The H5MD Mosaic module

H5MD is a modular file format for trajectory files in molecular simulation, based on HDF5. It defines how the typically large time-dependent datasets in trajectories are stored, but it does not define a description for the simulation universe itself because such descriptions are very domain specific. The combination of H5MD and Mosaic provides a complete specification for self-contained trajectory files, i.e. trajectory files that do not require additional information for their interpretation.

The H5MD specification consists of a basic format specification plus so-called modules for additional domain-specific specifications. The combination of H5MD and Mosaic is thus defined in the following by a specification of the “Mosaic module” for H5MD.

Objective

The Mosaic module provides a way to store the definition of a simulation universe and of subsets of the particles using Mosaic data items. These data items assign a number to each site of each atom. These numbers are the indices of the particle data in the trajectory.

Module name and version

The name of this module is mosaic. The module version is 0.1.0.

Mosaic root group

H5MD files applying the Mosaic module contain an additional group at the root level, i.e. next to the h5md group. This additional group is called mosaic and contains all Mosaic data items related to the trajectory.

The mosaic group contains one obligatory item, the simulation universe, in a group called universe. It may not contain more than one universe data item. It can contain any number of other Mosaic data items, whose names are subject to the same rules as the names of particle groups in H5MD.

Each subgroup of the H5MD particles group must have a corresponding Mosaic data item in the mosaic group that has the same name. This data item can either be the simulation universe, or a selection data item. Each H5MD particle corresponds to a Mosaic site. The site order defined by the Mosaic universe or selection thus assigns a site to each position in the particles group.

The box groups in the H5MD trajectory must be compatible with the simulation universe: the dimension must be 3, the boundary must be [none, none, none] for a universe with “infinite” cell shape and [periodic, periodic, periodic] for a universe of any other currently defined cell shape, and the edges must also be compatible with the universe’s cell shape.