/usr/share/pyshared/ase/gui/neb.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | # -*- coding: utf-8 -*-
from math import sqrt
import numpy as np
from ase.neb import fit0
def NudgedElasticBand(images):
N = images.repeat.prod()
natoms = images.natoms // N
R = images.P[:, :natoms]
E = images.E
F = images.F[:, :natoms]
s, E, Sfit, Efit, lines = fit0(E, F, R)
import pylab
import matplotlib
#matplotlib.use('GTK')
pylab.ion()
x = 2.95
pylab.figure(figsize=(x * 2.5**0.5, x))
pylab.plot(s, E, 'o')
for x, y in lines:
pylab.plot(x, y, '-g')
pylab.plot(Sfit, Efit, 'k-')
pylab.xlabel(u'path [Å]')
pylab.ylabel(u'energy [eV]')
pylab.title('Maximum: %.3f eV' % max(Efit))
pylab.show()
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