gmx::H5md Class Reference

#include <gromacs/fileio/h5md/h5md.h>

Description

Manager of an H5MD filehandle. The class is designed to read/write data according to de Buyl et al., 2014 (https://doi.org/10.1016/j.cpc.2014.01.018) and https://www.nongnu.org/h5md/h5md.html.

Public Member Functions
	H5md (const std::filesystem::path &fileName, H5mdFileMode mode)
	Open an H5MD file and manage its filehandle. More...
	H5md (const H5md &)=delete
H5md &	operator= (const H5md &)=delete
	H5md (H5md &&)=delete
H5md &	operator= (H5md &&)=delete
hid_t	fileid () const
	Return the HDF5 handle of the file. More...
void	flush (bool throwExceptionUponError=true)
	Write all unwritten data to the file. More...
void	setupFileFromInput (const gmx_mtop_t &topology, const t_inputrec &inputRecord)
	Set up the file from input data. More...
void	setupFromExistingFile ()
	Set up from an existing file. More...
void	setupFromExistingFileForAppending (int64_t restartingFromStep, int64_t numParticles)
	Set up from an existing file when restarting a simulation from a checkpoint. More...
bool	readNextFrame (t_trxframe *frame, const std::string &selectionName="system")
	Read the next frame of the trajectory. More...
void	writeNextFrame (ArrayRef< const RVec > positions, ArrayRef< const RVec > velocities, ArrayRef< const RVec > forces, const matrix box, int64_t step, double time)
	Write input data as the next frame of the trajectory. More...

Constructor & Destructor Documentation

gmx::H5md::H5md	(	const std::filesystem::path &	fileName,
		H5mdFileMode	mode
	)

Open an H5MD file and manage its filehandle.

Parameters

[in]	fileName	Name of the file to open. The same as the file path.
[in]	mode	The mode to open the file.

Exceptions

FileIOError

if fileName is specified and the file cannot be opened.

Member Function Documentation

hid_t gmx::H5md::fileid

(

)

const

Return the HDF5 handle of the file.

This handle is used as the root container of the file's data hierarchy, to which the tree of groups and data sets can be added.

Returns

The file handle.

void gmx::H5md::flush

(

bool

throwExceptionUponError = true

)

Write all unwritten data to the file.

Parameters

[in]

throwExceptionUponError

Whether to throw an exception if an error occurs. Assumes a valid file_ identifier.

Exceptions

FileIOError

If there were errors during flushing (and throwExceptionUponError is true).

bool gmx::H5md::readNextFrame	(	t_trxframe *	frame,
		const std::string &	selectionName = "system"
	)

Read the next frame of the trajectory.

Parameters

[out]	frame	Container to read data into.
[in]	selectionName	Name of group to read frame for.

Returns

True if a frame was read, otherwise false.

void gmx::H5md::setupFileFromInput	(	const gmx_mtop_t &	topology,
		const t_inputrec &	inputRecord
	)

Set up the file from input data.

Parameters

[in]	topology	Topology data of system.
[in]	inputRecord	Simulation parameters.

void gmx::H5md::setupFromExistingFile

(

)

Set up from an existing file.

Scans for trajectory data available in the /particles/system group of the HDF5 file. For trajectories written by GROMACS this group contains data for all atoms in the simulated system.

Note

Ignores trajectory data in other subgroups of /particles.

void gmx::H5md::setupFromExistingFileForAppending	(	int64_t	restartingFromStep,
		int64_t	numParticles
	)

Set up from an existing file when restarting a simulation from a checkpoint.

Scans for trajectory data available in the /particles/system group of the HDF5 file. For trajectories written by GROMACS this group contains data for all atoms in the simulated system.

Note

Ignores trajectory data in other subgroups of /particles.

Parameters

[in]	restartingFromStep	Step which we are restarting the simulation from
[in]	numParticles	Number of particles in system

Exceptions

gmx::FileIOError

if the existing file contents are not for a system of numParticles.

void gmx::H5md::writeNextFrame	(	ArrayRef< const RVec >	positions,
		ArrayRef< const RVec >	velocities,
		ArrayRef< const RVec >	forces,
		const matrix	box,
		int64_t	step,
		double	time
	)

Write input data as the next frame of the trajectory.

Parameters

[in]	positions	Position data to write (or empty if not to write).
[in]	velocities	Velocity data to write (or empty if not to write).
[in]	forces	Force data to write (or empty if not to write).
[in]	box	Simulation box for frame.
[in]	step	Simulation step for frame.
[in]	time	Simulation time for frame.

Exceptions

gmx::FileIOError

if position, velocity or force data is given but the corresponding data set has not been created, or if the size of the data buffers do not match the number of atoms of the system.

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

• src/gromacs/fileio/h5md/h5md.h
• src/gromacs/fileio/h5md/h5md.cpp