jax_md_mod.custom_quantity.self_diffusion_green_kubo

jax_md_mod.custom_quantity.self_diffusion_green_kubo#

self_diffusion_green_kubo(traj_state, time_step, t_cut)[source]#

Green-Kubo formulation to compute self-diffusion D via the velocity autocorrelation function (VACF).

\[D = \frac{1}{dim} Int_0^{t_cut} VACF(\tau) d\tau\]
Parameters:

  • traj_state – TrajectoryState containing a finely resolved trajectory.

  • time_step – Time lag between 2 adjacent states in the trajetcory. The simulation time step, in the usual case where every state is retained.

  • t_cut – Cut-off time: Biggest time-difference to consider in the VACF.

Returns:

A tuple (D, VACF). Estimate of self-diffusion D and VACF that can be used for additional post-processing / analysis.

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