def get_odos(self, stack=True, xlim=[-10, 10], ylim=[0, 50], sigma=0.15):
dos_vasprun = Vasprun(os.path.join(self.path, "vasprun.xml"), parse_projected_eigen=True)
dos_data = dos_vasprun.complete_dos
plotter = DosPlotter(stack=stack, sigma=sigma)
o_dos = dos_data.get_spd_dos()
plotter.add_dos_dict(o_dos)
plotter.save_plot(f'{self.path}-odos.png', img_format=u'png', xlim=xlim, ylim=ylim)
class DosPlotterTest(unittest.TestCase):
def setUp(self):
try:
import scipy
except ImportError:
raise SkipTest("scipy not present. Skipping...")
with open(os.path.join(test_dir, "complete_dos.json"), "r") as f:
self.dos = CompleteDos.from_dict(json.load(f))
self.plotter = DosPlotter(sigma=0.2, stack=True)
def test_add_dos_dict(self):
try:
import scipy
except ImportError:
raise SkipTest("scipy not present. Skipping...")
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 0)
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 4)
def test_get_dos_dict(self):
try:
import scipy
except ImportError:
raise SkipTest("scipy not present. Skipping...")
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
for el in ["Li", "Fe", "P", "O"]:
self.assertIn(el, d)
def get_dos_plot(args):
v = Vasprun(args.dos_file)
dos = v.complete_dos
all_dos = OrderedDict()
all_dos["Total"] = dos
structure = v.final_structure
if args.site:
for i in range(len(structure)):
site = structure[i]
all_dos["Site " + str(i) + " " + site.specie.symbol] = \
dos.get_site_dos(site)
if args.element:
syms = [tok.strip() for tok in args.element[0].split(",")]
all_dos = {}
for el, dos in dos.get_element_dos().items():
if el.symbol in syms:
all_dos[el] = dos
if args.orbital:
all_dos = dos.get_spd_dos()
plotter = DosPlotter()
plotter.add_dos_dict(all_dos)
return plotter.get_plot()
def get_dos_plot(args):
"""
Plot DOS.
Args:
args (dict): Args from argparse.
"""
v = Vasprun(args.dos_file)
dos = v.complete_dos
all_dos = OrderedDict()
all_dos["Total"] = dos
structure = v.final_structure
if args.site:
for i, site in enumerate(structure):
all_dos["Site " + str(i) + " " +
site.specie.symbol] = dos.get_site_dos(site)
if args.element:
syms = [tok.strip() for tok in args.element[0].split(",")]
all_dos = {}
for el, dos in dos.get_element_dos().items():
if el.symbol in syms:
all_dos[el] = dos
if args.orbital:
all_dos = dos.get_spd_dos()
plotter = DosPlotter()
plotter.add_dos_dict(all_dos)
return plotter.get_plot()
def plot_dos(args):
v = Vasprun(args.filename[0])
dos = v.complete_dos
all_dos = OrderedDict()
all_dos["Total"] = dos
structure = v.final_structure
if args.site:
for i in xrange(len(structure)):
site = structure[i]
all_dos["Site " + str(i) + " " + site.specie.symbol] = \
dos.get_site_dos(site)
if args.element:
syms = [tok.strip() for tok in args.element[0].split(",")]
all_dos = {}
for el, dos in dos.get_element_dos().items():
if el.symbol in syms:
all_dos[el] = dos
if args.orbital:
all_dos = dos.get_spd_dos()
plotter = DosPlotter()
plotter.add_dos_dict(all_dos)
if args.file:
plotter.get_plot().savefig(args.file[0])
else:
plotter.show()
def dos_graph_soc(rawdatadir, savedir):
dosrun = Vasprun("{}/vasprun.xml".format(rawdatadir),
soc=True,
parse_dos=True)
dos = dosrun.complete_dos
orbitals = {
"s": Orbital.s,
"p_y": Orbital.py,
"p_z": Orbital.pz,
"p_x": Orbital.px,
"d_xy": Orbital.dxy,
"d_yz": Orbital.dyz,
"d_z2-r2": Orbital.dz2,
"d_xz": Orbital.dxz,
"d_x2-y2": Orbital.dx2
}
spinor_component = {
"mtot": SpinNonCollinear.mtot,
"mx": SpinNonCollinear.mx,
"my": SpinNonCollinear.my,
"mz": SpinNonCollinear.mz
}
for m in spinor_component:
dosplot = DosPlotter()
if m == "mtot":
dosplot.add_dos("Total DOS with SOC", dos.tdos)
dosplot.add_dos_dict(dos.get_element_dos())
plt = dosplot.get_plot(xlim=[-3, 3],
soc=True,
spinor_component=spinor_component[m],
element_colors=True)
plt.grid()
plt.savefig("{}/DOSGraph_{}_{}".format(savedir, m,
"DOS by Element with SOC"))
plt.close()
for m in spinor_component:
dosplot = DosPlotter()
if m == "mtot":
dosplot.add_dos("Total DOS with SOC", dos.tdos)
dosplot.add_dos_dict(dos.get_orbital_dos())
plt = dosplot.get_plot(xlim=[-3, 3],
soc=True,
spinor_component=spinor_component[m])
plt.grid()
plt.savefig("{}/DOSGraph_{}_{}".format(savedir, m,
"DOS by Orbital with SOC"))
plt.close()
# Get detailed info about band gap (source: vasprun.xml)
dos_graph_soc.e_fermi = float(dosrun.efermi)
dos_graph_soc.electronic_gap = \
dosrun.tdos.get_gap_alt(xlim=[-3,3],e_fermi=dos_graph_soc.e_fermi,
tol=0.001,abs_tol=False,
spin=SpinNonCollinear.mtot)
return
def main():
parser = argparse.ArgumentParser(
description='''Convenient DOS Plotter for Feff runs.
Author: Alan Dozier
Version: 1.0
Last updated: April, 2013''')
parser.add_argument('filename',
metavar='filename',
type=str,
nargs=1,
help='ldos%% file set to plot')
parser.add_argument('filename1',
metavar='filename1',
type=str,
nargs=1,
help='feff.inp input file ')
parser.add_argument('-s',
'--site',
dest='site',
action='store_const',
const=True,
help='plot site projected DOS')
parser.add_argument('-e',
'--element',
dest='element',
action='store_const',
const=True,
help='plot element projected DOS')
parser.add_argument('-o',
'--orbital',
dest="orbital",
action='store_const',
const=True,
help='plot orbital projected DOS')
args = parser.parse_args()
f = LDos.from_file(args.filename1[0], args.filename[0])
dos = f.complete_dos
all_dos = OrderedDict()
all_dos['Total'] = dos
structure = f.complete_dos.structure
if args.site:
for i, site in enumerate(structure):
all_dos['Site ' + str(i) + " " + site.specie.symbol] = \
dos.get_site_dos(site)
if args.element:
all_dos.update(dos.get_element_dos())
if args.orbital:
all_dos.update(dos.get_spd_dos())
plotter = DosPlotter()
plotter.add_dos_dict(all_dos)
plotter.show()
def get_dos(self, dos):
task_id = dos['task_id']
dos_obj = self.vaspdb.get_dos(task_id)
energies = dos_obj.energies
efermi = dos_obj.efermi
gap = dos_obj.get_gap()
densities_up = dos_obj.densities[Spin.up]
densities_dn = dos_obj.densities[Spin.down]
#densities = densities_up + densities_dn
densities = dos_obj.get_densities()
#print('Fermi energy: {}'.format(efermi))
#print('gap: {}'.format(gap))
tdos = np.vstack((energies, densities))
#print(tdos)
#print(type(densities))
plotter = DosPlotter()
# Adds a DOS with a label.
#plotter.add_dos("Total DOS", dos)
# Alternatively, you can add a dict of DOSs. This is the typical
# form returned by CompleteDos.get_spd/element/others_dos().
#plotter.add_dos_dict({"dos1": dos1, "dos2": dos2})
dosplot = plotter.add_dos_dict(dos_obj.get_element_dos())
#dosplot = plotter.add_dos_dict(dos_obj.get_spd_dos())
#plotter.show()
self.head = [
'energies', 'total_dos', 'total_dos_spin_up', 'total_dos_spin_down'
]
self.unit = ['eV', '', '', '']
self.data = np.vstack(
(energies, densities, densities_up, -densities_dn)).T
self.parameter = dos['input']['incar']
class DosPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "complete_dos.json"), "r") as f:
self.dos = CompleteDos.from_dict(json.load(f))
self.plotter = DosPlotter(sigma=0.2, stack=True)
def test_add_dos_dict(self):
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 0)
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 4)
def test_get_dos_dict(self):
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
for el in ["Li", "Fe", "P", "O"]:
self.assertIn(el, d)
class DosPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "complete_dos.json"), "r",
encoding='utf-8') as f:
self.dos = CompleteDos.from_dict(json.load(f))
self.plotter = DosPlotter(sigma=0.2, stack=True)
def test_add_dos_dict(self):
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 0)
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 4)
def test_get_dos_dict(self):
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
for el in ["Li", "Fe", "P", "O"]:
self.assertIn(el, d)
# Minimal baseline testing for get_plot. not a true test. Just checks that
# it can actually execute.
def test_get_plot(self):
# Disabling latex is needed for this test to work.
from matplotlib import rc
rc('text', usetex=False)
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
plt = self.plotter.get_plot()
self.plotter.save_plot("dosplot.png")
self.assertTrue(os.path.isfile("dosplot.png"))
os.remove("dosplot.png")
class DosPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "complete_dos.json"), "r",
encoding='utf-8') as f:
self.dos = CompleteDos.from_dict(json.load(f))
self.plotter = DosPlotter(sigma=0.2, stack=True)
def test_add_dos_dict(self):
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 0)
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 4)
def test_get_dos_dict(self):
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
for el in ["Li", "Fe", "P", "O"]:
self.assertIn(el, d)
# Minimal baseline testing for get_plot. not a true test. Just checks that
# it can actually execute.
def test_get_plot(self):
# Disabling latex is needed for this test to work.
from matplotlib import rc
rc('text', usetex=False)
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
plt = self.plotter.get_plot()
self.plotter.save_plot("dosplot.png")
self.assertTrue(os.path.isfile("dosplot.png"))
os.remove("dosplot.png")
class DosPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "complete_dos.json"), "r",
encoding='utf-8') as f:
self.dos = CompleteDos.from_dict(json.load(f))
self.plotter = DosPlotter(sigma=0.2, stack=True)
def test_add_dos_dict(self):
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 0)
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 4)
def test_get_dos_dict(self):
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
for el in ["Li", "Fe", "P", "O"]:
self.assertIn(el, d)
def main():
parser = argparse.ArgumentParser(description='''Convenient DOS Plotter for Feff runs.
Author: Alan Dozier
Version: 1.0
Last updated: April, 2013''')
parser.add_argument('filename', metavar='filename', type=str, nargs=1,
help='ldos%% file set to plot')
parser.add_argument('filename1', metavar='filename1', type=str, nargs=1,
help='feff.inp input file ')
parser.add_argument('-s', '--site', dest='site', action='store_const',
const=True, help='plot site projected DOS')
parser.add_argument('-e', '--element', dest='element', action='store_const',
const=True, help='plot element projected DOS')
parser.add_argument('-o', '--orbital', dest="orbital", action='store_const',
const=True, help='plot orbital projected DOS')
args = parser.parse_args()
f = LDos.from_file(args.filename1[0], args.filename[0])
dos = f.complete_dos
all_dos = OrderedDict()
all_dos['Total'] = dos
structure = f.complete_dos.structure
if args.site:
for i, site in enumerate(structure):
all_dos['Site ' + str(i) + " " + site.specie.symbol] = \
dos.get_site_dos(site)
if args.element:
all_dos.update(dos.get_element_dos())
if args.orbital:
all_dos.update(dos.get_spd_dos())
plotter = DosPlotter()
plotter.add_dos_dict(all_dos)
plotter.show()
def main():
parser = argparse.ArgumentParser(
description="""Convenient DOS Plotter for Feff runs.
Author: Alan Dozier
Version: 1.0
Last updated: April, 2013"""
)
parser.add_argument("filename", metavar="filename", type=str, nargs=1, help="ldos%% file set to plot")
parser.add_argument("filename1", metavar="filename1", type=str, nargs=1, help="feff.inp input file ")
parser.add_argument("-s", "--site", dest="site", action="store_const", const=True, help="plot site projected DOS")
parser.add_argument(
"-e", "--element", dest="element", action="store_const", const=True, help="plot element projected DOS"
)
parser.add_argument(
"-o", "--orbital", dest="orbital", action="store_const", const=True, help="plot orbital projected DOS"
)
args = parser.parse_args()
f = LDos.from_file(args.filename1[0], args.filename[0])
dos = f.complete_dos
all_dos = OrderedDict()
all_dos["Total"] = dos
structure = f.complete_dos.structure
if args.site:
for i, site in enumerate(structure):
all_dos["Site " + str(i) + " " + site.specie.symbol] = dos.get_site_dos(site)
if args.element:
all_dos.update(dos.get_element_dos())
if args.orbital:
all_dos.update(dos.get_spd_dos())
plotter = DosPlotter()
plotter.add_dos_dict(all_dos)
plotter.show()
'/home/jinho93/oxides/perobskite/lanthanum-aluminate/periodic_step/vasp/stengel/001/vca/AlO2'
)
os.chdir(
'/home/jinho93/oxides/perobskite/lanthanum-aluminate/slab/14/asym/to_Al')
# os.chdir('/home/jinho93/new/oxides/perobskite/lanthanum-aluminate/slab/7')
vrun = Vasprun('vasprun.xml')
cdos = vrun.complete_dos
s = vrun.final_structure
dsp = DosPlotter()
dos_dict = {}
i: Site
for n, i in enumerate(s.sites):
if i.species_string == 'La':
dos_dict[f'{n}'] = cdos.get_site_dos(i)
dsp.add_dos_dict(dos_dict)
dsp.show(xlim=(-10, 5), ylim=(0, 2))
# %%
aldos = cdos.get_site_dos(s.sites[0])
dx = aldos.energies[1] - aldos.energies[0]
o = np.sum(
aldos.get_densities(Spin.up)[np.logical_and(aldos.energies > -2,
aldos.energies < 0)]) * dx
print(o)
# %%
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter
from collections import OrderedDict
vaspout = Vasprun("vasprun.xml")
dos = vaspout.complete_dos
all_dos = OrderedDict()
all_dos["Total"] = dos
plt = DosPlotter()
plt.add_dos_dict(all_dos)
plt = plt.get_plot(xlim=[-10,10],ylim=[0,1.5])
plt.savefig('dos.pdf')
def main():
"""
Main function.
"""
parser = argparse.ArgumentParser(
description="""Convenient DOS Plotter for Feff runs.
Author: Alan Dozier
Version: 1.0
Last updated: April, 2013""")
parser.add_argument(
"filename",
metavar="filename",
type=str,
nargs=1,
help="ldos%% file set to plot",
)
parser.add_argument("filename1",
metavar="filename1",
type=str,
nargs=1,
help="feff.inp input file ")
parser.add_argument(
"-s",
"--site",
dest="site",
action="store_const",
const=True,
help="plot site projected DOS",
)
parser.add_argument(
"-e",
"--element",
dest="element",
action="store_const",
const=True,
help="plot element projected DOS",
)
parser.add_argument(
"-o",
"--orbital",
dest="orbital",
action="store_const",
const=True,
help="plot orbital projected DOS",
)
args = parser.parse_args()
f = LDos.from_file(args.filename1[0], args.filename[0])
dos = f.complete_dos
all_dos = {}
all_dos["Total"] = dos
structure = f.complete_dos.structure
if args.site:
for i, site in enumerate(structure):
all_dos["Site " + str(i) + " " +
site.specie.symbol] = dos.get_site_dos(site)
if args.element:
all_dos.update(dos.get_element_dos())
if args.orbital:
all_dos.update(dos.get_spd_dos())
plotter = DosPlotter()
plotter.add_dos_dict(all_dos)
plotter.show()
from pymatgen.io.vasp import Vasprun, Element
from pymatgen.electronic_structure.plotter import DosPlotter
v = Vasprun('AgTe_dos/vasprun.xml')
cdos = v.complete_dos
element_dos = cdos.get_element_dos()
element_orbital = cdos.get_element_spd_dos(el=Element("Te"))
#print(cdos.pdos)
#px = cdos.get_site_orbital_dos(site=v.final_structure.sites[0],orbital=0)
#py = cdos.get_site_orbital_dos(site=v.final_structure.sites[0],orbital=2)
#pz = cdos.get_site_orbital_dos(site=v.final_structure.sites[0],orbital=1)
plotter = DosPlotter(zero_at_efermi=True)
plotter.add_dos_dict(element_dos)
#plotter.add_dos_dict(px)
#plotter.add_dos_dict(py)
#plotter.add_dos_dict(pz)
plotter.show(xlim=[-4, 4], ylim=[0, 10])
def dos_graph(rawdatadir,
savedir,
total_dos=True,
by_element=False,
by_orbital=False):
dosrun = Vasprun("{}/vasprun.xml".format(rawdatadir), parse_dos=True)
dos = dosrun.complete_dos
# Get basic plot
dos_graph.e_fermi = float(dosrun.efermi)
dos_graph.band_gap = float(dosrun.eigenvalue_band_properties[0])
dosplot = DosPlotter()
#dosplot = DosPlotter(sigma=0.1)
if total_dos == True:
dosplot.add_dos("Total DOS", dos)
if by_element == True:
dosplot.add_dos_dict(dos.get_element_dos())
if by_orbital == True:
dosplot.add_dos_dict(dos.get_spd_dos())
plt = dosplot.get_plot(xlim=[-3, 3], ylim=[-15, 15], element_colors=True)
plt.grid()
plt.savefig("{}/DOSGraph".format(savedir))
plt.close()
# Get plot for comparison with SOC total DOS plot
dosplot = DosPlotter()
dosplot.add_dos("Total DOS without SOC", dos)
dosplot.add_dos_dict(dos.get_element_dos())
plt = dosplot.get_plot_total(xlim=[-3, 3], element_colors=True)
plt.grid()
plt.savefig("{}/DOSGraph_tot_DOS by Element without SOC".format(savedir))
plt.close()
dosplot = DosPlotter()
orbitals = {
"s": Orbital.s,
"p_y": Orbital.py,
"p_z": Orbital.pz,
"p_x": Orbital.px,
"d_xy": Orbital.dxy,
"d_yz": Orbital.dyz,
"d_z2-r2": Orbital.dz2,
"d_xz": Orbital.dxz,
"d_x2-y2": Orbital.dx2
}
dosplot.add_dos("Total DOS without SOC", dos)
dosplot.add_dos_dict(dos.get_orbital_dos())
plt = dosplot.get_plot_total(xlim=[-3, 3])
plt.grid()
plt.savefig("{}/DOSGraph_tot_DOS by Orbital without SOC".format(savedir))
plt.close()
"""
# Get quick info about band gap (source: EIGENVAL)
eigenval = Eigenval("{}/EIGENVAL".format(rawdatadir))
dos_graph.band_properties = eigenval.eigenvalue_band_properties
"""
# Get detailed info about band gap and CB/VB in each spin channel
# (source: vasprun.xml)
dos_graph.majority_vbm = \
dosrun.tdos.get_cbm_vbm_alt(xlim=[-3,3],e_fermi=dos_graph.e_fermi,
tol=0.3,abs_tol=True,spin=Spin.up)[1]
dos_graph.majority_cbm = \
dosrun.tdos.get_cbm_vbm_alt(xlim=[-3,3],e_fermi=dos_graph.e_fermi,
tol=0.3,abs_tol=True,spin=Spin.up)[0]
dos_graph.minority_vbm = \
dosrun.tdos.get_cbm_vbm_alt(xlim=[-3,3],e_fermi=dos_graph.e_fermi,
tol=0.3,abs_tol=True,spin=Spin.down)[1]
dos_graph.minority_cbm = \
dosrun.tdos.get_cbm_vbm_alt(xlim=[-3,3],e_fermi=dos_graph.e_fermi,
tol=0.3,abs_tol=True,spin=Spin.down)[0]
dos_graph.majority_gap = \
dosrun.tdos.get_gap_alt(xlim=[-3,3],e_fermi=dos_graph.e_fermi,
tol=0.3,abs_tol=True,spin=Spin.up)
dos_graph.minority_gap = \
dosrun.tdos.get_gap_alt(xlim=[-3,3],e_fermi=dos_graph.e_fermi,
tol=0.3,abs_tol=True,spin=Spin.down)
dos_graph.electronic_gap = \
dosrun.tdos.get_gap_alt(xlim=[-3,3],e_fermi=dos_graph.e_fermi,
tol=0.3,abs_tol=True,spin=None)
return
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
"""
reads in vasprun.xml file and plots the density of states
"""
# To use matplotlib on Hipergator, uncomment the following 2 lines:
# import matplotlib
# matplotlib.use('Agg')
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter
if __name__ == "__main__":
# readin the density of states from vasprun.xml file
run = Vasprun("vasprun.xml", parse_projected_eigen=True)
complete_dos = run.complete_dos
print('cbm and vbm ', complete_dos.get_cbm_vbm())
print('gap = ', complete_dos.get_gap())
# get orbital projected DOS.
spd_dos = complete_dos.get_spd_dos()
plotter = DosPlotter()
plotter.add_dos_dict(spd_dos)
plotter.save_plot('dos.eps')
help='feff.inp input file ')
parser.add_argument('-s', '--site', dest='site', action='store_const',
const=True, help='plot site projected DOS')
parser.add_argument('-e', '--element', dest='element', action='store_const',
const=True, help='plot element projected DOS')
parser.add_argument('-o', '--orbital', dest="orbital", action='store_const',
const=True, help='plot orbital projected DOS')
args = parser.parse_args()
f = FeffLdos.from_file(args.filename1[0], args.filename[0])
dos = f.complete_dos
all_dos = OrderedDict()
all_dos['Total'] = dos
structure = f.complete_dos.structure
if args.site:
for i in xrange(len(structure)):
site = structure[i]
all_dos['Site ' + str(i) + " " + site.specie.symbol] = \
dos.get_site_dos(site)
if args.element:
all_dos.update(dos.get_element_dos())
if args.orbital:
all_dos.update(dos.get_spd_dos())
plotter = DosPlotter()
plotter.add_dos_dict(all_dos)
plotter.show()
#!/nfshome/villa/anaconda3/bin/python
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter, DosPlotter
vaspout = Vasprun("./vasprun.xml")
# Initializes plotter with some optional args. Defaults are usually
# fine,
complete_dos = vaspout.complete_dos
plt = DosPlotter()
plt.add_dos_dict(complete_dos.get_spd_dos())
tdos = vaspout.tdos
# Adds a DOS with a label.
plt.add_dos("Total", tdos)
#plt.get_plot()
plt.save_plot('dos_mg.pdf', img_format='pdf', xlim=[-7, 6], ylim=[0, 20])
help='plot element projected DOS')
parser.add_argument('-o',
'--orbital',
dest="orbital",
action='store_const',
const=True,
help='plot orbital projected DOS')
args = parser.parse_args()
f = FeffLdos.from_file(args.filename1[0], args.filename[0])
dos = f.complete_dos
all_dos = OrderedDict()
all_dos['Total'] = dos
structure = f.complete_dos.structure
if args.site:
for i in xrange(len(structure)):
site = structure[i]
all_dos['Site ' + str(i) + " " + site.specie.symbol] = \
dos.get_site_dos(site)
if args.element:
all_dos.update(dos.get_element_dos())
if args.orbital:
all_dos.update(dos.get_spd_dos())
plotter = DosPlotter()
plotter.add_dos_dict(all_dos)
plotter.show()
out = Outcar('./OUTCAR')
print('Total Magnetic Moment:', out.total_mag)
if make_dosplot:
# read in BSDOSPlotter function to plot DOS and BS
from pymatgen.electronic_structure.plotter import DosPlotter
# make and save a plot of the band structure and DOS
dos = vsp.complete_dos
energy_range = (-10, 7) # eV, change if desired to change plotting range
# create DosPlotter object with smearing
edosplot = DosPlotter(sigma=dos_smearing)
# plot Total DOS and element-projected dos
edosplot.add_dos("Total DOS", dos)
edosplot.add_dos_dict(dos.get_element_dos())
plt = edosplot.get_plot(xlim=energy_range)
plt.plot((-20, 20), (0, 0), 'k--')
plt.savefig('Element_DOS_plot.png')
# create DosPlotter object with smearing
odosplot = DosPlotter(sigma=dos_smearing)
# plot Total DOS and orbital-projected dos
odosplot.add_dos("Total DOS", dos)
odosplot.add_dos_dict(dos.get_spd_dos())
plt = odosplot.get_plot(xlim=energy_range)
plt.plot((-20, 20), (0, 0), 'k--')
plt.savefig('Orbital_DOS_plot.png')
print('Generated DOS plots')
import numpy as np
os.chdir(
'/home/jinho93/oxides/perobskite/lanthanum-aluminate/periodic_step/vasp/from-2012/1.0ps/full'
)
os.chdir(
'/home/jinho93/oxides/perobskite/lanthanum-aluminate/periodic_step/vasp/from-100/300k'
)
os.chdir(
'/home/jinho93/oxides/perobskite/lanthanum-aluminate/periodic_step/vasp/from-100/ini'
)
vrun = Vasprun('vasprun.xml')
cdos = vrun.complete_dos
dsp = DosPlotter()
dsp.add_dos_dict(cdos.get_element_dos())
dsp.show()
eldos = cdos.get_element_dos()
for i, j in eldos.items():
if i == Element.La:
tmp = [cdos.energies - cdos.efermi, j.densities[Spin.up]]
tmp = np.transpose(np.array(tmp))
np.savetxt('La.dat', tmp)
elif i == Element.O:
tmp = [cdos.energies - cdos.efermi, j.densities[Spin.up]]
tmp = np.transpose(np.array(tmp))
np.savetxt('O.dat', tmp)
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
"""
reads in vasprun.xml file and plots the density of states
"""
# To use matplotlib on Hipergator, uncomment the following 2 lines:
# import matplotlib
# matplotlib.use('Agg')
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter
if __name__ == "__main__":
# readin the density of states from vasprun.xml file
run = Vasprun("vasprun.xml", parse_projected_eigen=True)
complete_dos = run.complete_dos
print('cbm and vbm ', complete_dos.get_cbm_vbm())
print('gap = ', complete_dos.get_gap())
# get orbital projected DOS.
spd_dos = complete_dos.get_spd_dos()
plotter = DosPlotter()
plotter.add_dos_dict(spd_dos)
plotter.save_plot('dos.eps')
from pymatgen.io.vasp import Vasprun, Element
from pymatgen.electronic_structure.plotter import DosPlotter
v = Vasprun('AgTe_dos/vasprun.xml')
cdos = v.complete_dos
element_dos = cdos.get_element_dos()
element_orbital = cdos.get_element_spd_dos(el=Element("Ag"))
plotter = DosPlotter()
plotter.add_dos_dict(element_orbital)
plotter.show(xlim=[-4, 4], ylim=[0, 10])
spd_dos = cdos.get_spd_dos
#print spd_dos
element_dos = cdos.get_element_dos
#element_spd_dos = cdos.get_element_spd_dos(el)
dosplotter = DosPlotter()
Totaldos = dosplotter.add_dos('Total DOS', tdos)
Integrateddos = dosplotter.add_dos('Integrated DOS', idos)
#Pdos = dosplotter.add_dos('Partial DOS',pdos)
#Spd_dos = dosplotter.add_dos('spd DOS',spd_dos)
#Element_dos = dosplotter.add_dos('Element DOS',element_dos)
#Element_spd_dos = dosplotter.add_dos('Element_spd DOS',element_spd_dos)
dos_dict = {
'Total DOS': tdos,
'Integrated DOS': idos
} #'Partial DOS':pdos,'spd DOS':spd_dos,'Element DOS':element_dos}#'Element_spd DOS':element_spd_dos
add_dos_dict = dosplotter.add_dos_dict(dos_dict)
get_dos_dict = dosplotter.get_dos_dict()
dos_plot = dosplotter.get_plot()
##dosplotter.save_plot("MAPbI3_dos",img_format="png")
##dos_plot.show()
bsplotter = BSPlotter(bs)
bs_plot_data = bsplotter.bs_plot_data()
bs_plot = bsplotter.get_plot()
#bsplotter.save_plot("MAPbI3_bs",img_format="png")
#bsplotter.show()
ticks = bsplotter.get_ticks()
print ticks
bsplotter.plot_brillouin()
bsdos = BSDOSPlotter(
tick_fontsize=10,
egrid_interval=20,
from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter
dsp = DosPlotter()
vrun = Vasprun('vasprun.xml')
dsp.add_dos_dict(
vrun.complete_dos.get_site_spd_dos(vrun.final_structure.sites[0]))
dsp.show()
from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter
from pymatgen.io.vasp.outputs import Vasprun, Procar
from pymatgen.core.ion import Ion
v = Vasprun('vasprun.xml')
cdos = v.complete_dos
#el = cdos.Structure.composition
eles = cdos.structure.composition.elements
for ele in eles:
plotter = DosPlotter()
ele_or_dos = cdos.get_element_spd_dos(ele)
plotter.add_dos_dict(ele_or_dos)
plotter.show(xlim=[-8, 8], ylim=[0, 1000])
exit(0)
print cdos.Structure
#print el.elements
#exit(0)
#orbital_dos = cdos.get_spd_dos()
#plotter = DosPlotter()
#plotter.add_dos_dict(orbital_dos)
#plotter.show(xlim=[-8, 8], ylim=[0, 1000])
'second': (0.5, 0.6),
}
for key, val in en.items():
s: PeriodicSite = None
dosN = Dos(cdos.efermi, cdos.energies,
{k: np.zeros(d.shape)
for k, d in cdos.densities.items()})
dosMetal = Dos(
cdos.efermi, cdos.energies,
{k: np.zeros(d.shape)
for k, d in cdos.densities.items()})
for s in find_ind(cdos.structure, *val):
if s.specie.__str__() == 'N':
sum_orbital(dosN, cdos.get_site_spd_dos(s)[OrbitalType.p])
elif s.specie.__str__() == 'Ni':
sum_orbital(dosMetal, cdos.get_site_spd_dos(s)[OrbitalType.d])
dosN.densities = dosN.get_smeared_densities(0.03)
dosMetal.densities = dosMetal.get_smeared_densities(0.03)
sum_spin(dosN)
sum_spin(dosMetal)
dosN = integrate(dosN)
dosMetal = integrate(dosMetal)
dp.add_dos_dict({key + "dosN": dosN, key + "dosM": dosMetal})
dp.show()
# write_dos(key + '_N_mag.dat', integrate(dosN))
# write_dos(key + '_Cu_mag.dat', integrate(dosMetal))
import os
from pymatgen.electronic_structure.plotter import DosPlotter
from pymatgen.io.vasp.outputs import Vasprun, Element, Dos
os.chdir('/home/jinho93/molecule/ddt/vasp/2-sub/triplet/')
vrun = Vasprun('vasprun.xml')
# mpr = MPRester('DhmFQPuibZo8JtXn')
dos = vrun.complete_dos
# dos: CompleteDos = mpr.get_dos_by_material_id('mp-352')
eldos = dos.get_element_dos()
dos.get_site_spd_dos()
dos.get_site_t2g_eg_resolved_dos()
i: Element
j: Dos
print(vrun.final_structure.composition.element_composition)
#for i, j in eldos.items():
# vasprun.final_structure.num_sites
#eldos.pop(Element.Mo)
#eldos.pop(Element.S)
dsp = DosPlotter()
dsp.add_dos_dict(eldos)
dsp.show(xlim=(-3, 5))
#%% from matplotlib.pyplot import xlim from pymatgen.io.vasp.outputs import Vasprun, Element from pymatgen.electronic_structure.plotter import DosPlotter path = '/home/jinho93/oxides/perobskite/lanthanum-aluminate/bulk/hse/dos/' # path = '/home/jinho93/oxides/perobskite/lanthanum-aluminate/periodic_step/vasp/stengel/bulk/dos/' vrun = Vasprun(path + 'vasprun.xml') dsp = DosPlotter(zero_at_efermi=True) dsp.add_dos_dict(vrun.complete_dos.get_element_spd_dos(Element.La)) dsp.show(xlim=(-10, 8)) # %%
