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, boost::mpi::communicator comm=boost::mpi::communicator())
	Constructor.
	~File ()=default
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	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 103 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, boost::mpi::communicator  comm = boost::mpi::communicator()  )

inline

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.
comm	The MPI communicator.

Definition at line 118 of file h5md_core.hpp.

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 197 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 279 of file h5md_core.cpp.

file_path()

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

inline

Retrieve the path to the hdf5 file.

Returns

The path as a string.

Definition at line 155 of file h5md_core.hpp.

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 478 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 185 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 173 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 167 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 161 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 179 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 203 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 191 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 356 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