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 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)
if args.file:
plotter.get_plot().savefig(args.file[0])
else:
plotter.show()
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 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 plot_dos(vasprun_path: str):
try:
v = Vasprun(vasprun_path)
except xml.etree.ElementTree.ParseError:
print("\tskipped due to parse error")
return
tdos = v.tdos
plt = DosPlotter()
plt.add_dos("Total DOS", tdos)
plt.show()
def pdos(vasprun):
# Load the vasprun.xml file
out = Vasprun(os.path.abspath(vasprun))
# Extract the types of species in the structure
species = out.initial_structure.types_of_specie
# Extract the complete DOS
element_dos = out.complete_dos.get_element_dos()
# Initialize the DosPlotter
plotter = DosPlotter()
# Add the element projected DOS to the DOSplotter
for specie in species:
plotter.add_dos(specie.name, element_dos[specie])
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()
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()
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])
'/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)
# %%
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()
@Time1 : 2020-05-09 10:27:36
@Time2 : 2020/5/9 10:27
@Month1 : 5月
@Month2 : 五月
"""
from pymatgen.electronic_structure.plotter import DosPlotter, BSPlotter, BSDOSPlotter
from pymatgen.io.vasp import Vasprun, BSVasprun
vasprun_file = './AlEuO3_Perovskite_DOS/vasprun.xml'
vasprun = Vasprun(vasprun_file)
tdos = vasprun.tdos
plotter = DosPlotter()
plotter.add_dos('Total DOS', tdos)
# plotter.show(xlim=[-20, 20], ylim=[-6, 6])
plotter.show()
completeDos = vasprun.complete_dos
element_dos = completeDos.get_element_dos()
plotter = DosPlotter()
plotter.add_dos_dict(element_dos)
plotter.add_dos('Total DOS', tdos)
plotter.show()
spd_dos = completeDos.get_spd_dos()
plotter = DosPlotter()
plotter.add_dos_dict(spd_dos)
plotter.add_dos('Total DOS', tdos)
plotter.show()
bsvasprun_file = './AlEuO3_Perovskite_BS/vasprun.xml'
cdos = vrun.complete_dos
atoms = []
i: Site
dos = {
'd_in':
Dos(cdos.efermi, cdos.energies, {Spin.up: np.zeros_like(cdos.energies)}),
'd_out':
Dos(cdos.efermi, cdos.energies, {Spin.up: np.zeros_like(cdos.energies)})
}
for i in vrun.final_structure.sites:
if i.species_string == 'V':
atoms.append(i)
for j in atoms:
for n, k in dos.items():
if n == 'd_in':
dos[n] = k.__add__(cdos.get_site_orbital_dos(j, Orbital.dxy))
else:
dos[n] = k.__add__(cdos.get_site_orbital_dos(j, Orbital.dyz))
dos[n] = k.__add__(cdos.get_site_orbital_dos(j, Orbital.dxz))
dsp.add_dos_dict(dos)
dsp.show()
# %%
for n, k in dos.items():
with open(f'{n}.dat', 'w') as f:
f.write(k.__str__())
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))
# pure
h8, e4, d4 = 4, -5, -1
for orb in [Orbital.dxy, Orbital.dyz, Orbital.dz2, Orbital.dxz, Orbital.dx2]:
dos_dict[orb.name] = cdos.get_site_orbital_dos(structure.sites[h8], orb)
# dos_dict[orb.__str__()].densities = dos_dict[orb.__str__()].get_smeared_densities(0.1)
def save_dos_dict():
arr = [
np.concatenate(
[cdos.energies - cdos.efermi, (cdos.energies - cdos.efermi)[::-1]])
]
for i in dos_dict.values():
tmp = np.concatenate(
[i.densities[Spin.up], -i.densities[Spin.down][::-1]])
arr.append(tmp)
arr = np.array(arr)
np.savetxt('output.dat', arr.transpose(), delimiter='\t')
if __name__ == '__main__':
from pymatgen.electronic_structure.plotter import DosPlotter
from VASP.vasprun_related.FeN.MAE import Coupling
dsp = DosPlotter()
dsp.add_dos_dict(dos_dict)
dsp.show(xlim=(-2, 1), ylim=(-1.5, 1.5))
save_dos_dict()
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()
'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))
if b[0] == 1 and b[1] == 0:
ter += 1
elif b[0] == 2 and b[1] == 0:
brig += 1
print(ter, brig)
# %%
import numpy as np
import macrodensity as md
arr = np.genfromtxt('/home/jinho93/molecule/dems/25/100/temp.dat')
arr = arr[:, 3]
mac = md.macroscopic_average(arr, 1, 0.1)
import matplotlib.pyplot as plt
plt.plot(mac)
np.savetxt('/home/jinho93/mac.dat', mac)
# %%
a = np.genfromtxt('mac.dat')
# %%
print(a)
# %%
from pymatgen.io.vasp import Vasprun
from pymatgen import Element
from pymatgen.electronic_structure.plotter import DosPlotter
dsp = DosPlotter()
vrun = Vasprun('vasprun.xml')
dsp.add_dos('total', vrun.tdos)
dsp.show(xlim=(-1, 1.5))
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])
#%% 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)) # %%
