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from math import cos, pi, sqrt
import numpy as np
import pytest
from ase import Atoms, data
from ase.lattice.cubic import FaceCenteredCubic
symb = 'Cu'
Z = data.atomic_numbers[symb]
a0 = data.reference_states[Z]['a'] # type: ignore[index]
def checkang(a, b, phi):
"Check the angle between two vectors."
cosphi = np.dot(a, b) / sqrt(np.dot(a, a) * np.dot(b, b))
assert np.abs(cosphi - cos(phi)) < 1e-10
@pytest.fixture()
def atoms():
# (100) oriented block
atoms = FaceCenteredCubic(size=(5, 5, 5), symbol=symb, pbc=(1, 1, 0))
assert len(atoms) == 5 * 5 * 5 * 4
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 2)
checkang(c[1], c[2], pi / 2)
assert np.abs(5 * a0 - c[2, 2]) < 1e-10
return atoms
def test_vacuum_one_direction(atoms):
vac = 10.0
atoms.center(axis=2, vacuum=vac)
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 2)
checkang(c[1], c[2], pi / 2)
assert np.abs(4.5 * a0 + 2 * vac - c[2, 2]) < 1e-10
def test_vacuum_all_directions(atoms):
vac = 4.0
atoms.center(vacuum=vac)
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 2)
checkang(c[1], c[2], pi / 2)
assert np.abs(4.5 * a0 + 2 * vac - c[0, 0]) < 1e-10
assert np.abs(4.5 * a0 + 2 * vac - c[1, 1]) < 1e-10
assert np.abs(4.5 * a0 + 2 * vac - c[2, 2]) < 1e-10
@pytest.fixture()
def atoms_guc():
return FaceCenteredCubic(size=(5, 5, 5),
directions=[[1, 0, 0], [0, 1, 0], [1, 0, 1]],
symbol=symb, pbc=(1, 1, 0))
def test_general_unit_cell(atoms_guc):
atoms = atoms_guc
assert len(atoms) == 5 * 5 * 5 * 2
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 4)
checkang(c[1], c[2], pi / 2)
assert np.abs(2.5 * a0 - c[2, 2]) < 1e-10
def test_vacuum_one_direction_guc(atoms_guc):
atoms = atoms_guc
vac = 10.0
atoms.center(axis=2, vacuum=vac)
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 4)
checkang(c[1], c[2], pi / 2)
assert np.abs(2 * a0 + 2 * vac - c[2, 2]) < 1e-10
# Recenter without specifying vacuum
atoms.center()
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 4)
checkang(c[1], c[2], pi / 2)
assert np.abs(2 * a0 + 2 * vac - c[2, 2]) < 1e-10
a2 = atoms.copy()
# Add vacuum in all directions
vac = 4.0
atoms.center(vacuum=vac)
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 4)
checkang(c[1], c[2], pi / 2)
assert np.abs(4.5 * a0 + 2 * vac - c[1, 1]) < 1e-10
assert np.abs(2 * a0 + 2 * vac - c[2, 2]) < 1e-10
# One axis at the time:
for i in range(3):
a2.center(vacuum=vac, axis=i)
assert abs(atoms.positions - a2.positions).max() < 1e-12
assert abs(atoms.cell - a2.cell).max() < 1e-12
def test_center_empty():
atoms = Atoms()
atoms.center()
assert atoms == Atoms()
def test_center_nocell():
atoms = Atoms('H', positions=[[1., 2., 3.]])
atoms.center()
assert atoms.positions == pytest.approx(0)
def test_center_about1():
atoms = Atoms('H', positions=[[1., 2., 3.]])
atoms.center(vacuum=10.0, about=(0, 0, 0), axis=2)
assert atoms.positions[0, 0] != pytest.approx(0)
assert atoms.positions[0, 1] != pytest.approx(0)
assert atoms.positions[0, 2] == pytest.approx(0)
def test_center_about2():
atoms = Atoms('H', positions=[[1., 2., 3.]])
atoms.center(vacuum=10.0, about=(0, 5, 0), axis=(1, 2))
assert atoms.positions[0, 0] != pytest.approx(0)
assert atoms.positions[0, 1] == pytest.approx(5)
assert atoms.positions[0, 2] == pytest.approx(0)
def test_center_about3():
atoms = Atoms('H', positions=[[1., 2., 3.]])
atoms.center(vacuum=10.0, about=(10, 5, 2), axis=(0, 1, 2))
assert atoms.positions[0, 0] == pytest.approx(10)
assert atoms.positions[0, 1] == pytest.approx(5)
assert atoms.positions[0, 2] == pytest.approx(2)
def test_center_about4():
atoms = Atoms('H', positions=[[1., 2., 3.]])
atoms.center(vacuum=10.0, about=(0, 0, 0))
assert atoms.positions[0, 0] == pytest.approx(0)
assert atoms.positions[0, 1] == pytest.approx(0)
assert atoms.positions[0, 2] == pytest.approx(0)
def test_center_about_fail():
atoms = Atoms('H', positions=[[1., 2., 3.]])
atoms.set_cell([10, 10, 10])
atoms.center(about=(0, 0, 0), axis=2)
assert atoms.positions[0, 0] == pytest.approx(1)
assert atoms.positions[0, 1] == pytest.approx(2)
assert atoms.positions[0, 2] == pytest.approx(0)
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