Definitions corresponding to bulk_hdf5.hpp. More...

#include <bitset>
#include <cstdint>
#include <H5Cpp.h>
#include <bulk_hdf5.hpp>

Include dependency graph for bulk_hdf5.cpp:

Functions
void	alma::write_string_attribute (H5Location &loc, const std::string &name, const std::string &value)
	Add a string-valued attribute to an HDF5 file, group, or dataset. More...

template<typename T >
void	alma::create_eigen_dataset (CommonFG &loc, const Eigen::DenseBase< T > &data, const std::string &name, const std::string &units)
	Create a dataset from an Eigen object. More...

void	alma::write_file_attributes (H5File &file, const std::string &description)
	Write some metadata to the HDF5 file as attributes. More...

void	alma::create_groups (H5File &file)
	Create some predefined groups in the HDF5 file. More...

void	alma::save_bulk_hdf5 (const char *filename, const std::string &description, const Crystal_structure &cell, const Symmetry_operations &symmetries, const Gamma_grid &grid, const std::vector< Threeph_process > &processes, const boost::mpi::communicator &comm)
	Save all relevant information about a bulk material to an HDF5 file. More...

std::string	alma::read_file_attributes (H5File &file)
	Read an HDF5 file's metadata and check if the versions are compatible. More...

std::tuple< std::string, std::unique_ptr< Crystal_structure >, std::unique_ptr< Symmetry_operations >, std::unique_ptr< Gamma_grid >, std::unique_ptr< std::vector< Threeph_process > > >	alma::load_bulk_hdf5 (const char *filename, const boost::mpi::communicator &comm)
	Reconstruct all data structures from a file saved with save_bulk_hdf5(). More...

std::vector< std::string >	alma::list_scattering_subgroups (const char *filename, const boost::mpi::communicator &comm)
	Return the names of all subgroups in the "/scattering" group of an HDF5 file. More...

Scattering_subgroup	alma::load_scattering_subgroup (const char *filename, const std::string &groupname, const boost::mpi::communicator &comm)
	Read the scattering rates stored in a subgroup from the "/scattering" group. More...

void	alma::write_scattering_subgroup (const char *filename, const Scattering_subgroup &group, const boost::mpi::communicator &comm)
	Add a subgroup to the "/scattering" group of the HDF5 file. More...

Variables
constexpr std::size_t	ABSORPTION_BIT = 0
	Constants used to build the "/threeph_processes/type" dataset. More...

constexpr std::size_t	GAUSSIAN_BIT = 1

constexpr std::size_t	VP2_BIT = 2

Detailed Description

Definitions corresponding to bulk_hdf5.hpp.

Function Documentation

◆ create_eigen_dataset()

template<typename T >

void alma::create_eigen_dataset	(	CommonFG &	loc,
		const Eigen::DenseBase< T > &	data,
		const std::string &	name,
		const std::string &	units
	)

Create a dataset from an Eigen object.

All objects are assumed to be 2D, and their contents are assumed to be double-precission floating point numbers.

Parameters

[in,out]	loc	- the HDF5 file or group
[in]	data	- the Eigen object
[in]	name	- the name of the dataset
[in]	units	- the units of the data

◆ create_groups()

void alma::create_groups ( H5File & file )

Create some predefined groups in the HDF5 file.

Parameters

[in,out] file - the hdf5 file

◆ list_scattering_subgroups()

std::vector< std::string > alma::list_scattering_subgroups	(	const char *	filename,
		const boost::mpi::communicator &	comm
	)

Return the names of all subgroups in the "/scattering" group of an HDF5 file.

An empty vector is returned both when the "/scattering" group does not exist and when it exists but does not contain any subset.

Parameters

[in]	filename	- path to the HDF5 file
[in]	comm	- MPI communicator used to coordinate with all other processes

Returns: a vector of subgroup names

◆ load_bulk_hdf5()

std::tuple< std::string, std::unique_ptr< Crystal_structure >, std::unique_ptr< Symmetry_operations >, std::unique_ptr< Gamma_grid >, std::unique_ptr< std::vector< Threeph_process > > > alma::load_bulk_hdf5	(	const char *	filename,
		const boost::mpi::communicator &	comm
	)

Reconstruct all data structures from a file saved with save_bulk_hdf5().

Parameters

[in]	filename	- path to the HDF5 file
[in]	comm	- MPI communicator used to determine which part of the data to load in this process.

Returns: a tuple with all the information in the file, namely: description - a free-format description cell - description of the unit cell symmetries - symmetry operations of the unit cell grid - phonon spectrum on a refular grid processes - allowed three-phonon processes

◆ load_scattering_subgroup()

Scattering_subgroup alma::load_scattering_subgroup	(	const char *	filename,
		const std::string &	groupname,
		const boost::mpi::communicator &	comm
	)

Read the scattering rates stored in a subgroup from the "/scattering" group.

The existence of the group is not checked.

Parameters

[in]	filename	- path to the HDF5 file
[in]	groupname	- name of the group
[in]	comm	- MPI communicator used to coordinate with all other processes

Returns: a Scattering_subgroup structure

◆ read_file_attributes()

std::string alma::read_file_attributes ( H5File & file )

Read an HDF5 file's metadata and check if the versions are compatible.

Parameters

[in] file - the HDF5 file

Returns: the description stored in the file

◆ save_bulk_hdf5()

void alma::save_bulk_hdf5	(	const char *	filename,
		const std::string &	description,
		const Crystal_structure &	cell,
		const Symmetry_operations &	symmetries,
		const Gamma_grid &	grid,
		const std::vector< Threeph_process > &	processes,
		const boost::mpi::communicator &	comm
	)

Save all relevant information about a bulk material to an HDF5 file.

Parameters

[in]	filename	- path to the HDF5 file. It can be NULL for all processes except the one with rank == 0.
[in]	description	- a free-format description
[in]	cell	- description of the unit cell
[in]	symmetries	- symmetry operations of the unit cell
[in]	grid	- phonon spectrum on a refular grid
[in]	processes	- allowed three-phonon processes
[in]	comm	- MPI communicator used to coordinate with all other processes

◆ write_file_attributes()

void alma::write_file_attributes	(	H5File &	file,
		const std::string &	description
	)

Write some metadata to the HDF5 file as attributes.

Parameters

[in,out]	file	- the HDF5 file
[in]	description	- a free-format description

◆ write_scattering_subgroup()

void alma::write_scattering_subgroup	(	const char *	filename,
		const Scattering_subgroup &	group,
		const boost::mpi::communicator &	comm
	)

Add a subgroup to the "/scattering" group of the HDF5 file.

The existence of the group is not checked.

Parameters

[in]	filename	- path to the HDF5 file
[in]	group	- information about the group
[in]	comm	- MPI communicator used to coordinate with all other processes

◆ write_string_attribute()

void alma::write_string_attribute	(	H5Location &	loc,
		const std::string &	name,
		const std::string &	value
	)

Add a string-valued attribute to an HDF5 file, group, or dataset.

Note that UTF-8 encoding is assumed.

Parameters

[in,out]	loc	- HDF5 file, group, or dataset
[in]	name	- attribute identifier
[in]	value	- attribute value

Variable Documentation

◆ ABSORPTION_BIT

constexpr std::size_t ABSORPTION_BIT = 0

Constants used to build the "/threeph_processes/type" dataset.

See below for details.

Functions

Variables

Detailed Description

Function Documentation

◆ create_eigen_dataset()

◆ create_groups()

◆ list_scattering_subgroups()

◆ load_bulk_hdf5()

◆ load_scattering_subgroup()

◆ read_file_attributes()

◆ save_bulk_hdf5()

◆ write_file_attributes()

◆ write_scattering_subgroup()

◆ write_string_attribute()

Variable Documentation

◆ ABSORPTION_BIT