On my site, I host data on particle motion, including the motion of molecules in gases and liquids, as well as the motion of Lagrangian particles in turbulence. Most of these systems, like turbulence, exhibit intrinsically smooth time dynamics and can be simulated using conventional time-stepping algorithms such as direct numerical simulation (DNS). However, I also host data on the dynamics of hard-sphere fluids — statistical systems with intrinsically discrete, collision-based dynamics modeled using event-driven algorithms.
The data for hard-sphere systems is obtained using the DynamO particle simulator. DynamO outputs data in XML format and is designed to provide processed data. I, on the other hand, offer raw trajectory data for users to process themselves. I consider HDF5 to be a more convenient format for this purpose. Below, I describe how I store DynamO output in HDF5.