dynsight.descriptors.orientational_order_param¶

dynsight.descriptors.orientational_order_param(universe, neigh_list_per_frame, order=6)[source]¶

Compute the magnitude of the orientational order parameter.

\[| \psi^{(n)}_i | = \frac{1}{N_i} \sum_{j=1}^{N_{i}} e^{i n \theta_{ij}}\]

where n is the symmetry order.

Warning

Particles are considered as laying in the (x, y) plane. z-coordinates are ignored.

Parameters:

universe (Universe) – contains the coordinates at each frame.
neigh_list_per_frame (list[list[AtomGroup]]) – A frame-by-frame list of the neighbors of each atom, output of listNeighboursAlongTrajectory().
order (int) – the order of the symmetry measured by the descriptor. Default is 6, corresponding to the hexatic order parameter.

Returns:

An array of shape (n_atoms, n_frames), with the values of psi.

Return type:

NDArray[np.float64]

Example

import numpy as np
from dynsight.trajectory import Trj
from dynsight.descriptors import orientational_order_param

trj = Trj.init_from_xyz(path / "trajectory.xyz", dt=1.0)
neig_counts, _ = trj.get_coord_number(r_cut=3.0)

psi = orientational_order_param(
    universe=trj.universe,
    neigh_list_per_frame=neig_counts,
)