#!/usr/bin/env python
# -*- coding: utf-8; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
# vim:fenc=utf-8:et:sw=4:ts=4:sts=4:tw=0
import os, sys
import numpy as np
from progressbar import ProgressBar, Percentage, Bar, ETA, FileTransferSpeed, \
RotatingMarker, ReverseBar, SimpleProgress
from oppvasp.plotutils import DisplacementPlot
dp = DisplacementPlot()
dp.read_trajectory( dir = './' )
# Find the diffusivity of all atoms:
m = 65
D = np.zeros(m)
pbar = ProgressBar(widgets=['Henter diff koeff...',Percentage(),Bar()], maxval = m).start()
for at in range(m):
pbar.update(at)
D[at] = dp.get_diffusion_coeff(at)[0]
pbar.finish()
# Find the 3 atoms with the highest diffusivity:
arg = np.argsort(D)
include_atoms = arg[:-4:-1] # return the last three values (not including -4)
#pbar = ProgressBar(widgets=['Smoothen trajectories...',Percentage(),Bar()], maxval = m).start()
styles = [ { 'color' : c } for c in ['red','blue','black'] ]
first_step = 0
last_step = -1
if len(sys.argv) > 1:
first_step = int(sys.argv[1])
print "Starting from step %i" % (first_step)
if len(sys.argv) > 2:
last_step = int(sys.argv[2])
print "Ending at step %i" % (last_step)
# Read trajectory:
traj = read_trajectory(unwrap_pbcs=True, poscar_file='POSCAR')
traj.set_selection(first_step, last_step)
# Make plot
dp = DisplacementPlot(traj)
dp.add_plot(what='D', atom_no=0, smoothen=True, linear_fit=False)
#dp.ax1.legend(('All atoms', 'P'), ncol = 1, loc = 'upper left', frameon = False)
D = dp.get_diffusion_coeff([0])[0]
td = np.zeros((D.shape[0], 2))
td[:, 0] = dp.trajs[0].time
td[:, 1] = D
np.savetxt('out.csv', td, delimiter='\t')
Ds = D[-1]
Dm = np.mean(D[:])
dp.ax1.axhline(Dm, color='red')
dp.ax1.text(0.95,
0.95,
