#!/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.vasp.parsers import IterativeVasprunParser, PoscarParser

from oppvasp.md import Trajectory

xml_filename = 'vasprun.xml'

npz_filename = 'trajectory.npz'

vtf_filename = 'trajectory.vtf'

if len(sys.argv) > 1:

npz_filename = sys.argv[1]

if os.path.isfile(npz_filename):

traj = Trajectory(filename = npz_filename)

else:

p = IterativeVasprunParser(xml_filename)

traj = p.get_all_trajectories()

traj.save(npz_filename)

basis = traj.basis

atoms = traj.atoms

nsteps = traj.length # NSW

nions = traj.num_atoms

positions = traj.positions

forces = traj.forces

total_energy = traj.total_energy

f = open(vtf_filename,'w')

# A bond is formed whenever two atoms are within (R1 + R2) x 0.6 of each other,

# where R1 and R2 are the respective radii of candidate atoms.

R = 2.0

def writeAtomDef(b,e,c):

f.write(str)

f.write("# Structure block\n")

b=0; e=0; c=-1

for at in atoms:

if c != at and e > 0:

writeAtomDef(b,e,c)

b = e

c = at

e += 1

writeAtomDef(b,e-1,c)

def norm(v):

return np.sqrt(np.dot(v,v))

def getUnitCell(i):

return a,b,c,alpha,beta,gamma

pbar = ProgressBar(widgets=[u'الرجاء الانتظار',Bar()], maxval = nsteps).start()

for i in range(nsteps):

pbar.update(i)

f.write("\n# Energy: %.3f\n" % total_energy[i])

f.write("timestep\n")

uc = getUnitCell(i)

f.write("pbc %.2f %.2f %.2f %.1f %.1f %.1f\n" % uc)

for j in range(nions):

# convert to cartesian (Angstrom):

at_pos = np.dot(positions[i,j], basis[i])

at_force = forces[i,j]

# should probably looking into optimization here

f.write("%.8f %.8f %.8f %.8f %.8f %.8f\n" % tuple(list(at_pos) + list(at_force)))

pbar.finish()

f.close()

print "Wrote %s" % (vtf_filename)