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, )