#!/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 optparse import OptionParser

from oppvasp.vasp.parsers import read_trajectory

from oppvasp.plotutils import DisplacementPlot

################################# OPTIONS ########################################

# Parse cmd line args

parser = OptionParser()

pdf_file = os.path.splitext(os.path.basename(sys.argv[0]))[0] + '.pdf'

parser.add_option('--pdf', dest = 'pdf_file', default = pdf_file, help = 'Destination PDF')

parser.add_option('--xml', dest = 'xml_file', default = 'vasprun.xml', help = 'Input vasprun.xml')

parser.add_option('--poscar', dest = 'poscar_file', default = 'POSCAR', help = 'Input POSCAR')

parser.add_option('-f', '--firststep', metavar='STEP', dest = 'first_step', type='int', default = 1, help = 'First ion step to include')

parser.add_option('-l', '--laststep', metavar='STEP', dest = 'last_step', type='int', default = -1, help = 'Last ion step to include')

parser.add_option('-a', '--atom', metavar='ATOM', dest = 'atom_no', type='int', default = 0, help = 'Index of atom to watch (first index is 0)')

(options, args) = parser.parse_args()

print "Range: %i:%i. Atom: %i" % (options.first_step, options.last_step, options.atom_no)

############################## MAIN SCRIPT ######################################

# Read trajectory:

traj = read_trajectory(xml_file = options.xml_file, unwrap_pbcs = True, poscar_file = options.poscar_file)

traj.set_selection(options.first_step, options.last_step)

# Make plot

dp = DisplacementPlot(traj)

dp.add_plot( what = 'r2', smoothen = True, style = { 'linestyle' : '--', 'dashes' : (3,1), 'color' : 'black' } ) # avg r^2 for all atoms

#dp.add_plot( what = 'x', atom_no = 0, smoothen = True, linear_fit = True)

dp.add_plot( what = 'r2', atom_no = 0, smoothen = True, linear_fit = False)

#dp.add_plot( what = 'r', atom_no = 0, smoothen = True, linear_fit = True)

#dp.add_plot( what = 'x', atom_no = 0, smoothen = False, style = { 'zorder' : -1, 'alpha': 0.4, 'color': 'gray' } )

ymax = 0

ymin = 0

for p in dp.plotdata:

ymax_tmp = np.max(p['y'])

if ymax_tmp > ymax:

ymax = ymax_tmp

ymin_tmp = np.min(p['y'])

if ymin_tmp < ymin:

ymin = ymin_tmp

ymax = (ymax)*1.1

ymin = (ymin)*1.1

dp.ax1.set_ylim(ymin,ymax)

dp.save_plot(options.pdf_file)