def get_atoms_adsorbate(): # We need the relaxed slab here! slab = Atoms([ Atom('Cu', [-1.028468159509163, -0.432387156877267, -0.202086055768265]), Atom('Cu', [0.333333333333333, 0.333333333333333, -2.146500000000000]), Atom('Cu', [1.671531840490805, -0.432387156877287, -0.202086055768242]), Atom('Cu', [3.033333333333334, 0.333333333333333, -2.146500000000000]), Atom('Cu', [4.371531840490810, -0.432387156877236, -0.202086055768261]), Atom('Cu', [5.733333333333333, 0.333333333333333, -2.146500000000000]), Atom('Cu', [7.071531840490944, -0.432387156877258, -0.202086055768294]), Atom('Cu', [8.433333333333335, 0.333333333333333, -2.146500000000000]), Atom('Cu', [0.321531840490810, 1.905881433340708, -0.202086055768213]), Atom('Cu', [1.683333333333333, 2.671601923551318, -2.146500000000000]), Atom('Cu', [3.021531840490771, 1.905881433340728, -0.202086055768250]), Atom('Cu', [4.383333333333334, 2.671601923551318, -2.146500000000000]), Atom('Cu', [5.721531840490857, 1.905881433340735, -0.202086055768267]), Atom('Cu', [7.083333333333333, 2.671601923551318, -2.146500000000000]), Atom('Cu', [8.421531840490820, 1.905881433340739, -0.202086055768265]), Atom('Cu', [9.783333333333335, 2.671601923551318, -2.146500000000000]), Atom('Cu', [1.671531840490742, 4.244150023558601, -0.202086055768165]), Atom('Cu', [3.033333333333334, 5.009870513769302, -2.146500000000000]), Atom('Cu', [4.371531840490840, 4.244150023558694, -0.202086055768265]), Atom('Cu', [5.733333333333333, 5.009870513769302, -2.146500000000000]), Atom('Cu', [7.071531840490880, 4.244150023558786, -0.202086055768352]), Atom('Cu', [8.433333333333335, 5.009870513769302, -2.146500000000000]), Atom('Cu', [9.771531840491031, 4.244150023558828, -0.202086055768371]), Atom('Cu', [11.133333333333335, 5.009870513769302, -2.146500000000000]), Atom('Cu', [3.021531840490714, 6.582418613776583, -0.202086055768197]), Atom('Cu', [4.383333333333334, 7.348139103987287, -2.146500000000000]), Atom('Cu', [5.721531840490814, 6.582418613776629, -0.202086055768203]), Atom('Cu', [7.083333333333333, 7.348139103987287, -2.146500000000000]), Atom('Cu', [8.421531840490985, 6.582418613776876, -0.202086055768357]), Atom('Cu', [9.783333333333335, 7.348139103987287, -2.146500000000000]), Atom('Cu', [11.121531840490929, 6.582418613776676, -0.202086055768221]), Atom('Cu', [12.483333333333334, 7.348139103987287, -2.146500000000000]), ]) mask = [a.position[2] < -1 for a in slab] slab.set_constraint(FixAtoms(mask=mask)) a = 2.70 c = 1.59 * a h = 1.85 d = 1.10 x = slab.positions[0, 2] / (c / 2) * 100 molecule = Atoms('2N', positions=[(0., 0., h), (0., 0., h + d)]) molecule.set_calculator(EMT()) slab.extend(molecule) return slab
def get_atoms(): srf = Atoms('Cu64', [(1.2763, 1.2763, 4.0000), (3.8290, 1.2763, 4.0000), (6.3816, 1.2763, 4.0000), (8.9343, 1.2763, 4.0000), (1.2763, 3.8290, 4.0000), (3.8290, 3.8290, 4.0000), (6.3816, 3.8290, 4.0000), (8.9343, 3.8290, 4.0000), (1.2763, 6.3816, 4.0000), (3.8290, 6.3816, 4.0000), (6.3816, 6.3816, 4.0000), (8.9343, 6.3816, 4.0000), (1.2763, 8.9343, 4.0000), (3.8290, 8.9343, 4.0000), (6.3816, 8.9343, 4.0000), (8.9343, 8.9343, 4.0000), (0.0000, 0.0000, 5.8050), (2.5527, 0.0000, 5.8050), (5.1053, 0.0000, 5.8050), (7.6580, 0.0000, 5.8050), (0.0000, 2.5527, 5.8050), (2.5527, 2.5527, 5.8050), (5.1053, 2.5527, 5.8050), (7.6580, 2.5527, 5.8050), (0.0000, 5.1053, 5.8050), (2.5527, 5.1053, 5.8050), (5.1053, 5.1053, 5.8050), (7.6580, 5.1053, 5.8050), (0.0000, 7.6580, 5.8050), (2.5527, 7.6580, 5.8050), (5.1053, 7.6580, 5.8050), (7.6580, 7.6580, 5.8050), (1.2409, 1.2409, 7.6081), (3.7731, 1.2803, 7.6603), (6.3219, 1.3241, 7.6442), (8.8935, 1.2669, 7.6189), (1.2803, 3.7731, 7.6603), (3.8188, 3.8188, 7.5870), (6.3457, 3.8718, 7.6649), (8.9174, 3.8340, 7.5976), (1.3241, 6.3219, 7.6442), (3.8718, 6.3457, 7.6649), (6.3945, 6.3945, 7.6495), (8.9576, 6.3976, 7.6213), (1.2669, 8.8935, 7.6189), (3.8340, 8.9174, 7.5976), (6.3976, 8.9576, 7.6213), (8.9367, 8.9367, 7.6539), (0.0582, 0.0582, 9.4227), (2.5965, -0.2051, 9.4199), (5.1282, 0.0663, 9.4037), (7.6808, -0.0157, 9.4235), (-0.2051, 2.5965, 9.4199), (2.1913, 2.1913, 9.6123), (5.0046, 2.5955, 9.4873), (7.5409, 2.5336, 9.4126), (0.0663, 5.1282, 9.4037), (2.5955, 5.0046, 9.4873), (5.3381, 5.3381, 9.6106), (7.8015, 5.0682, 9.4237), (-0.0157, 7.6808, 9.4235), (2.5336, 7.5409, 9.4126), (5.0682, 7.8015, 9.4237), (7.6155, 7.6155, 9.4317)]) c2 = Atoms('C2', [(3.2897, 3.2897, 10.6627), (4.2113, 4.2113, 10.6493)]) srf.extend(c2) srf.pbc = (1, 1, 0) srf.set_cell([10.2106, 10.2106, 20.6572], scale_atoms=False) mask = [a.index < 32 for a in srf] c1 = FixedPlane(-1, (1 / np.sqrt(2), 1 / np.sqrt(2), 1)) c2 = FixedPlane(-2, (1 / np.sqrt(2), 1 / np.sqrt(2), 1)) constraint = FixAtoms(mask=mask) srf.set_constraint([constraint, c1, c2]) return srf