def testPointDefectConstruction(self):
identifiers=[(2, (0, 0)), (3, (0, 0)), ]
surface = Ge001
defect = SurfacePointDefect(
surface=surface,
identifiers=identifiers)
pos1 = defect.removedAtoms(coordinates='orth_surface').get_positions().mean(0)
pos = [pos1]
name = 'Test'
added_atoms = Atoms('Ag', pos)
test = Diamond001PointDefect(
name=name,
symbol='Ge',
identifiers=identifiers,
added_atoms=added_atoms,
)
self.assertEqual(test.name(), name)
def __init__(self,
probe_symbol,
surface_symbol,
):
self.__probe_symbol = probe_symbol
surface = BodyCenteredCubic111(surface_symbol)
l = vectorLength(surface.cell()[1])/3
x, y = self.probePlacement(l)
positions = [(x,y,2.210),
(x, y + l, 0.92),
(x + l*np.cos(np.pi/6), y-l*np.sin(np.pi/6), 0.92),
(x - l*np.cos(np.pi/6),y-l*np.sin(np.pi/6), 0.92),
]
added_atoms = Atoms(probe_symbol*len(positions), positions)
SurfacePointDefect.__init__(
self,
surface=surface,
added_atoms=added_atoms,
)