def perform_es_corr(self, lattice, q, step=1e-4):
"""
Perform Electrostatic Freysoldt Correction
Args:
lattice: Pymatgen lattice object
q (int): Charge of defect
step (float): step size for numerical integration
Return:
Electrostatic Point Charge contribution to Freysoldt Correction (float)
"""
logger.info(
"Running Freysoldt 2011 PC calculation (should be equivalent to sxdefectalign)"
)
logger.debug("defect lattice constants are (in angstroms)" +
str(lattice.abc))
[a1, a2, a3] = ang_to_bohr * np.array(lattice.get_cartesian_coords(1))
logging.debug("In atomic units, lat consts are (in bohr):" +
str([a1, a2, a3]))
vol = np.dot(a1, np.cross(a2, a3)) # vol in bohr^3
def e_iso(encut):
gcut = eV_to_k(encut) # gcut is in units of 1/A
return scipy.integrate.quad(
lambda g: self.q_model.rho_rec(g * g)**2, step,
gcut)[0] * (q**2) / np.pi
def e_per(encut):
eper = 0
for g2 in generate_reciprocal_vectors_squared(a1, a2, a3, encut):
eper += (self.q_model.rho_rec(g2)**2) / g2
eper *= (q**2) * 2 * round(np.pi, 6) / vol
eper += (q**2) * 4 * round(np.pi,
6) * self.q_model.rho_rec_limit0 / vol
return eper
eiso = converge(e_iso, 5, self.madetol, self.energy_cutoff)
logger.debug("Eisolated : %f", round(eiso, 5))
eper = converge(e_per, 5, self.madetol, self.energy_cutoff)
logger.info("Eperiodic : %f hartree", round(eper, 5))
logger.info("difference (periodic-iso) is %f hartree",
round(eper - eiso, 6))
logger.info("difference in (eV) is %f",
round((eper - eiso) * hart_to_ev, 4))
es_corr = round((eiso - eper) / self.dielectric * hart_to_ev, 6)
logger.info("Defect Correction without alignment %f (eV): ", es_corr)
return es_corr
def perform_es_corr(self, lattice, q, step=1e-4):
"""
Peform Electrostatic Freysoldt Correction
"""
logger.info("Running Freysoldt 2011 PC calculation (should be " "equivalent to sxdefectalign)")
logger.debug("defect lattice constants are (in angstroms)" + str(lattice.abc))
[a1, a2, a3] = ang_to_bohr * np.array(lattice.get_cartesian_coords(1))
logging.debug("In atomic units, lat consts are (in bohr):" + str([a1, a2, a3]))
vol = np.dot(a1, np.cross(a2, a3)) # vol in bohr^3
def e_iso(encut):
gcut = eV_to_k(encut) # gcut is in units of 1/A
return scipy.integrate.quad(lambda g: self.q_model.rho_rec(g * g)**2, step, gcut)[0] * (q**2) / np.pi
def e_per(encut):
eper = 0
for g2 in generate_reciprocal_vectors_squared(a1, a2, a3, encut):
eper += (self.q_model.rho_rec(g2)**2) / g2
eper *= (q**2) * 2 * round(np.pi, 6) / vol
eper += (q**2) * 4 * round(np.pi, 6) \
* self.q_model.rho_rec_limit0 / vol
return eper
eiso = converge(e_iso, 5, self.madetol, self.energy_cutoff)
logger.debug("Eisolated : %f", round(eiso, 5))
eper = converge(e_per, 5, self.madetol, self.energy_cutoff)
logger.info("Eperiodic : %f hartree", round(eper, 5))
logger.info("difference (periodic-iso) is %f hartree", round(eper - eiso, 6))
logger.info("difference in (eV) is %f", round((eper - eiso) * hart_to_ev, 4))
es_corr = round((eiso - eper) / self.dielectric * hart_to_ev, 6)
logger.info("Defect Correction without alignment %f (eV): ", es_corr)
return es_corr
def test_converges(self):
self.assertAlmostEqual(converge(np.sqrt, 0.1, 0.1, 1.0),
0.6324555320336759)
def test_converges(self):
self.assertAlmostEqual(converge(np.sqrt, 0.1, 0.1, 1.0),
0.6324555320336759)
