def plot_to_file(self, outfile=''):
import matplotlib
matplotlib.use('pdf')
import matplotlib.pyplot as plt
fig = plt.figure()
ax1 = fig.add_subplot(2, 1, 1)
ax2 = fig.add_subplot(2, 1, 2)
self.plot_rdf(ax1)
self.getStructureFactor()
self.plot_sq(ax2)
if outfile == '':
outfile = os.path.splitext(sys.argv[0])[0] + '.pdf'
sys.stdout.write("Writing %s... " % os.path.basename(outfile))
sys.stdout.flush()
plt.savefig(outfile)
sys.stdout.write("done!\n")
if __name__ == '__main__':
print " --> Reading trajectory"
traj = read_trajectory(unwrap_pbcs=False)
#for at in range(0,65):
at = [10]
pl = PairDistributionFunctionPlot(traj, n_bins='auto', atoms=at)
pl.plot_to_file('%s_%s_%d.pdf' %
(os.getcwd().split('/').pop(), 'rdf', at[0]))
def plot_to_file(self, outfile = ''):
import matplotlib
matplotlib.use('pdf')
import matplotlib.pyplot as plt
fig = plt.figure()
ax1 = fig.add_subplot(2,1,1)
ax2 = fig.add_subplot(2,1,2)
self.plot_rdf(ax1)
self.getStructureFactor()
self.plot_sq(ax2)
if outfile == '':
outfile = os.path.splitext(sys.argv[0])[0] + '.pdf'
sys.stdout.write("Writing %s... " % os.path.basename(outfile))
sys.stdout.flush()
plt.savefig(outfile)
sys.stdout.write("done!\n")
if __name__ == '__main__':
print " --> Reading trajectory"
traj = read_trajectory(unwrap_pbcs = False)
#for at in range(0,65):
at = [10]
pl = PairDistributionFunctionPlot(traj, n_bins = 'auto', atoms = at)
pl.plot_to_file('%s_%s_%d.pdf' % (os.getcwd().split('/').pop(), 'rdf', at[0] ))
#print "y",y.shape
print self.y.shape
y = self.y[:mp]
return float(y[y < treshold].shape[0]) / y.shape[0]
#print y[not y>treshold].shape
if __name__ == "__main__":
from oppvasp import read_trajectory
from oppvasp.vasp.parsers import PoscarParser
#atom = 42
atom = 0
traj = read_trajectory( './', unwrap_pbcs = False )
poscar = '/Users/danmichael/Documents/Studier/Master/notur/hipersol/templates/si64/POSCAR'
pl = DistanceFromLatticeSites(trajectory = traj,
lattice = PoscarParser(poscar).get_structure(),
atom = atom, nn = 1, step = 50
)
first = True
def on_enter_site(obj):
global first
if first:
sys.stdout.write('\033[31;1mEntered lattice site at %.2f\033[0m\n' % obj['x'])
first = False
pl.entered_site.subscribe(on_enter_site)
pl.plot_to_file('%s_%s.pdf' % (os.getcwd().split('/').pop(), 'dist_from_lattice' ), verbose = False)
#dp.analyse()
def plot_to_file(self,outfile):
import matplotlib
matplotlib.use('pdf')
from oppvasp.plotutils import prepare_canvas
prepare_canvas('8 cm')
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subplot(1,1,1)
fig.subplots_adjust(left=0.17, bottom=0.20, right=0.80, top=0.95)
self.plot(ax)
plt.savefig(outfile)
if __name__ == '__main__':
from oppvasp import read_trajectory
traj = read_trajectory(unwrap_pbcs = True)
atom = 0
pl = DisplacementPlot(traj, atom = atom)
pl.plot_to_file('%s_%s.pdf' % (os.getcwd().split('/').pop(), 'displacement' ))
##!/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 import read_trajectory
#from oppvasp.plotutils import DisplacementPlot
def plot_to_file(self, outfile):
import matplotlib
matplotlib.use('pdf')
from oppvasp.plotutils import prepare_canvas
prepare_canvas('8 cm')
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
fig.subplots_adjust(left=0.17, bottom=0.20, right=0.80, top=0.95)
self.plot(ax)
plt.savefig(outfile)
if __name__ == '__main__':
from oppvasp import read_trajectory
traj = read_trajectory(unwrap_pbcs=True)
atom = 0
pl = DisplacementPlot(traj, atom=atom)
pl.plot_to_file('%s_%s.pdf' %
(os.getcwd().split('/').pop(), 'displacement'))
##!/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 import read_trajectory
#from oppvasp.plotutils import DisplacementPlot
