def charges_annotation(E_Fermi, E_for, charge, ax, text_size):
""" Add an annotation giving the charge of the formation energy at the beginning of the line
:param E_Fermi: Fermi energy range
:param E_for: defect formation energy for a given charge 'charge'
:param charge: charge associated with the defect formation energy
:param ax: matplotlib.axes object
:param text_size: size of the text
"""
if float(charge) > 0:
index = np.where(np.abs(E_for - ax.get_ylim()[0]) < 5e-4)[0]
if len(index) != 0:
coordinates = (E_Fermi[index[-1]], E_for[index[-1]]) # coordinates of the annotation
hor_al = 'center' # horizontal alignment of the annotation
ver_al = 'bottom' # vertical alignment of the annotation
else:
coordinates = (E_Fermi[0] + 0.01 * E_Fermi[-1], E_for[0] + float(charge) * 0.05 * E_Fermi[-1])
hor_al = 'left'
ver_al = 'center'
else:
index = np.where(np.abs(E_for - ax.get_ylim()[1]) < 5e-4)[0]
if len(index) != 0:
coordinates = (E_Fermi[index[0]], E_for[index[0]])
hor_al = 'center'
ver_al = 'top'
else:
coordinates = (E_Fermi[0] + 0.01 * E_Fermi[-1], E_for[0] + float(charge) * 0.05 * E_Fermi[-1])
hor_al = 'left'
ver_al = 'center'
annotation = ax.annotate('$q = %s$' % bf.float_to_str(charge), xy=coordinates,
bbox=dict(boxstyle='square', fc='1', pad=0.05),
ha=hor_al, va=ver_al, fontsize=text_size)
annotation.draggable()
def plot_transition_levels(self):
""" Plot the transition levels of the study """
E_Fermi = np.linspace(self.tpp.E_range[0], self.tpp.E_range[1], 30000) # range of fermi energies
transition_levels = self.get_transition_levels(E_Fermi) # all transition levels in the range of fermi energies
gap = self.gaps[self.tpp.gap_choice]
# ------------------------------------------- FIGURE PARAMETERS -----------------------------------------------
fig, ax = transition_figure_parameters(self.tpp)
ax.set_xlim(-0.01, 1.2)
# -------------------------------------------- PLOT PARAMETERS ------------------------------------------------
ax.stackplot([0, 0, 1.1, 1.1], [[0, ax.get_ylim()[0]-1, ax.get_ylim()[0]-1, 0]], colors=['grey'], linewidths=4)
ax.plot([0, 0, 1.1, 1.1], [ax.get_ylim()[1], gap, gap, ax.get_ylim()[1]], color='black', linewidth=4)
ax.annotate(' $VBM$', xy=(1.1, 0.0), fontsize=self.tpp.text_size, va='center', ha='left').draggable()
ax.annotate(' $CBM$', xy=(1.1, gap), fontsize=self.tpp.text_size, va='center', ha='left').draggable()
for transition in transition_levels:
ax.plot([0.1, 1], [transition[0], transition[0]], linewidth=2, color='black')
charges = sorted(list(set(np.concatenate([f[2:] for f in transition_levels]))), reverse=True)
tr_fermi = [f[0] for f in transition_levels]
for charge, tr in zip(charges, [tr_fermi[0] - 0.06] + list(tr_fermi[:-1] + np.diff(tr_fermi)/2.0) + [tr_fermi[-1] + 0.06]):
ax.annotate('$' + bf.float_to_str(charge) + '$', xy=(0.55, tr), fontsize=self.tpp.text_size,
va='center', ha='center').draggable()
fig.tight_layout()
fig.show()
def plot_formation_energy(self):
""" Plot the defect formation energy as a function of the Fermi level energy """
E_Fermi = np.linspace(self.fpp.E_range[0], np.max(self.gaps.values() +
[self.fpp.E_range[1]]), 10000) # energies of the Fermi level
E_for = [f.E_for_0 + f.Defect_Cell.charge * E_Fermi for f
in self.defect_cell_studies.itervalues()] # corresponding formation energies
E_for_low = np.transpose([self.get_formation_energy_low_EF(f) for f in E_Fermi])[1]
transition_levels = self.get_transition_levels(E_Fermi)
# ------------------------------------------- FIGURE PARAMETERS ------------------------------------------------
fig, ax = formation_figure_parameters(self.fpp)
# -------------------------------------------- PLOT PARAMETERS -------------------------------------------------
[ax.plot(E_Fermi, f, color='black', linewidth=1.5) for f in E_for] # formation energies
ax.plot(E_Fermi, E_for_low, color='black', linewidth=4) # lowest formation energy
[ax.plot([f[1], f[1]], [ax.get_ylim()[0], ax.get_ylim()[1]], label=f[0], linewidth=2, linestyle='--')
for f in self.gaps.iteritems()]
if self.fpp.display_charges is True:
charges = [f.Defect_Cell.charge for f in self.defect_cell_studies.itervalues()]
[charges_annotation(E_Fermi, f, g, ax, self.fpp.text_size - 3) for f, g in zip(E_for, charges)]
if self.fpp.display_transition_levels is True:
for level in transition_levels:
ax.plot([level[0], level[0]], [ax.get_ylim()[0], level[1]], linestyle='--', color='black')
text = r'$\epsilon(' + bf.float_to_str(level[3]) + '/' + bf.float_to_str(level[2]) + ')$'
annotation = ax.annotate(text, xy=(level[0], ax.get_ylim()[0] + 0.1 * np.diff(ax.get_ylim())[0]),
ha='center', va='top', fontsize=self.fpp.text_size - 2, backgroundcolor='w')
annotation.draggable()
legend = ax.legend(loc='best', fancybox=True, fontsize=self.fpp.text_size - 2)
legend.draggable()
fig.tight_layout()
fig.show()
def __init__(self, Host_Cell, Defect_Cell, DefectS, spheres_radius, z_e, z_h, geometry, e_r, mk_1_1, DE_VBM, DE_CBM,
potential_alignment_correction=True, moss_burstein_correction=True, phs_correction=True,
vbm_correction=True, makov_payne_correction=True):
"""
:param Host_Cell: Cell object of the host cell calculation
:param Defect_Cell: Cell object of the defect cell calculation
:param DefectS: list of Defect objects
:param spheres_radius: radius of the spheres in angstrom (float)
:param z_e: number of electrons in the PHS
:param z_h: number of holes in the PHS
:param geometry: geometry of the host cell
:param e_r: relative permittivity
:param mk_1_1: value of the first term of the Makov-Payne correction in the case q = 1 & e_r = 1
:param DE_VBM: correction of the VBM
:param DE_CBM: correction of the CBM
:param potential_alignment_correction: if True, the potential alignment correction is done
:param moss_burstein_correction: if True, the Moss-Burstein correction is done
:param phs_correction: if True, the PHS correction is done
:param vbm_correction: if True, the VBM correction is done
:param makov_payne_correction: if True, the Makov-Payne correction is done
"""
self.Host_Cell = Host_Cell
self.Defect_Cell = Defect_Cell
self.DefectS = DefectS
self.spheres_radius = spheres_radius
# Check that the Host Cell and the Defect Cell have the same cristal parameters
if Host_Cell.cell_parameters != Defect_Cell.cell_parameters:
raise bf.PydefDefectCellError("The host cell is not consistent with the defect cell")
# if Defect_Cell.isym != 0:
# raise bf.PydefDefectCellError('You should se ISYM to 0')
# Title of the defects for display (name of the defects + charge of the cell)
if len(DefectS) == 1:
self.defects_title = self.DefectS[0].name + '^{' + bf.float_to_str(int(self.Defect_Cell.charge)) + '}'
else:
self.defects_title = '(' + ' & '.join([f.name for f in self.DefectS]) + ')^{' \
+ bf.float_to_str(int(self.Defect_Cell.charge)) + '}'
# Title of the Defect Cell Study for display
self.title = Host_Cell.display_rname + ' - ' + self.defects_title
# --------------------------------------------- CORRECTIONS ---------------------------------------------------
if potential_alignment_correction is True:
self.pa_corr_temp = zc.potential_alignment_correction(Host_Cell, Defect_Cell, DefectS,
spheres_radius, False)[-1]
self.pa_corr = self.pa_corr_temp * Defect_Cell.charge
else:
self.pa_corr = 0.0
if moss_burstein_correction is True:
self.mb_corr = zc.moss_burstein_correction(Host_Cell, Defect_Cell, DefectS, spheres_radius)
else:
self.mb_corr = [0.0, 0.0]
if phs_correction is True:
self.phs_corr = zc.phs_correction(z_h, z_e, DE_VBM, DE_CBM)
else:
self.phs_corr = [0.0, 0.0]
if vbm_correction is True:
self.vbm_corr = zc.vbm_correction(Defect_Cell, DE_VBM)
else:
self.vbm_corr = 0.0
if makov_payne_correction is True:
self.mp_corr = zc.makov_payne_correction(Defect_Cell, geometry, e_r, mk_1_1)
else:
self.mp_corr = 0.0
# Total correction
self.tot_corr = self.pa_corr + sum(self.mb_corr) + sum(self.phs_corr) + self.vbm_corr + self.mp_corr
self.E_for_0 = Defect_Cell.energy - Host_Cell.energy + sum([f.n * f.chem_pot for f in DefectS]) \
+ Defect_Cell.charge * Host_Cell.VBM + self.tot_corr