Band Structure of NiO¶
Germain Salvato Vallverdu germain.vallverdu@univ-pau.fr¶
Short examples to show how to extract or plot the band structure from a VASP calculation using pymagen.
Written using:
- pymatgen==2018.3.13
First, load used packages :
import pymatgen as mg
from pymatgen.io.vasp.outputs import BSVasprun, Vasprun
from pymatgen import Spin
from pymatgen.electronic_structure.plotter import BSPlotter, BSDOSPlotter, DosPlotter
import matplotlib.pyplot as plt
%matplotlib inline
I work in a directory that contains the calculations of the NiO band structure. Look at this example to learn how to obtain a band structure from VASP calculations.
ls
1) Read vasprun.xml and extract the band structure¶
run = BSVasprun("vasprun.xml", parse_projected_eigen=True)
bs = run.get_band_structure("KPOINTS")
You can obtain some information about the band structure :
print("number of bands", bs.nb_bands)
print("number of kpoints", len(bs.kpoints))
bs.is_metal()
bs.is_spin_polarized
2) Extract a given band or eigenvalues¶
The bands attribute of the BaandStructure object is a dictionnary of arrays that contains all the bands. The shape is the following :
{Spin.up: np.array((nb_bands, nb_kpoints)), Spin.down: np.array((nb_bands, nb_kpoints))}bs.bands
bs.bands[Spin.up].shape
The 9th bands of spin down is extracted by :
bs.bands[Spin.down][9, :]
In order to print a band and the corresponding k-points :
n = 0
for kpoints, e in zip(bs.kpoints, bs.bands[Spin.down][9, :]):
n += 1
if n == 11:
print("...")
if 10 < n < 190:
continue
print("kx = %5.3f ky = %5.3f kz = %5.3f eps(k) = %8.4f" % (tuple(kpoints.frac_coords) + (e,)))
3) Plot a simple band structure¶
bsplot = BSPlotter(bs)
# get the plot
bsplot.get_plot(ylim=(-20, 10), zero_to_efermi=True)
print(bs.efermi)
# add some features
ax = plt.gca()
ax.set_title("NiO Band Structure", fontsize=20)
xlim = ax.get_xlim()
ax.hlines(0, xlim[0], xlim[1], linestyles="dashed", color="black")
# add legend
ax.plot((), (), "b-", label="spin up")
ax.plot((), (), "r--", label="spin down")
ax.legend(fontsize=16, loc="upper left")
3.1) Extract data from the plot¶
You can get data from the plot and in particular the (x, y) coordinates of each band.
data = bsplot.bs_plot_data()
data.keys()
For example, here, you print the abscissa and the energy of the 9th band. Keep in mind that here the data are the ones used to do the plot. Thus the zero to fermi translation is already done according to the BSPlotter class.
ibands = 9 # band number from 0 --> number of bands
spin = str(Spin.up)
for xpath, epath in zip(data["distances"], data["energy"]):
print(20 * "-")
for x, bands in zip(xpath, epath[spin][ibands]):
print("%8.4f %8.4f" % (x, bands))
Same as above but in a plot.
ibands = 9 # band number from 0 --> number of bands
spin = str(Spin.up)
for xpath, epath in zip(data["distances"], data["energy"]):
plt.plot(xpath, epath[spin][ibands])
The same again but merging the slices of the band.
ibands = 1 # band number from 0 --> number of bands
spin = str(Spin.up)
x = list()
y = list()
for xpath, epath in zip(data["distances"], data["energy"]):
x += xpath
y += epath[spin][ibands]
plt.plot(x, y)
4) Plot DOS¶
Read the DOS from another calculations.
dosrun = Vasprun("../DOS_SMEAR/vasprun.xml", parse_dos=True)
dos = dosrun.complete_dos
print(dosrun.efermi)
print(dos.efermi)
dosplot = DosPlotter(sigma=0.1)
dosplot.add_dos("Total DOS", dos)
dosplot.add_dos_dict(dos.get_element_dos())
plt = dosplot.get_plot()
plt.grid()
5) Plot Bands and DOS¶
bs = run.get_band_structure("KPOINTS", efermi=dos.efermi)
bsdosplot = BSDOSPlotter(
bs_projection="elements",
dos_projection="elements",
vb_energy_range=22,
egrid_interval=2.5
)
plt = bsdosplot.get_plot(bs, dos=dos)
bsdosplot = BSDOSPlotter(
bs_projection="elements",
dos_projection="elements",
vb_energy_range=11,
cb_energy_range=10,
egrid_interval=2
)
plt = bsdosplot.get_plot(bs, dos=dos)
