Writer::H5md::File Class Reference

Class for writing H5MD files. More...

#include <h5md_core.hpp>

Public Member Functions
	File (std::filesystem::path file_path, std::filesystem::path script_path, std::vector< std::string > const &output_fields, std::string mass_unit, std::string length_unit, std::string time_unit, std::string force_unit, std::string velocity_unit, std::string charge_unit, int chunk_size)
	Constructor.
	~File ()
void	close ()
	Method to perform the renaming of the temporary file from "filename" + ".bak" to "filename".
void	write (const ParticleRange &particles, double time, int step, BoxGeometry const &geometry)
	Write data to the hdf5 file.
auto const &	file_path () const
	Retrieve the path to the hdf5 file.
auto const &	script_path () const
	Retrieve the path to the simulation script.
auto const &	mass_unit () const
	Retrieve the set mass unit.
auto const &	length_unit () const
	Retrieve the set length unit.
auto const &	time_unit () const
	Retrieve the set time unit.
auto const &	force_unit () const
	Retrieve the set force unit.
auto const &	velocity_unit () const
	Retrieve the set velocity unit.
auto const &	charge_unit () const
	Retrieve the set charge unit.
auto const &	chunk_size () const
	Retrieve the set chunk size.
std::vector< std::string >	valid_fields () const
	Build the list of valid output fields.
void	flush ()
	Method to enforce flushing the buffer to disk.

Detailed Description

Class for writing H5MD files.

Definition at line 75 of file h5md_core.hpp.

Constructor & Destructor Documentation

File()

Writer::H5md::File::File	(	std::filesystem::path	file_path,
		std::filesystem::path	script_path,
		std::vector< std::string > const &	output_fields,
		std::string	mass_unit,
		std::string	length_unit,
		std::string	time_unit,
		std::string	force_unit,
		std::string	velocity_unit,
		std::string	charge_unit,
		int	chunk_size
	)

Constructor.

Parameters

file_path	Name for the hdf5 file on disk.
script_path	Path to the simulation script.
output_fields	Properties to write to disk.
mass_unit	The unit for mass.
length_unit	The unit for length.
time_unit	The unit for time.
force_unit	The unit for force.
velocity_unit	The unit for velocity.
charge_unit	The unit for charge.
chunk_size	The chunk size for DataSet in hdf5 file

Definition at line 702 of file h5md_core.cpp.

References chunk_size().

~File()

Writer::H5md::File::~File

(

)

Definition at line 727 of file h5md_core.cpp.

References close().

Member Function Documentation

charge_unit()

auto const & Writer::H5md::File::charge_unit ( ) const

inline

Retrieve the set charge unit.

Returns

The unit as a string.

Definition at line 158 of file h5md_core.hpp.

Referenced by ScriptInterface::Writer::H5md::H5md().

chunk_size()

auto const & Writer::H5md::File::chunk_size ( ) const

inline

Retrieve the set chunk size.

Definition at line 163 of file h5md_core.hpp.

Referenced by File(), and ScriptInterface::Writer::H5md::H5md().

close()

void Writer::H5md::File::close

(

)

Method to perform the renaming of the temporary file from "filename" + ".bak" to "filename".

Definition at line 371 of file h5md_core.cpp.

Referenced by ~File().

file_path()

auto const & Writer::H5md::File::file_path ( ) const

inline

Retrieve the path to the hdf5 file.

Returns

The path as a file system object.

Definition at line 116 of file h5md_core.hpp.

Referenced by ScriptInterface::Writer::H5md::H5md().

flush()

void Writer::H5md::File::flush

(

)

Method to enforce flushing the buffer to disk.

This pushes all buffers to the Virtual File Driver (VFD) layer. However, the file superblock, which contains the address space information (End of Allocation, EOA), won't be flushed. Therefore, the file won't necessarily be in a guaranteed consistent state for a read operation by another HDF5 parser. Only the close() method can flush the EOA.

Definition at line 695 of file h5md_core.cpp.

force_unit()

auto const & Writer::H5md::File::force_unit ( ) const

inline

Retrieve the set force unit.

Returns

The unit as a string.

Definition at line 146 of file h5md_core.hpp.

Referenced by ScriptInterface::Writer::H5md::H5md().

length_unit()

auto const & Writer::H5md::File::length_unit ( ) const

inline

Retrieve the set length unit.

Returns

The unit as a string.

Definition at line 134 of file h5md_core.hpp.

Referenced by ScriptInterface::Writer::H5md::H5md().

mass_unit()

auto const & Writer::H5md::File::mass_unit ( ) const

inline

Retrieve the set mass unit.

Returns

The unit as a string.

Definition at line 128 of file h5md_core.hpp.

Referenced by ScriptInterface::Writer::H5md::H5md().

script_path()

auto const & Writer::H5md::File::script_path ( ) const

inline

Retrieve the path to the simulation script.

Returns

The path as a file system object.

Definition at line 122 of file h5md_core.hpp.

Referenced by ScriptInterface::Writer::H5md::H5md().

time_unit()

auto const & Writer::H5md::File::time_unit ( ) const

inline

Retrieve the set time unit.

Returns

The unit as a string.

Definition at line 140 of file h5md_core.hpp.

Referenced by ScriptInterface::Writer::H5md::H5md().

valid_fields()

std::vector< std::string > Writer::H5md::File::valid_fields

(

)

const

Build the list of valid output fields.

Returns

The list as a vector of strings.

Definition at line 697 of file h5md_core.cpp.

References Writer::H5md::fields_map, and stream.

velocity_unit()

auto const & Writer::H5md::File::velocity_unit ( ) const

inline

Retrieve the set velocity unit.

Returns

The unit as a string.

Definition at line 152 of file h5md_core.hpp.

Referenced by ScriptInterface::Writer::H5md::H5md().

write()

void Writer::H5md::File::write	(	const ParticleRange &	particles,
		double	time,
		int	step,
		BoxGeometry const &	geometry
	)

Write data to the hdf5 file.

Parameters

particles	Particle range for which to write data.
time	Simulation time.
step	Simulation step (monotonically increasing).
geometry	The box dimensions.

Definition at line 567 of file h5md_core.cpp.

References Particle::force(), Writer::H5md::H5MD_OUT_BONDS, Writer::H5md::H5MD_OUT_BOX_L, Writer::H5md::H5MD_OUT_CHARGE, Writer::H5md::H5MD_OUT_FORCE, Writer::H5md::H5MD_OUT_IMG, Writer::H5md::H5MD_OUT_LE_DIR, Writer::H5md::H5MD_OUT_LE_NORMAL, Writer::H5md::H5MD_OUT_LE_OFF, Writer::H5md::H5MD_OUT_MASS, Writer::H5md::H5MD_OUT_POS, Writer::H5md::H5MD_OUT_TYPE, Writer::H5md::H5MD_OUT_VEL, Particle::id(), BoxGeometry::lees_edwards_bc(), Particle::mass(), Particle::q(), ParticleRange::size(), stream, Particle::type(), Particle::v(), Writer::H5md::write_box(), Writer::H5md::write_dataset(), Writer::H5md::write_le_dir(), Writer::H5md::write_le_normal(), and Writer::H5md::write_le_off().

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

• h5md_core.hpp
• h5md_core.cpp