plt.setp(fig[i].get_xticklabels(), visible=True)
for tick in fig[i].xaxis.get_major_ticks():
tick.label1.set_fontweight('bold')
print 'Done formatting!'
for i, nm in enumerate(nms):
s = ReadStruct('../../crystal_files/INPUT_'+nm)
s.normalise()
vbmax, cbmin = map(offst, lims[nm])
print nm
print vbmax, cbmin
fig[i].axvspan(offst(-5), vbmax, facecolor='0.85', linewidth=0)
fig[i].axvspan( cbmin, offst(1), facecolor='0.85', linewidth=0)
E, up, down = get_at_pdos(nm, 3, total=True)
fig[i].plot(offst(E), up, '-', color='slateblue', linewidth=3)
fig[i].plot(offst(E), down, '-', color='slateblue', linewidth=3)
_, u2, d2 = np.zeros(len(E)), np.zeros(len(up)), np.zeros(len(down))
print sc_lims[nm][0], sc_lims[nm][1]
for j, at in enumerate(s.atoms):
if at.z < sc_lims[nm][0] or at.z > sc_lims[nm][1]:
if at.z < ox_lims[nm][0] or at.z > ox_lims[nm][1]:
x, y1, y2 = get_at_pdos(nm, j+1)
u2 += y1
d2 += y2
fig[i].plot(offst(E), u2, '-', color='crimson', linewidth=3)
fig[i].plot(offst(E), d2, '-', color='crimson', linewidth=3)
'hfo2si_c1ox':(-2.62, -0.74),
'hfo2si_c2ox':(-2.48, -0.32),
'hfo2si_c3ox':(-2.43, -0.04)}
a = np.zeros(6, dtype=int)
y = [[] for i in range(len(a))]
for nm in nms:
s = ReadStruct('../../crystal_files/INPUT_'+nm)
for i, at in enumerate(s.atoms):
if at.species == 'Hf':
nbs = neighbours_from_file(i+1, nm)
nbs = [nb for nb in nbs if (nb.length < 3. and nb.atom_type == 'Hf')]
a[len(nbs)] +=1
E, up, down = get_at_pdos(nm, i+1)
vbm, cbm = lims[nm]
dos = integrate_dos(E, up, down, emin=vbm, emax=cbm) # tweak emin and emax
y[len(nbs)].append(dos)
xs, ys = np.array([]), np.array([])
for x, p in enumerate(y):
g = np.array([x]*len(p))
xs = np.append(xs, g)
ys = np.append(ys, p)
fig = plt.axes(xlim=(-1, 5))
fig.scatter(xs, ys, marker='o', facecolors='none')
#fig.boxplot(y[:], showfliers=False)
plt.setp(fig[i].get_xticklabels(), visible=True)
for tick in fig[i].xaxis.get_major_ticks():
tick.label1.set_fontweight('bold')
print 'Done formatting!'
for i, nm in enumerate(nms):
s = ReadStruct('../../crystal_files/INPUT_'+nm)
o = lambda k : k - offsets[nm]['VBM']
fig[i].axvspan(-1, 0, facecolor='0.85', linewidth=0)
fig[i].axvspan(offsets[nm]['CBM']-offsets[nm]['VBM'], 3, facecolor='0.85', linewidth=0)
E, up, down = get_at_pdos(nm, 3, total=True)
fig[i].plot(o(E), up, '-', color='slateblue', linewidth=3)
fig[i].plot(o(E), down, '-', color='slateblue', linewidth=3)
p1, p2 = np.zeros(600), np.zeros(600)
for ii, at in enumerate(s.atoms):
nbs = neighbours_from_file(ii+1, nm)
nbs = [nb for nb in nbs if (nb.atom_type == 'Hf' and nb.length < 3.)]
if at.species == 'Si' and nbs:
print [(nb.atom_type, nb.length) for nb in nbs]
_, u, d = get_at_pdos(nm, ii+1)
p1 += u
p2 += d
fig[i].plot(o(E), p1, '-', color='#66FFCC', linewidth=3)
fig[i].plot(o(E), p2, '-', color='#66FFCC', linewidth=3)
s = ReadStruct('../../crystal_files/INPUT_'+nm)
zero = offsets[nm]['VBM']
zeros_before = int(np.fabs(zero/dE))
zeros_after = 600 - zeros_before
#it = (i+1 for i in range(len(s)))
it = (a for a in s.atoms)
for i, at in enumerate(s.atoms):
if at.species=='Si':
nbs = neighbours_from_file(i+1, nm)
nbs = [nb for nb in nbs if (nb.length < 3 and nb.atom_type == 'Hf')]
E, y_u, y_d = get_at_pdos(nm, i+1)
Y_u = np.concatenate((np.zeros(zeros_before), y_u, np.zeros(zeros_after)), axis=0)
Y_d = np.concatenate((np.zeros(zeros_before), y_d, np.zeros(zeros_after)), axis=0)
if len(nbs) > 1:
Y= Y + Y_u - Y_d
Y_tot= Y_tot + Y_u - Y_d
fig.plot(X, Y, 'r', linewidth=2)
fig.plot(X, Y_tot, 'k', linewidth=2)
plt.setp(fig.get_xticklabels(), visible=True)
plt.gcf().set_size_inches(20., 3.5)
plt.xlabel('Energy [eV]', fontweight='bold', fontsize=20)
plt.savefig('dos_Si_HfBonded.png', dpi=100, bbox_inches='tight')
