def get_Y(lim_low, lim_high):
X = np.linspace(-5., 5., 600*2)
Y = np.zeros(600*2)
YU = np.zeros(600*2)
YD = np.zeros(600*2)
Yp = np.zeros(600*2)
YpU = np.zeros(600*2)
YpD = np.zeros(600*2)
no_eprimes = 0
for c in cells_to_check:
print c
zero = offsets[c]['VBM']
zeros_before = int(np.fabs(zero/dE))
zeros_after = 600 - zeros_before
#plt.plot([offsets[c]['Ef']-offsets[c]['VBM'],]*2, [-30,30], 'r--')
for eprime in eprime_dict[c]:
s = get_spin_mom(eprime, c)
if lim_low <= np.fabs(s) <= lim_high:
print s, eprime
x, y_u, y_d = get_at_pdos(c, eprime)
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)
Y = Y + Y_u - Y_d
if to_switch[c][eprime]:
print c, eprime, 'switch'
YU -= Y_d
YD -= Y_u
else:
YU += Y_u
YD += Y_d
if 'ox' not in c:
at_e = ReadStruct('../../crystal_files/INPUT_'+c,
'crystal').atoms[eprime-1]
p_str= ReadStruct('../../crystal_files/INPUT_'+c+'p', 'crystal')
i_x, at_p = get_similar(at_e, p_str)
x, yy_u, yy_d = get_at_pdos(c+'p', i_x)
Yp_u = np.concatenate((np.zeros(zeros_before),
yy_u,
np.zeros(zeros_after)), axis=0)
Yp_d = np.concatenate((np.zeros(zeros_before),
yy_d,
np.zeros(zeros_after)), axis=0)
Yp = Yp + Yp_u - Yp_d
if to_switch[c][eprime]:
print c, eprime, 'switch'
YpU -= Yp_d
YpD -= Yp_u
else:
YpU += Yp_u
YpD += Yp_d
no_eprimes = no_eprimes + 1
return X, YU, YD, no_eprimes
}
for c in ['c'+ i for i in map(str, range(2, 7))]:
print c,
for eprime in eprime_dict[c]:
print eprime,
x, y_u, y_d = get_at_pdos(c, eprime)
x = [o(p) for p in x]
plt.plot(x, y_u, 'k-', linewidth=2)
nps, = plt.plot(x, y_d, 'k-', label='Unpassivated', linewidth=2)
# Get the Atom object of the eprime
at_e = ReadStruct('../../crystal_files/INPUT_'+c,
'crystal').atoms[eprime-1]
p_str= ReadStruct('../../crystal_files/INPUT_'+c+'p', 'crystal')
# get equivalent atom from passified structure
i_x, at_p = get_similar(at_e, p_str)
print '{:5.3f}'.format(distance(at_e, at_p)),
x, y_u, y_d = get_at_pdos(c+'p', i_x)
x = [o(p) for p in x]
plt.plot(x, y_u, 'r-', linewidth=2.5)
ps,= plt.plot(x, y_d, 'r-', label='H passivated', linewidth=2.5)
print
minor_locator = MultipleLocator(0.10)
plt.gca().xaxis.set_minor_locator(minor_locator)
plt.gca().tick_params(which='minor', length=5, width=2)
plt.gca().tick_params(which='major', length=10, width=2, labelsize=15)
plt.legend(handles=[nps, ps], ncol=2, fontsize=20)
plt.axvspan(o(-5),o(-3.313), facecolor='0.85', linewidth=0)
plt.axvspan(o(-2.27),o(0.0), facecolor='0.85', linewidth=0)