root / ase / test / center.py @ 1
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"Test that atoms.center() works when adding vacuum ()"
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import numpy as np |
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from math import pi, sqrt, cos |
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from ase import data |
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from ase.lattice.cubic import FaceCenteredCubic |
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def checkang(a, b, phi): |
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"Check the angle between two vectors."
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cosphi = np.dot(a,b) / sqrt(np.dot(a,a) * np.dot(b,b)) |
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assert np.abs(cosphi - cos(phi)) < 1e-10 |
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symb = "Cu"
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Z = data.atomic_numbers[symb] |
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a0 = data.reference_states[Z]['a']
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# (100) oriented block
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atoms = FaceCenteredCubic(size=(5,5,5), symbol="Cu", pbc=(1,1,0)) |
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assert len(atoms) == 5*5*5*4 |
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c = atoms.get_cell() |
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checkang(c[0], c[1], pi/2) |
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checkang(c[0], c[2], pi/2) |
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checkang(c[1], c[2], pi/2) |
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assert np.abs(5 * a0 - c[2,2]) < 1e-10 |
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# Add vacuum in one direction
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vac = 10.0
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atoms.center(axis=2, vacuum=vac)
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c = atoms.get_cell() |
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checkang(c[0], c[1], pi/2) |
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checkang(c[0], c[2], pi/2) |
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checkang(c[1], c[2], pi/2) |
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assert np.abs(4.5 * a0 + 2* vac - c[2,2]) < 1e-10 |
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# Add vacuum in all directions
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vac = 4.0
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atoms.center(vacuum=vac) |
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c = atoms.get_cell() |
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checkang(c[0], c[1], pi/2) |
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checkang(c[0], c[2], pi/2) |
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checkang(c[1], c[2], pi/2) |
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assert np.abs(4.5 * a0 + 2* vac - c[0,0]) < 1e-10 |
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assert np.abs(4.5 * a0 + 2* vac - c[1,1]) < 1e-10 |
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assert np.abs(4.5 * a0 + 2* vac - c[2,2]) < 1e-10 |
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# Now a general unit cell
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atoms = FaceCenteredCubic(size=(5,5,5), directions=[[1,0,0], [0,1,0], [1,0,1]], |
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symbol="Cu", pbc=(1,1,0)) |
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assert len(atoms) == 5*5*5*2 |
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c = atoms.get_cell() |
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checkang(c[0], c[1], pi/2) |
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checkang(c[0], c[2], pi/4) |
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checkang(c[1], c[2], pi/2) |
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assert np.abs(2.5 * a0 - c[2,2]) < 1e-10 |
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# Add vacuum in one direction
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vac = 10.0
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atoms.center(axis=2, vacuum=vac)
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c = atoms.get_cell() |
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checkang(c[0], c[1], pi/2) |
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checkang(c[0], c[2], pi/4) |
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checkang(c[1], c[2], pi/2) |
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assert np.abs(2 * a0 + 2* vac - c[2,2]) < 1e-10 |
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# Recenter without specifying vacuum
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atoms.center() |
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c = atoms.get_cell() |
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checkang(c[0], c[1], pi/2) |
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checkang(c[0], c[2], pi/4) |
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checkang(c[1], c[2], pi/2) |
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assert np.abs(2 * a0 + 2* vac - c[2,2]) < 1e-10 |
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# Add vacuum in all directions
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vac = 4.0
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atoms.center(vacuum=vac) |
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c = atoms.get_cell() |
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checkang(c[0], c[1], pi/2) |
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checkang(c[0], c[2], pi/4) |
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checkang(c[1], c[2], pi/2) |
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assert np.abs(4.5 * a0 + 2* vac - c[1,1]) < 1e-10 |
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assert np.abs(2 * a0 + 2* vac - c[2,2]) < 1e-10 |
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