HDF5 library. More...

#include <hdf5_tree.hpp>

Classes
class	HDF5_attribute

class	HDF5_dataset
	Auxiliary class to handle HDF5 Dataset object. More...

class	HDF5_dataspace
	Auxiliary class to handle HDF5 Dataspace object. More...

class	HDF5_group
	Auxiliary class to handle HDF5 Group object. More...

Public Member Functions
	HDF5_tree (const std::string &file_name__, hdf5_access_t access__)
	Constructor to create the HDF5 tree. More...

	~HDF5_tree ()
	Destructor. More...

HDF5_tree	create_node (int idx)
	Create node by integer index. More...

HDF5_tree	create_node (std::string const &name)
	Create node by name. More...

template<typename T , int N>
void	write (const std::string &name, sddk::mdarray< std::complex< T >, N > const &data)

template<typename T , int N>
void	write (std::string const &name__, sddk::mdarray< T, N > const &data__)
	Write a multidimensional array by name. More...

template<typename T , int N>
void	write (int name_id, sddk::mdarray< T, N > const &data)
	Write a multidimensional array by integer index. More...

template<typename T >
void	write (const std::string &name, T const *data, int size)
	Write a buffer. More...

template<typename T >
void	write (const std::string &name, T data)
	Write a scalar. More...

template<typename T >
void	write (int name_id, std::vector< T > const &vec)
	Write a vector by id. More...

template<typename T >
void	write (const std::string &name, std::vector< T > const &vec)
	Write a vector by name. More...

template<typename T >
void	write_attribute (const std::string &name, const T &data) const
	Write attribute. More...

template<typename T >
void	write_attribute (const std::string &name, const T &data, const std::string &dataset_name) const
	Write attribute. More...

void	write_attribute (const std::string &name, const std::string &data, hid_t base_string_type=H5T_FORTRAN_S1) const
	Write string attribute. More...

void	write_attribute (const std::string &name, const std::string &data, const std::string &dataset_name, hid_t base_string_type=H5T_FORTRAN_S1) const
	Write string attribute. More...

template<std::size_t N>
void	write_attribute (const std::string &name, const char(&data)[N], hid_t base_string_type=H5T_FORTRAN_S1) const
	Write string attribute. More...

template<std::size_t N>
void	write_attribute (const std::string &name, const char(&data)[N], const std::string &dataset_name, hid_t base_string_type=H5T_FORTRAN_S1) const
	Write string attribute. More...

template<typename T >
void	write_attribute (const std::string &name, const std::vector< T > &data) const
	Write array attribute. More...

template<typename T >
void	write_attribute (const std::string &name, const std::vector< T > &data, const std::string &dataset_name) const
	Write array attribute. More...

template<typename T >
void	write_attribute (const std::string &name, const std::initializer_list< T > &data) const
	Write array attribute. More...

template<typename T >
void	write_attribute (const std::string &name, const std::initializer_list< T > &data, const std::string &dataset_name) const
	Write array attribute. More...

template<int N>
void	read (const std::string &name, sddk::mdarray< std::complex< double >, N > &data)

template<typename T , int N>
void	read (const std::string &name, sddk::mdarray< T, N > &data)

template<typename T , int N>
void	read (int name_id, sddk::mdarray< T, N > &data)

template<typename T >
void	read (std::string const &name, T *data, int size)
	Read a vector or a scalar. More...

template<typename T >
void	read (int name_id, std::vector< T > &vec)

template<typename T >
void	read (std::string const &name, std::vector< T > &vec)

HDF5_tree	operator[] (std::string const &path__)

HDF5_tree	operator[] (int idx__)

Private Member Functions
	HDF5_tree (hid_t file_id__, const std::string &path__)
	Constructor to create branches of the HDF5 tree. More...

hid_t	string_type (const std::string &data, hid_t base_string_type) const
	Create HDF5 string type from std::string. More...

template<typename T >
hid_t	array_type (const std::vector< T > &data) const
	Create HDF5 array type from std::vector. More...

template<typename T >
void	write (const std::string &name, T const *data, std::vector< int > const &dims)
	Write a multidimensional array. More...

template<typename T >
void	write_attribute (const std::string &name, const T *const data, hid_t type_id) const

template<typename T >
void	write_attribute (const std::string &name, const T *const data, hid_t type_id, const std::string &dataset_name) const

template<typename T >
void	read (const std::string &name, T *data, std::vector< int > const &dims)
	Read a multidimensional array. More...

Private Attributes
std::string	file_name_
	HDF5 file name. More...

std::string	path_
	path inside HDF5 file More...

hid_t	file_id_ {-1}
	HDF5 file handler. More...

bool	root_node_ {true}
	True if this is a root node. More...

Detailed Description

Interface to the HDF5 library.

Definition at line 85 of file hdf5_tree.hpp.

Constructor & Destructor Documentation

◆ HDF5_tree() [1/2]

sirius::HDF5_tree::HDF5_tree	(	hid_t	file_id__,
		const std::string &	path__
	)

inlineprivate

Constructor to create branches of the HDF5 tree.

Definition at line 273 of file hdf5_tree.hpp.

◆ HDF5_tree() [2/2]

sirius::HDF5_tree::HDF5_tree	(	const std::string &	file_name__,
		hdf5_access_t	access__
	)

inline

Constructor to create the HDF5 tree.

Definition at line 377 of file hdf5_tree.hpp.

◆ ~HDF5_tree()

sirius::HDF5_tree::~HDF5_tree ( )

inline

Destructor.

Definition at line 413 of file hdf5_tree.hpp.

Member Function Documentation

◆ string_type()

hid_t sirius::HDF5_tree::string_type	(	const std::string &	data,
		hid_t	base_string_type
	)		const

inlineprivate

Create HDF5 string type from std::string.

Definition at line 281 of file hdf5_tree.hpp.

◆ array_type()

template<typename T >

hid_t sirius::HDF5_tree::array_type ( const std::vector< T > & data ) const

inlineprivate

Create HDF5 array type from std::vector.

Definition at line 293 of file hdf5_tree.hpp.

◆ write() [1/8]

template<typename T >

void sirius::HDF5_tree::write	(	const std::string &	name,
		T const *	data,
		std::vector< int > const &	dims
	)

inlineprivate

Write a multidimensional array.

Definition at line 301 of file hdf5_tree.hpp.

◆ write_attribute() [1/12]

template<typename T >

void sirius::HDF5_tree::write_attribute	(	const std::string &	name,
		const T *const	data,
		hid_t	type_id
	)		const

inlineprivate

Write attribure to current GROUP

Parameters

name	Name of the attribute
data	Attribute data
type_id	Attribute type ID

Definition at line 324 of file hdf5_tree.hpp.

◆ write_attribute() [2/12]

template<typename T >

void sirius::HDF5_tree::write_attribute	(	const std::string &	name,
		const T *const	data,
		hid_t	type_id,
		const std::string &	dataset_name
	)		const

inlineprivate

Write attribure to DATASET within the GROUP

Parameters

name	Name of the attribute
data	Attribute data
type_id	Attribute type ID
dataset_name	Dataset in current group to wich attach the attribute

Definition at line 342 of file hdf5_tree.hpp.

◆ read() [1/7]

template<typename T >

void sirius::HDF5_tree::read	(	const std::string &	name,
		T *	data,
		std::vector< int > const &	dims
	)

inlineprivate

Read a multidimensional array.

Definition at line 358 of file hdf5_tree.hpp.

◆ create_node() [1/2]

HDF5_tree sirius::HDF5_tree::create_node ( int idx )

inline

Create node by integer index.

Create node at the current location using integer index as a name.

Definition at line 424 of file hdf5_tree.hpp.

◆ create_node() [2/2]

HDF5_tree sirius::HDF5_tree::create_node ( std::string const & name )

inline

Create node by name.

Create node with the given name at the current location.

Definition at line 431 of file hdf5_tree.hpp.

◆ write() [2/8]

template<typename T , int N>

void sirius::HDF5_tree::write	(	const std::string &	name,
		sddk::mdarray< std::complex< T >, N > const &	data
	)

inline

Definition at line 442 of file hdf5_tree.hpp.

◆ write() [3/8]

template<typename T , int N>

void sirius::HDF5_tree::write	(	std::string const &	name__,
		sddk::mdarray< T, N > const &	data__
	)

inline

Write a multidimensional array by name.

Definition at line 454 of file hdf5_tree.hpp.

◆ write() [4/8]

template<typename T , int N>

void sirius::HDF5_tree::write	(	int	name_id,
		sddk::mdarray< T, N > const &	data
	)

inline

Write a multidimensional array by integer index.

Definition at line 465 of file hdf5_tree.hpp.

◆ write() [5/8]

template<typename T >

void sirius::HDF5_tree::write	(	const std::string &	name,
		T const *	data,
		int	size
	)

inline

Write a buffer.

Definition at line 473 of file hdf5_tree.hpp.

◆ write() [6/8]

template<typename T >

void sirius::HDF5_tree::write	(	const std::string &	name,
		T	data
	)

inline

Write a scalar.

Definition at line 482 of file hdf5_tree.hpp.

◆ write() [7/8]

template<typename T >

void sirius::HDF5_tree::write	(	int	name_id,
		std::vector< T > const &	vec
	)

inline

Write a vector by id.

Definition at line 491 of file hdf5_tree.hpp.

◆ write() [8/8]

template<typename T >

void sirius::HDF5_tree::write	(	const std::string &	name,
		std::vector< T > const &	vec
	)

inline

Write a vector by name.

Definition at line 499 of file hdf5_tree.hpp.

◆ write_attribute() [3/12]

template<typename T >

void sirius::HDF5_tree::write_attribute	(	const std::string &	name,
		const T &	data
	)		const

inline

Write attribute.

Definition at line 506 of file hdf5_tree.hpp.

◆ write_attribute() [4/12]

template<typename T >

void sirius::HDF5_tree::write_attribute	(	const std::string &	name,
		const T &	data,
		const std::string &	dataset_name
	)		const

inline

Write attribute.

Definition at line 513 of file hdf5_tree.hpp.

◆ write_attribute() [5/12]

void sirius::HDF5_tree::write_attribute	(	const std::string &	name,
		const std::string &	data,
		hid_t	base_string_type = `H5T_FORTRAN_S1`
	)		const

inline

Write string attribute.

Definition at line 519 of file hdf5_tree.hpp.

◆ write_attribute() [6/12]

void sirius::HDF5_tree::write_attribute	(	const std::string &	name,
		const std::string &	data,
		const std::string &	dataset_name,
		hid_t	base_string_type = `H5T_FORTRAN_S1`
	)		const

inline

Write string attribute.

Definition at line 526 of file hdf5_tree.hpp.

◆ write_attribute() [7/12]

template<std::size_t N>

void sirius::HDF5_tree::write_attribute	(	const std::string &	name,
		const char(&)	data[N],
		hid_t	base_string_type = `H5T_FORTRAN_S1`
	)		const

inline

Write string attribute.

Definition at line 534 of file hdf5_tree.hpp.

◆ write_attribute() [8/12]

template<std::size_t N>

void sirius::HDF5_tree::write_attribute	(	const std::string &	name,
		const char(&)	data[N],
		const std::string &	dataset_name,
		hid_t	base_string_type = `H5T_FORTRAN_S1`
	)		const

inline

Write string attribute.

Definition at line 541 of file hdf5_tree.hpp.

◆ write_attribute() [9/12]

template<typename T >

void sirius::HDF5_tree::write_attribute	(	const std::string &	name,
		const std::vector< T > &	data
	)		const

inline

Write array attribute.

Definition at line 549 of file hdf5_tree.hpp.

◆ write_attribute() [10/12]

template<typename T >

void sirius::HDF5_tree::write_attribute	(	const std::string &	name,
		const std::vector< T > &	data,
		const std::string &	dataset_name
	)		const

inline

Write array attribute.

Definition at line 556 of file hdf5_tree.hpp.

◆ write_attribute() [11/12]

template<typename T >

void sirius::HDF5_tree::write_attribute	(	const std::string &	name,
		const std::initializer_list< T > &	data
	)		const

inline

Write array attribute.

Definition at line 563 of file hdf5_tree.hpp.

◆ write_attribute() [12/12]

template<typename T >

void sirius::HDF5_tree::write_attribute	(	const std::string &	name,
		const std::initializer_list< T > &	data,
		const std::string &	dataset_name
	)		const

inline

Write array attribute.

Definition at line 570 of file hdf5_tree.hpp.

◆ read() [2/7]

template<int N>

void sirius::HDF5_tree::read	(	const std::string &	name,
		sddk::mdarray< std::complex< double >, N > &	data
	)

inline

Definition at line 577 of file hdf5_tree.hpp.

◆ read() [3/7]

template<typename T , int N>

void sirius::HDF5_tree::read	(	const std::string &	name,
		sddk::mdarray< T, N > &	data
	)

inline

Definition at line 588 of file hdf5_tree.hpp.

◆ read() [4/7]

template<typename T , int N>

void sirius::HDF5_tree::read	(	int	name_id,
		sddk::mdarray< T, N > &	data
	)

inline

Definition at line 598 of file hdf5_tree.hpp.

◆ read() [5/7]

template<typename T >

void sirius::HDF5_tree::read	(	std::string const &	name,
		T *	data,
		int	size
	)

inline

Read a vector or a scalar.

Definition at line 606 of file hdf5_tree.hpp.

◆ read() [6/7]

template<typename T >

void sirius::HDF5_tree::read	(	int	name_id,
		std::vector< T > &	vec
	)

inline

Definition at line 614 of file hdf5_tree.hpp.

◆ read() [7/7]

template<typename T >

void sirius::HDF5_tree::read	(	std::string const &	name,
		std::vector< T > &	vec
	)

inline

Definition at line 620 of file hdf5_tree.hpp.

◆ operator[]() [1/2]

HDF5_tree sirius::HDF5_tree::operator[] ( std::string const & path__ )

inline

Definition at line 625 of file hdf5_tree.hpp.

◆ operator[]() [2/2]

HDF5_tree sirius::HDF5_tree::operator[] ( int idx__ )

inline

Definition at line 631 of file hdf5_tree.hpp.

Member Data Documentation

◆ file_name_

std::string sirius::HDF5_tree::file_name_

private

HDF5 file name.

Definition at line 89 of file hdf5_tree.hpp.

◆ path_

std::string sirius::HDF5_tree::path_

private

path inside HDF5 file

Definition at line 92 of file hdf5_tree.hpp.

◆ file_id_

hid_t sirius::HDF5_tree::file_id_ {-1}

private

HDF5 file handler.

Definition at line 95 of file hdf5_tree.hpp.

◆ root_node_

bool sirius::HDF5_tree::root_node_ {true}

private

True if this is a root node.

Definition at line 98 of file hdf5_tree.hpp.

The documentation for this class was generated from the following file:

hdf5_tree.hpp

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ HDF5_tree() [1/2]

◆ HDF5_tree() [2/2]

◆ ~HDF5_tree()

Member Function Documentation

◆ string_type()

◆ array_type()

◆ write() [1/8]

◆ write_attribute() [1/12]

◆ write_attribute() [2/12]

◆ read() [1/7]

◆ create_node() [1/2]

◆ create_node() [2/2]

◆ write() [2/8]

◆ write() [3/8]

◆ write() [4/8]

◆ write() [5/8]

◆ write() [6/8]

◆ write() [7/8]

◆ write() [8/8]

◆ write_attribute() [3/12]

◆ write_attribute() [4/12]

◆ write_attribute() [5/12]

◆ write_attribute() [6/12]

◆ write_attribute() [7/12]

◆ write_attribute() [8/12]

◆ write_attribute() [9/12]

◆ write_attribute() [10/12]

◆ write_attribute() [11/12]

◆ write_attribute() [12/12]

◆ read() [2/7]

◆ read() [3/7]

◆ read() [4/7]

◆ read() [5/7]

◆ read() [6/7]

◆ read() [7/7]

◆ operator[]() [1/2]

◆ operator[]() [2/2]

Member Data Documentation

◆ file_name_

◆ path_

◆ file_id_

◆ root_node_