h5amep file format

Based on the Hierarchical Data Format version 5 (HDF5), HDFGroup/hdf5, AMEP introduces a new file format h5amep to store simulation data and additional metadata. This format is used in the backend of AMEP. The HDF5 files are structured into groups and datasets. The h5amep format has the following groups, subgroups, and attributes:

h5amep root
\amep
\info
    \authors
    \software
\scripts
\params
\type
\particles or \fields
\frames
    \steps
    \times
    \[frame0]
        \coords
        \velocities
        \...
    \[frame1]
        \...
    \...

The group amep contains information about the AMEP version that has been used to create the h5amep file. The group info contains the saved information about authors and software. The scripts group gives the possibility to save text files such as simulation scripts and log files that correspond to the simulation data. In the params group, AMEP stores parameters such as the simulation timestep for example. Additional simulation parameters can be added. The attribute type contains a flag about the type of data stored in the h5amep file. This can be either "particle" or "field". The groups particles and fields contain user-defined information about the particles and the fields used in the simulation, respectively. Finally, the group frames contains multiple datasets and subgroups with the simulation data. The dataset steps stores a list of all the frame numbers (i.e., the number of timesteps for each frame) and the dataset times the corresponding (physical) time, while the individual frames of the simulation are stored in subgroups of frames named by their simulation step. Within an individual frame, the simulation data is stored, e.g., coordinates and velocities for particle-based simulations or density and concentrations for continuum simulations, as separate datasets.

This section is an excerpt of the AMEP publication.