xyz2nmode module

This module contains classes to project an XYZ trajectory file into normal-mode coordinates.

class xyz2nmode.prob_dist_on_nm(phonon_info_file, ref_struc, traj_file, prefix, start_frame=1, end_frame=None, remove_rot_trans=True, par_exec=True, mode_list=None, freq_scaled=True, nmode_traj=True, hist_start=- 5.0, hist_end=5.0, hist_nbin=1001)

Bases: object

This class projects a whole trajectory into normal modes and computes probability distribution. This can be done either with serial or parallel (using MPI4Py) execution.

Arguments:

phonon_info_file = A string. Path to the ipi-restart file of the phonon calculation or phonon file generated by pyepfd.

ref_struc = A string. Path to the geometry optimized xyz file.

traj_file = A string.. Path to the actual trajectory (XYZ) file.

prefix = A string. Prefix for the output files.

start_frame = An intiger. Starting frame of the trajectory. Default 1.

end_frame = An intiger. End frame of the trajectory up to which is considered for the statistics. Default: index of the last frame in the trajectory.

par_exec = A boolean. If true parallel execution would be preferred provided MPI4PY is available.

mode_list = A list of integers. Supplied modes on which projection must be made. Default all active modes based on the acoustic sum rule in the phonon_info_file.

freq_scaled = A Boolean. If True then the output would be in frequency scaled unit. If frequency scaled then correspondig result would be equivalent to V(x) = 0.5*x**2.

nmode_traj = A Boolean. If True it would write the whole trajectory in normal mode coordinates.

hist_start = A float. Grid points from where histogram of probability density would begin. Default -5.0.

hist_end = A float. Grid points from where histogram of probability density would end.

hist_nbin = An integer. Number of bins on the probability density histogram