md.simulation_hooks.MoleculeStream

class md.simulation_hooks.MoleculeStream(store_velocities: bool)

DataStream for logging atom types, positions and velocities to the group ‘molecules’ of the main hdf5 dataset. Positions and velocities are stored in a n_steps x n_replicas x n_molecules x 6 array, where n_steps is the number of simulation steps, n_replicas and n_molecules are the number of simulation replicas and different molecules. The first 3 of the final 6 components are the Cartesian positions and the last 3 the velocities in atomic units. Atom types, the numbers of replicas, molecules and atoms, as well as the length of the time step in atomic units (for spectra) are stored in the group attributes.

Parameters:

store_velocities (bool) – store atoms velocities in addition to positions