md.simulation_hooks.PropertyStream

class md.simulation_hooks.PropertyStream(target_properties: List[str] | None = None)

Main routine for logging the properties predicted by the calculator to the group ‘properties’ of hdf5 dataset. Stores properties in a flattened array and writes names, shapes and positions to the group data section. Since this routine determines property shapes based on the system.properties dictionary, at least one computations needs to be performed beforehand. Properties are stored in an array of the shape n_steps x n_replicas x n_molecules x n_properties, where n_steps is the number of simulation steps, n_replicas and n_molecules is the number of simulation replicas and different molecules and n_properties is the length of the flattened property array.

Parameters:

target_properties (list) – List of properties to be written to the hdf5 database. If no list is given, defaults to None, which means all properties are stored.