Descriptors¶

tICA¶

many_body_tica

tICA (time-lagged Independent Component Analysis) is a dimensionality reduction method. Time-series data are mapped to components characterizing the slowest processes, by maximizing the data correlation function at a given lag-time.

This module allows to perform tICA on trajectories from many-body systems, where the observables under analysis are single-particle descriptors, which should not be mixed within the tICs.

This module uses the TICA class from the deeptime.decomposition package (see the documentation page). deeptime requires numpy <= 2.1.

Velocity alignment¶

velocity_alignment

Computes the average velocity alignment between the central particle and the neighboring ones. The alignment is computed as the cosine between the velocities. Thus, the output is a number between 1 (perfect alignment) and -1 (perfect anti-alignment).

Orinetational order parameter¶

orientational_order_param

Computes orientational order parameter for the neighbors of each atom in the trajectory. The output is a real number between 0 and 1, where 1 corresponds to a perfect order, and 0 to completely random positions.