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plot_vasp.py
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def smooth(y, box_pts):
import numpy as np
box = np.ones(box_pts)/box_pts
y_smooth = np.convolve(y, box, mode='same')
return y_smooth
def dos(vasprun_path = './vasprun.xml', t2g_list = [], eg_list = [], emin = -10, emax= 10, y_axis = [0,20], tdos = True, avg_points = 10, file_name=None):
import matplotlib.pyplot as plt
import numpy as np
import collections
import scipy as sp
import pymatgen as mg
import pymatgen.io.vasp.outputs as vio
from pymatgen.electronic_structure.core import Spin, Orbital
from pymatgen.electronic_structure import dos
vasprun = vio.Vasprun(vasprun_path)
dos_size = len(vasprun.pdos[0][Orbital.dz2][Spin.up][:])
atom_list = vasprun.atomic_symbols
atoms = collections.OrderedDict()
for i in range(0,len(atom_list)):
if not atom_list[i] in atoms:
atoms[atom_list[i]] = [i]
else:
atoms[atom_list[i]].append(i)
d_list = ['dxz','dyz','dxy','dx2','dz2']
f_list = ['f_1','f_2','f_3','f0','f1','f2','f3']
A_d = np.zeros(dos_size)
A_f = np.zeros(dos_size)
A_f_dos = False
B_t2g = np.zeros(dos_size)
B_eg = np.zeros(dos_size)
O_p = np.zeros(dos_size)
A_d_dn = np.zeros(dos_size)
A_f_dn = np.zeros(dos_size)
B_t2g_dn = np.zeros(dos_size)
B_eg_dn = np.zeros(dos_size)
O_p_dn = np.zeros(dos_size)
# is magnetic?
if Spin.down in vasprun.tdos.densities:
mag = True
else:
mag = False
for species, atoms in atoms.items():
if species in ['Mo','V','Cu']:
B_species = species
for i in atoms:
for eg in eg_list:
B_eg += np.array(vasprun.pdos[i][Orbital[eg]][Spin.up])
if mag:
B_eg_dn += np.array(vasprun.pdos[i][Orbital[eg]][Spin.down])
for t2g in t2g_list:
B_t2g += np.array(vasprun.pdos[i][Orbital[t2g]][Spin.up])
if mag:
B_t2g_dn += np.array(vasprun.pdos[i][Orbital[t2g]][Spin.down])
elif species == 'O':
for i in atoms:
O_p += np.array(vasprun.pdos[i][Orbital.px][Spin.up])
O_p += np.array(vasprun.pdos[i][Orbital.py][Spin.up])
O_p += np.array(vasprun.pdos[i][Orbital.pz][Spin.up])
if mag:
O_p_dn += np.array(vasprun.pdos[i][Orbital.px][Spin.down])
O_p_dn += np.array(vasprun.pdos[i][Orbital.py][Spin.down])
O_p_dn += np.array(vasprun.pdos[i][Orbital.pz][Spin.down])
elif not species == 'O' and not species in ['Mo','V', 'Cu']:
A_species = species
for i in atoms:
for orb in d_list:
A_d += np.array(vasprun.pdos[i][Orbital[orb]][Spin.up])
if mag:
A_d_dn += np.array(vasprun.pdos[i][Orbital[orb]][Spin.down])
if np.array(vasprun.pdos[i][Orbital.f_1]):
A_f_dos = True
for orb in f_list:
A_f += np.array(vasprun.pdos[i][Orbital[orb]][Spin.up])
if mag:
A_f += np.array(vasprun.pdos[i][Orbital[orb]][Spin.down])
fig, (ax1) = plt.subplots(1,1,sharex="col",figsize=(12,6))
ax1.fill_between(vasprun.tdos.energies - vasprun.efermi,
smooth(vasprun.tdos.densities[Spin.up], avg_points), 0,
color='gray', linewidth=0,alpha=0.3, label='tdos')
ax1.plot(vasprun.tdos.energies - vasprun.efermi , smooth(B_t2g, avg_points),
"-", label = str(B_species)+r" t$_{2g}$", color = 'C0', linewidth = 2)
ax1.plot(vasprun.tdos.energies - vasprun.efermi, smooth(B_eg, avg_points),
"-", label = str(B_species)+r" e$_g$", color = 'C1', linewidth = 2)
ax1.plot(vasprun.tdos.energies - vasprun.efermi , smooth(O_p, avg_points),
"-", label = r"$O_p$", color = 'C2', linewidth = 2)
# A site
ax1.plot(vasprun.tdos.energies - vasprun.efermi , smooth(A_d, avg_points),
"-", label = str(A_species)+r"$_d$", color = 'C3', linewidth = 2)
# A site f dos
if A_f_dos:
ax1.plot(vasprun.tdos.energies - vasprun.efermi , smooth(A_f, avg_points),
"-", label = str(A_species)+r"$_f$", color = 'C4', linewidth = 2)
if mag:
ax1.fill_between(vasprun.tdos.energies - vasprun.efermi,
-1*smooth(vasprun.tdos.densities[Spin.down], avg_points), 0,
color='gray', linewidth=0,alpha=0.3)
ax1.plot(vasprun.tdos.energies - vasprun.efermi , -1*smooth(B_t2g_dn, avg_points),
"-", color = 'C0', linewidth = 2)
ax1.plot(vasprun.tdos.energies - vasprun.efermi, -1*smooth(B_eg_dn, avg_points),
"-", color = 'C1', linewidth = 2)
ax1.plot(vasprun.tdos.energies - vasprun.efermi , -1*smooth(O_p_dn, avg_points),
"-", color = 'C2', linewidth = 2)
# A site
ax1.plot(vasprun.tdos.energies - vasprun.efermi , -1*smooth(A_d_dn, avg_points),
"-", color = 'C3' , linewidth = 2)
# A site f dos
if A_f_dos:
ax1.plot(vasprun.tdos.energies - vasprun.efermi , -1*smooth(A_f_dn, avg_points),
"-", color = 'C4' , linewidth = 2)
ax1.set_xlim(emin,emax)
ax1.set_ylim(y_axis[0],y_axis[1])
ax1.set_xlabel(r"$E - E_F$ (eV)")
ax1.set_ylabel(r"$\rho \ \left( states/eV \right)$")
ax1.vlines(x=0, ymin=-1000, ymax=1000, color="k", lw=2)
ax1.hlines(y=0, xmin=-1000, xmax=1000, color="k", lw=1)
ax1.xaxis.set_ticks_position('both')
ax1.legend(loc='upper right', ncol=1,numpoints=1,handlelength=1,fancybox=True,
labelspacing=0.2,borderaxespad=0.5,borderpad=0.35,handletextpad=0.4)
ax1.tick_params(direction='in',pad=2)
if file_name:
plt.savefig(file_name,dpi=600, bbox_inches='tight',transparent=True, pad_inches=0.01)
plt.show()
return vasprun