pwtools.crys.smooth

pwtools.crys.smooth(traj, kern, method=1)[source]

Smooth Trajectory along timeaxis.

Each array in traj.attrs_nstep is smoothed by convolution with kern along timeaxis, i.e. coords, coords_frac, etot, … The kernel is only required to be a 1d array and is automatically broadcast to the shape of each array. A similar feature can be found in VMD -> Representations -> Trajectory.

Parameters:

  • traj (Trajectory) –

  • kern (1d array) – Convolution kernel (smoothing window, see smooth()).

  • method (int) –

    Choose how to do the convolution:

    1 : loops over 1d convolutions, easy on memory, sometimes faster than method=2 (default)
    2 : up to 3d kernel by broadcasting, can be very memory hungry for big traj (i.e. 1e5 timesteps, 128 atoms)

Returns:

tr – Has the same nstep and timestep as the input Trajectory.

Return type:

Trajectory

Examples

>>> kern = scipy.signal.hann(101)
>>> trs = smooth(tr, kern)