def calc_impurity_energy(self, structure, elements):
if structure not in ['oct38-center', 'oct38-face', 'oct38-edge']:
raise ValueError("Cannot calculate impurity energy for '%s'" %
(structure, ))
if len(elements) != 2:
raise ValueError("Tuple of elements must be of length two")
if self.debug:
print "Calculating impurity energy..."
print 40 * "*"
print "Structure: %s" % (structure, )
print "Elements: %s\n" % (elements, )
name, impurity = structure.split('-')
sym = reference_states[atomic_numbers[elements[1]]]['symmetry']
latticeconstant = self.get_lattice_constant_a(sym, (elements[1], ))
if name == 'oct38':
sites = {'center': 10, 'face': 9, 'edge': 0}
atoms = Octahedron(elements[1], 4, 1, latticeconstant)
atoms.set_calculator(self.get_calc())
dyn = BFGS(atoms, logfile=None, trajectory=None)
dyn.run(fmax=0.001, steps=100)
assert dyn.converged()
s_clean = dyn.get_number_of_steps()
e_clean = atoms.get_potential_energy()
atoms[sites[impurity]].symbol = elements[0]
dyn.run(fmax=0.001, steps=100)
assert dyn.converged()
s_impurity = dyn.get_number_of_steps()
e_impurity = atoms.get_potential_energy()
self.values[('impurity_energy', structure,
elements)] = e_impurity - e_clean
if self.debug:
print "BFGS steps: %i %i" % (s_clean, s_impurity)
print "Impurity energy: %.5f - %.5f = %.5f eV" % (
e_impurity, e_clean, e_impurity - e_clean)
print 40 * "-" + "\n"
