matlantis_features.features.md.post_features.diffusion.get_msd(positions_array: ndarray, masses: ndarray, element_indices: OrderedDict, com_indices: Optional[List[List[int]]] = None, direction: Optional[ndarray] = None, method: str = ‘normal’) → Tuple[ndarray, Optional[ndarray]]#

Calculate the mean squared displacement.

Parameters

  • positions_array (np.ndarray) – The atomic position of each atom in each step.

  • masses (np.ndarray) – The atomic number of each atom.

  • element_indices (OrderedDict) – The indices of atoms of each element.

  • com_indices (Optional[List[List[int]]], optional) – The indices of atoms who form a molecule. If it is used, the diffusion coefficient
    of the center of mass of molecules will be calculated. Defaults to None.

  • direction (Optional[np.ndarray], optional) – Calculate the diffusion coefficient along specific directions. It must be a nx3 array
    where n is number of directions. If None, only the diffusion coefficient along
    x, y and z directions is calculated. Defaults to None

  • method (str, optional) – The method to calculate mean square displacement (MSD). Now, two methods, i.e.
    “normal” and “segment”, are supported. Defaults to “normal”.

Returns

the mean square displacement of each atom, the mean square
displacement of each molecule.

Return type

tuple[np.ndarray, np.ndarray or None]