2.2.10. Loading IBIsCO and YASP files with MDAnalysis

MDAnalysis is able to read IBIsCO / YASP TRZ binary trajectories, including the coordinates and velocities as well as:

  • pressure
  • pressure_tensor
  • total_energy
  • potential_energy
  • kinetic_energy
  • temperature

Which are stored in the Timestep.data dictionary. For example to view the kinetic energy for each timestep:

for ts in u.trajectory:
    print(ts.data['kinetic_energy'])

Trajectory data are read and written in binary representation but because this depends on the machine hardware architecture, MDAnalysis always reads and writes TRZ trajectories in little-endian byte order.

For the implementation details, see MDAnalysis.coordinates.TRZ.

There is currently no support for reading a topology for this format, however the Reader is able to determine the number of atoms and provide a minimal topology (ie no names etc, only indices of atoms). To get a topology, it is required to convert an input into an XYZ or similar format.