exatomic.algorithms.displacement module

Computation of Displacement

exatomic.algorithms.displacement.absolute_squared_displacement(universe, ref_frame=None)

Compute the mean squared displacement per atom per time with respect to the referenced position.

Computes the squared displacement using the Atom dataframe. In the case where this dataframe only contains the in unit cell coordinates, this may not give desired results.

Parameters:

• universe (Universe) – The universe containing atomic positions

• ref_frame (int) – Which frame to use as the reference (default first frame)

Returns

df (DataFrame): Time dependent displacement per atom