gmx::H5mdParticleBlock Class Reference

#include <gromacs/fileio/h5md/h5md_particleblock.h>

Description

Class which manages trajectory data inside of a H5md particle group.

Per the H5md specification, trajectory data for subgroups is stored in the tree hierarchy as:

-- /particles/group1 -- box -- edges -- value: real[numFrames][3][3] -- position -- value: RVec[numFrames][numAtoms] -- step: int64_t[numFrames] -- (time): double[numFrames] (optional) -- velocity -- value: RVec[numFrames][numAtoms] -- step: int64_t[numFrames] -- (time): double[numFrames] (optional) -- force -- value: RVec[numFrames][numAtoms] -- step: int64_t[numFrames] -- (time): double[numFrames] (optional)

This class collects data sets for a single group into one object, providing access to H5mdTimeDataBlocks<RVec> for position, velocity and force using getters, and a H5mdFrameDataSet<real> for the simulation box.

Use the H5mdParticleBlockBuilder builder class to construct this object by adding selected data sets at will.

Public Member Functions
bool	hasBox () const
	Return whether the block stores a per-position-frame box value, else false.
bool	hasPosition () const
	Return whether the block stores a position block.
bool	hasVelocity () const
	Return whether the block stores a velocity block.
bool	hasForce () const
	Return whether the block stores a force block.
bool	hasTime () const
	Return whether time is stored in any of the managed data block sets.
int64_t	numParticles () const
	Return the number of particles for the managed blocks (0 if none are managed).
std::optional < H5mdFrameDataSet< real > > &	box ()
	Get the simulation box data set.
std::optional < H5mdTimeDataBlock< RVec > > &	position ()
	Get the position data set.
std::optional < H5mdTimeDataBlock< RVec > > &	velocity ()
	Get the velocity data set.
std::optional < H5mdTimeDataBlock< RVec > > &	force ()
	Get the force data set.

Friends
class	H5mdParticleBlockBuilder

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

• src/gromacs/fileio/h5md/h5md_particleblock.h
• src/gromacs/fileio/h5md/h5md_particleblock.cpp