Writer::H5md::File Class Reference

Class for writing H5MD files. More...

#include <h5md_core.hpp>

Public Member Functions
	File (std::string file_path, std::string 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)
	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.
std::string	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	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 101 of file h5md_core.hpp.

Constructor & Destructor Documentation

File()

Writer::H5md::File::File	(	std::string	file_path,
		std::string	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
	)

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.

Definition at line 505 of file h5md_core.cpp.

References file_path().

~File()

Writer::H5md::File::~File ( )

default

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 183 of file h5md_core.hpp.

Referenced by 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 300 of file h5md_core.cpp.

file_path()

std::string Writer::H5md::File::file_path

(

)

const

Retrieve the path to the hdf5 file.

Returns

The path as a string.

Definition at line 503 of file h5md_core.cpp.

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

flush()

void Writer::H5md::File::flush

(

)

Method to enforce flushing the buffer to disk.

Definition at line 501 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 171 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 159 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 153 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 string.

Definition at line 147 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 165 of file h5md_core.hpp.

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

valid_fields()

auto Writer::H5md::File::valid_fields ( ) const

inline

Build the list of valid output fields.

Returns

The list as a vector of strings.

Definition at line 189 of file h5md_core.hpp.

References Writer::H5md::fields_map.

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 177 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 377 of file h5md_core.cpp.

References BoxGeometry::folded_image_box(), BoxGeometry::folded_position(), 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, BoxGeometry::lees_edwards_bc(), ParticleRange::size(), 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