def vasputil_dosplot(options, args, dir):
#!/usr/bin/python
# -*- coding: utf-8 -*-
# vim: set fileencoding=utf-8
# Copyright (c) 2008, 2009, 2010 Janne Blomqvist
# This source code file is subject to the terms of the MIT (Expat)
# License. See the file LICENSE for details.
"""Example plotting script demonstrating how to use the vasputil.dos module
and the ase.calculators.vasp.VaspDos class."""
import sys, os
print dir
os.chdir(dir)
sys.path.append('/fslhome/bch/pythonscripts/ase-3.6.0.2515/')
sys.path.append('/fslhome/bch/pythonscripts/vasputil-5.7/')
sys.path.append('/fslhome/bch/pythonscripts/vasputil-5.7/scripts/')
sys.path.append('/fslhome/bch/pythonscripts/vasputil-5.7/scripts/vasputil')
import vasputil.dos as d
import ase.calculators.vasp as v
import matplotlib.pyplot as plt
from optparse import OptionParser
usage = """%prog [options] DOSCAR atom
atom is the index of the atom, starting from 0. If omitted, plots the total
DOS, or the integrated total DOS if additionally the -i option is present.
"""
parser = OptionParser(usage)
parser.add_option("-f", "--fermi", dest="fermi", help="Fermi energy")
parser.add_option("-o", "--orbital", dest="orb", help="Orbital, either \
string or integer. For non-spin polarized s=0, p=1, \
d=2, if spin polarized s+=0, s-=1 etc. If phase factors: s, py, pz, px, \
dxy, dyz, dz2, dxz, dx2, and equivalent as previous for spin polarized etc.")
parser.add_option('-i', '--integrated', dest='integ', action='store_true',
help='Show the integrated total DOS')
(options, argsdummy) = parser.parse_args()
# By default VaspDos constructor tries to read a file called "DOSCAR".
dc = v.VaspDos(args[0])
if options.fermi:
fermi = float(options.fermi)
dc.efermi = fermi
if options.orb:
try:
orb = int(options.orb)
except ValueError:
orb = options.orb
else:
orb = 0
en = dc.energy # This is the x-axis in a typical DOS plot.
fig = plt.figure()
ax = fig.add_subplot(111)
if len(args) == 2:
atom = int(args[1])
label = "Atom " + str(atom) + " orbital " + str(orb)
ax.plot(en, dc.site_dos(atom, orb), label=label)
elif options.integ:
label = 'Integrated total DOS'
if len(dc.integrated_dos.shape) == 1:
ax.plot(en, dc.integrated_dos, label=label)
else:
ul = label + ' spin up'
ax.plot(en, dc.integrated_dos[0, :], label=ul)
dl = label + ' spin down'
ax.plot(en, dc.integrated_dos[1, :], label=dl)
else:
label = 'Total DOS'
if len(dc.dos.shape) == 1:
ax.plot(en, dc.dos, label=label)
else:
ul = label + ' spin up'
ax.plot(en, dc.dos[0, :], label=ul)
dl = label + ' spin down'
ax.plot(en, dc.dos[1, :], label=dl)
d.set_labels()
plt.show()
plt.savefig('dos')
def vasputil_dosplot(options, args, dir):
#!/usr/bin/python
# -*- coding: utf-8 -*-
# vim: set fileencoding=utf-8
# Copyright (c) 2008, 2009, 2010 Janne Blomqvist
# This source code file is subject to the terms of the MIT (Expat)
# License. See the file LICENSE for details.
"""Example plotting script demonstrating how to use the vasputil.dos module
and the ase.calculators.vasp.VaspDos class."""
import sys, os
print dir
os.chdir(dir)
sys.path.append('/fslhome/bch/pythonscripts/ase-3.6.0.2515/')
sys.path.append('/fslhome/bch/pythonscripts/vasputil-5.7/')
sys.path.append('/fslhome/bch/pythonscripts/vasputil-5.7/scripts/')
sys.path.append('/fslhome/bch/pythonscripts/vasputil-5.7/scripts/vasputil')
import vasputil.dos as d
import ase.calculators.vasp as v
import matplotlib.pyplot as plt
from optparse import OptionParser
usage = """%prog [options] DOSCAR atom
atom is the index of the atom, starting from 0. If omitted, plots the total
DOS, or the integrated total DOS if additionally the -i option is present.
"""
parser = OptionParser(usage)
parser.add_option("-f", "--fermi", dest="fermi", help="Fermi energy")
parser.add_option("-o",
"--orbital",
dest="orb",
help="Orbital, either \
string or integer. For non-spin polarized s=0, p=1, \
d=2, if spin polarized s+=0, s-=1 etc. If phase factors: s, py, pz, px, \
dxy, dyz, dz2, dxz, dx2, and equivalent as previous for spin polarized etc."
)
parser.add_option('-i',
'--integrated',
dest='integ',
action='store_true',
help='Show the integrated total DOS')
(options, argsdummy) = parser.parse_args()
# By default VaspDos constructor tries to read a file called "DOSCAR".
dc = v.VaspDos(args[0])
if options.fermi:
fermi = float(options.fermi)
dc.efermi = fermi
if options.orb:
try:
orb = int(options.orb)
except ValueError:
orb = options.orb
else:
orb = 0
en = dc.energy # This is the x-axis in a typical DOS plot.
fig = plt.figure()
ax = fig.add_subplot(111)
if len(args) == 2:
atom = int(args[1])
label = "Atom " + str(atom) + " orbital " + str(orb)
ax.plot(en, dc.site_dos(atom, orb), label=label)
elif options.integ:
label = 'Integrated total DOS'
if len(dc.integrated_dos.shape) == 1:
ax.plot(en, dc.integrated_dos, label=label)
else:
ul = label + ' spin up'
ax.plot(en, dc.integrated_dos[0, :], label=ul)
dl = label + ' spin down'
ax.plot(en, dc.integrated_dos[1, :], label=dl)
else:
label = 'Total DOS'
if len(dc.dos.shape) == 1:
ax.plot(en, dc.dos, label=label)
else:
ul = label + ' spin up'
ax.plot(en, dc.dos[0, :], label=ul)
dl = label + ' spin down'
ax.plot(en, dc.dos[1, :], label=dl)
d.set_labels()
plt.show
# plt.close()
plt.savefig('dos')
ax.plot(en, dc.integrated_dos, label=label)
else:
ul = label + ' spin up'
ax.plot(en, dc.integrated_dos[0, :], label=ul)
dl = label + ' spin down'
ax.plot(en, dc.integrated_dos[1, :], label=dl)
else:
label = 'Total DOS'
if len(dc.dos.shape) == 1:
ax.plot(en, dc.dos, label=label)
else:
ul = label + ' spin up'
ax.plot(en, dc.dos[0, :], label=ul)
dl = label + ' spin down'
ax.plot(en, dc.dos[1, :], label=dl)
d.set_labels()
plt.show()
# For a more involved plot, create your own plot script or run interactively
# via 'ipython -pylab'
# Below are some example pylab commands for plotting
# For good plots in PS or PDF formats begin your script with
# from matplotlib import rc
# rc('ps', usedistiller='xpdf')
# rc('text', usetex=True)
#subplot(211)
# Get the s and p DOS of atom 1.
#plot(en, dc.site_dos(1, 0), "k-", label="Al s")
#plot(en, dc.site_dos(1, 1), "k-.", label="Al p")
def vasputil_dosplot(options, args, dir):
#!/usr/bin/python
# -*- coding: utf-8 -*-
# vim: set fileencoding=utf-8
# Copyright (c) 2008, 2009, 2010 Janne Blomqvist
# This source code file is subject to the terms of the MIT (Expat)
# License. See the file LICENSE for details.
"""Example plotting script demonstrating how to use the vasputil.dos module
and the ase.calculators.vasp.VaspDos class."""
import sys, os
print dir
os.chdir(dir)
sys.path.append('/fslhome/bch/pythonscripts/ase-3.6.0.2515/')
sys.path.append('/fslhome/bch/pythonscripts/vasputil-5.7/')
sys.path.append('/fslhome/bch/pythonscripts/vasputil-5.7/scripts/')
sys.path.append('/fslhome/bch/pythonscripts/vasputil-5.7/scripts/vasputil')
import vasputil.dos as d
import ase.calculators.vasp as v
import matplotlib.pyplot as plt
from optparse import OptionParser
usage = """%prog [options] DOSCAR atom
atom is the index of the atom, starting from 0. If omitted, plots the total
DOS, or the integrated total DOS if additionally the -i option is present.
"""
parser = OptionParser(usage)
parser.add_option("-f", "--fermi", dest="fermi", help="Fermi energy")
parser.add_option("-o",
"--orbital",
dest="orb",
help="Orbital, either \
string or integer. For non-spin polarized s=0, p=1, \
d=2, if spin polarized s+=0, s-=1 etc. If phase factors: s, py, pz, px, \
dxy, dyz, dz2, dxz, dx2, and equivalent as previous for spin polarized etc."
)
parser.add_option('-i',
'--integrated',
dest='integ',
action='store_true',
help='Show the integrated total DOS')
(options, argsdummy) = parser.parse_args()
# By default VaspDos constructor tries to read a file called "DOSCAR".
dc = v.VaspDos(args[0])
if options.fermi:
fermi = float(options.fermi)
dc.efermi = fermi
if options.orb:
try:
orb = int(options.orb)
except ValueError:
orb = options.orb
else:
orb = 0
en = dc.energy # This is the x-axis in a typical DOS plot.
fig = plt.figure()
ax = fig.add_subplot(111)
if len(args) == 2:
atom = int(args[1])
label = "Atom " + str(atom) + " orbital " + str(orb)
ax.plot(en, dc.site_dos(atom, orb), label=label)
elif options.integ:
label = 'Integrated total DOS'
if len(dc.integrated_dos.shape) == 1:
ax.plot(en, dc.integrated_dos, label=label)
else:
ul = label + ' spin up'
ax.plot(en, dc.integrated_dos[0, :], label=ul)
dl = label + ' spin down'
ax.plot(en, dc.integrated_dos[1, :], label=dl)
else:
label = 'Total DOS'
if len(dc.dos.shape) == 1:
ax.plot(en, dc.dos, label=label)
else:
ul = label + ' spin up'
ax.plot(en, dc.dos[0, :], label=ul)
dl = label + ' spin down'
ax.plot(en, dc.dos[1, :], label=dl)
d.set_labels()
plt.show()
plt.savefig('dos')
# For a more involved plot, create your own plot script or run interactively
# via 'ipython -pylab'
# Below are some example pylab commands for plotting
# For good plots in PS or PDF formats begin your script with
# from matplotlib import rc
# rc('ps', usedistiller='xpdf')
# rc('text', usetex=True)
#subplot(211)
# Get the s and p DOS of atom 1.
#plot(en, dc.site_dos(1, 0), "k-", label="Al s")
#plot(en, dc.site_dos(1, 1), "k-.", label="Al p")
#legend()
#xlim(-15,5)
#xticks(arange(0))
#subplot(212)
# s-DOS of atom 2.
#plot(en, dc.site_dos(2, 0), "k-", label="Al s")
#xlim(-15,5)
#ylim(0,.29)
# And to save the figs in EPS/PDF, use
# d.set_labels()
# savefig('tex_demo.eps')
# Fonts in legend touch upper border, test with your version of matplotlib
# savefig('tex_demo_xpdf.pdf')
# os.system('epstopdf tex_demo.eps')
# Finally, show picture
# show()
########### Colorline function ########## similar to cline in Matlab.
'''
ax.plot(en, dc.integrated_dos, label=label)
else:
ul = label + ' spin up'
ax.plot(en, dc.integrated_dos[0, :], label=ul)
dl = label + ' spin down'
ax.plot(en, dc.integrated_dos[1, :], label=dl)
else:
label = 'Total DOS'
if len(dc.dos.shape) == 1:
ax.plot(en, dc.dos, label=label)
else:
ul = label + ' spin up'
ax.plot(en, dc.dos[0, :], label=ul)
dl = label + ' spin down'
ax.plot(en, dc.dos[1, :], label=dl)
d.set_labels()
plt.show()
# For a more involved plot, create your own plot script or run interactively
# via 'ipython -pylab'
# Below are some example pylab commands for plotting
# For good plots in PS or PDF formats begin your script with
# from matplotlib import rc
# rc('ps', usedistiller='xpdf')
# rc('text', usetex=True)
#subplot(211)
# Get the s and p DOS of atom 1.
#plot(en, dc.site_dos(1, 0), "k-", label="Al s")
#plot(en, dc.site_dos(1, 1), "k-.", label="Al p")
def vasputil_dosplot(options, args, dir):
#!/usr/bin/python
# -*- coding: utf-8 -*-
# vim: set fileencoding=utf-8
# Copyright (c) 2008, 2009, 2010 Janne Blomqvist
# This source code file is subject to the terms of the MIT (Expat)
# License. See the file LICENSE for details.
"""Example plotting script demonstrating how to use the vasputil.dos module
and the ase.calculators.vasp.VaspDos class."""
import sys, os
print dir
os.chdir(dir)
sys.path.append('/fslhome/bch/pythonscripts/ase-3.6.0.2515/')
sys.path.append('/fslhome/bch/pythonscripts/vasputil-5.7/')
sys.path.append('/fslhome/bch/pythonscripts/vasputil-5.7/scripts/')
sys.path.append('/fslhome/bch/pythonscripts/vasputil-5.7/scripts/vasputil')
import vasputil.dos as d
import ase.calculators.vasp as v
import matplotlib.pyplot as plt
from optparse import OptionParser
usage = """%prog [options] DOSCAR atom
atom is the index of the atom, starting from 0. If omitted, plots the total
DOS, or the integrated total DOS if additionally the -i option is present.
"""
parser = OptionParser(usage)
parser.add_option("-f", "--fermi", dest="fermi", help="Fermi energy")
parser.add_option("-o", "--orbital", dest="orb", help="Orbital, either \
string or integer. For non-spin polarized s=0, p=1, \
d=2, if spin polarized s+=0, s-=1 etc. If phase factors: s, py, pz, px, \
dxy, dyz, dz2, dxz, dx2, and equivalent as previous for spin polarized etc.")
parser.add_option('-i', '--integrated', dest='integ', action='store_true',
help='Show the integrated total DOS')
(options, argsdummy) = parser.parse_args()
# By default VaspDos constructor tries to read a file called "DOSCAR".
dc = v.VaspDos(args[0])
if options.fermi:
fermi = float(options.fermi)
dc.efermi = fermi
if options.orb:
try:
orb = int(options.orb)
except ValueError:
orb = options.orb
else:
orb = 0
en = dc.energy # This is the x-axis in a typical DOS plot.
fig = plt.figure()
ax = fig.add_subplot(111)
if len(args) == 2:
atom = int(args[1])
label = "Atom " + str(atom) + " orbital " + str(orb)
ax.plot(en, dc.site_dos(atom, orb), label=label)
elif options.integ:
label = 'Integrated total DOS'
if len(dc.integrated_dos.shape) == 1:
ax.plot(en, dc.integrated_dos, label=label)
else:
ul = label + ' spin up'
ax.plot(en, dc.integrated_dos[0, :], label=ul)
dl = label + ' spin down'
ax.plot(en, dc.integrated_dos[1, :], label=dl)
else:
label = 'Total DOS'
if len(dc.dos.shape) == 1:
ax.plot(en, dc.dos, label=label)
else:
ul = label + ' spin up'
ax.plot(en, dc.dos[0, :], label=ul)
dl = label + ' spin down'
ax.plot(en, dc.dos[1, :], label=dl)
d.set_labels()
plt.show()
plt.savefig('dos')
# For a more involved plot, create your own plot script or run interactively
# via 'ipython -pylab'
# Below are some example pylab commands for plotting
# For good plots in PS or PDF formats begin your script with
# from matplotlib import rc
# rc('ps', usedistiller='xpdf')
# rc('text', usetex=True)
#subplot(211)
# Get the s and p DOS of atom 1.
#plot(en, dc.site_dos(1, 0), "k-", label="Al s")
#plot(en, dc.site_dos(1, 1), "k-.", label="Al p")
#legend()
#xlim(-15,5)
#xticks(arange(0))
#subplot(212)
# s-DOS of atom 2.
#plot(en, dc.site_dos(2, 0), "k-", label="Al s")
#xlim(-15,5)
#ylim(0,.29)
# And to save the figs in EPS/PDF, use
# d.set_labels()
# savefig('tex_demo.eps')
# Fonts in legend touch upper border, test with your version of matplotlib
# savefig('tex_demo_xpdf.pdf')
# os.system('epstopdf tex_demo.eps')
# Finally, show picture
# show()
########### Colorline function ########## similar to cline in Matlab.
'''
