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def test_geometry():
"""Test the ase.geometry module and ase.build.cut() function."""
import numpy as np
from ase.build import cut, bulk, fcc111
from ase.cell import Cell
from ase.geometry import get_layers, wrap_positions
from ase.spacegroup import crystal, get_spacegroup
al = crystal('Al', [(0, 0, 0)], spacegroup=225, cellpar=4.05)
# Cut out slab of 5 Al(001) layers
al001 = cut(al, nlayers=5)
correct_pos = np.array([[0., 0., 0.],
[0., 0.5, 0.2],
[0.5, 0., 0.2],
[0.5, 0.5, 0.],
[0., 0., 0.4],
[0., 0.5, 0.6],
[0.5, 0., 0.6],
[0.5, 0.5, 0.4],
[0., 0., 0.8],
[0.5, 0.5, 0.8]])
assert np.allclose(correct_pos, al001.get_scaled_positions())
# Check layers along 001
tags, levels = get_layers(al001, (0, 0, 1))
assert np.allclose(tags, [0, 1, 1, 0, 2, 3, 3, 2, 4, 4])
assert np.allclose(levels, [0., 2.025, 4.05, 6.075, 8.1])
# Check layers along 101
tags, levels = get_layers(al001, (1, 0, 1))
assert np.allclose(tags, [0, 1, 5, 3, 2, 4, 8, 7, 6, 9])
assert np.allclose(levels, [0.000, 0.752, 1.504, 1.880, 2.256, 2.632, 3.008,
3.384, 4.136, 4.888],
atol=0.001)
# Check layers along 111
tags, levels = get_layers(al001, (1, 1, 1))
assert np.allclose(tags, [0, 2, 2, 4, 1, 5, 5, 6, 3, 7])
assert np.allclose(levels, [0.000, 1.102, 1.929, 2.205, 2.756, 3.031, 3.858,
4.960],
atol=0.001)
# Cut out slab of three Al(111) layers
al111 = cut(al, (1, -1, 0), (0, 1, -1), nlayers=3)
correct_pos = np.array([[0.5, 0., 0.],
[0., 0.5, 0.],
[0.5, 0.5, 0.],
[0., 0., 0.],
[1 / 6., 1 / 3., 1 / 3.],
[1 / 6., 5 / 6., 1 / 3.],
[2 / 3., 5 / 6., 1 / 3.],
[2 / 3., 1 / 3., 1 / 3.],
[1 / 3., 1 / 6., 2 / 3.],
[5 / 6., 1 / 6., 2 / 3.],
[5 / 6., 2 / 3., 2 / 3.],
[1 / 3., 2 / 3., 2 / 3.]])
assert np.allclose(correct_pos, al111.get_scaled_positions())
# Cut out cell including all corner and edge atoms (non-periodic structure)
al = cut(al, extend=1.1)
correct_pos = np.array([[0., 0., 0.],
[0., 2.025, 2.025],
[2.025, 0., 2.025],
[2.025, 2.025, 0.],
[0., 0., 4.05],
[2.025, 2.025, 4.05],
[0., 4.05, 0.],
[2.025, 4.05, 2.025],
[0., 4.05, 4.05],
[4.05, 0., 0.],
[4.05, 2.025, 2.025],
[4.05, 0., 4.05],
[4.05, 4.05, 0.],
[4.05, 4.05, 4.05]])
assert np.allclose(correct_pos, al.positions)
# Create an Ag(111)/Si(111) interface
ag = crystal(['Ag'], basis=[(0, 0, 0)], spacegroup=225, cellpar=4.09)
si = crystal(['Si'], basis=[(0, 0, 0)], spacegroup=227, cellpar=5.43)
try:
assert get_spacegroup(ag).no == 225
assert get_spacegroup(si).no == 227
except ImportError:
pass
ag111 = cut(ag, a=(4, -4, 0), b=(4, 4, -8), nlayers=5) # noqa
si111 = cut(si, a=(3, -3, 0), b=(3, 3, -6), nlayers=5) # noqa
#
# interface = stack(ag111, si111)
# assert len(interface) == 1000
# assert np.allclose(interface.positions[::100],
# [[ 4.08125 , -2.040625 , -2.040625 ],
# [ 8.1625 , 6.121875 , -14.284375 ],
# [ 10.211875 , 0.00875 , 2.049375 ],
# [ 24.49041667, -4.07833333, -16.32208333],
# [ 18.37145833, 14.29020833, -24.48166667],
# [ 24.49916667, 12.25541667, -20.39458333],
# [ 18.36854167, 16.32791667, -30.60645833],
# [ 19.0575 , 0.01166667, 5.45333333],
# [ 23.13388889, 6.80888889, 1.36722222],
# [ 35.3825 , 5.45333333, -16.31333333]])
#
# Test the wrap_positions function.
positions = np.array([
[4.0725, -4.0725, -1.3575],
[1.3575, -1.3575, -1.3575],
[2.715, -2.715, 0.],
[4.0725, 1.3575, -1.3575],
[0., 0., 0.],
[2.715, 2.715, 0.],
[6.7875, -1.3575, -1.3575],
[5.43, 0., 0.]])
cell = np.array([[5.43, 5.43, 0.0], [5.43, -5.43, 0.0], [0.00, 0.00, 40.0]])
positions += np.array([6.1, -0.1, 10.1])
result_positions = wrap_positions(positions=positions, cell=cell)
correct_pos = np.array([
[4.7425, 1.2575, 8.7425],
[7.4575, -1.4575, 8.7425],
[3.385, 2.615, 10.1],
[4.7425, -4.1725, 8.7425],
[6.1, -0.1, 10.1],
[3.385, -2.815, 10.1],
[2.0275, -1.4575, 8.7425],
[0.67, -0.1, 10.1]])
assert np.allclose(correct_pos, result_positions)
positions = wrap_positions(positions, cell, pbc=[False, True, False])
correct_pos = np.array([
[4.7425, 1.2575, 8.7425],
[7.4575, -1.4575, 8.7425],
[3.385, 2.615, 10.1],
[10.1725, 1.2575, 8.7425],
[6.1, -0.1, 10.1],
[8.815, 2.615, 10.1],
[7.4575, 3.9725, 8.7425],
[6.1, 5.33, 10.1]])
assert np.allclose(correct_pos, positions)
# Test center away from values 0, 0.5
result_positions = wrap_positions(positions, cell,
pbc=[True, True, False],
center=0.2)
correct_pos = [[4.7425, 1.2575, 8.7425],
[2.0275, 3.9725, 8.7425],
[3.385, 2.615, 10.1],
[-0.6875, 1.2575, 8.7425],
[6.1, -0.1, 10.1],
[3.385, -2.815, 10.1],
[2.0275, -1.4575, 8.7425],
[0.67, -0.1, 10.1]]
assert np.allclose(correct_pos, result_positions)
# Test pretty_translation keyword
positions = np.array([
[0, 0, 0],
[0, 1, 1],
[1, 0, 1],
[1, 1, 0.]])
cell = np.diag([2, 2, 2])
result = wrap_positions(positions, cell, pbc=[True, True, True],
pretty_translation=True)
assert np.max(result) < 1 + 1E-10
assert np.min(result) > -1E-10
result = wrap_positions(positions - 5, cell, pbc=[True, True, True],
pretty_translation=True)
assert np.max(result) < 1 + 1E-10
result = wrap_positions(positions - 5, cell, pbc=[False, True, True],
pretty_translation=True)
assert np.max(result[:, 0]) < -3
assert np.max(result[:, 1:]) < 1 + 1E-10
# Get the correct crystal structure from a range of different cells
def checkcell(cell, name):
cell = Cell.ascell(cell)
lat = cell.get_bravais_lattice()
assert lat.name == name, (lat.name, name)
checkcell(bulk('Al').cell, 'FCC')
checkcell(bulk('Fe').cell, 'BCC')
checkcell(bulk('Zn').cell, 'HEX')
checkcell(fcc111('Au', size=(1, 1, 3), periodic=True).cell, 'HEX')
checkcell([[1, 0, 0], [0, 1, 0], [0, 0, 1]], 'CUB')
checkcell([[1, 0, 0], [0, 1, 0], [0, 0, 2]], 'TET')
checkcell([[1, 0, 0], [0, 2, 0], [0, 0, 3]], 'ORC')
checkcell([[1, 0, 0], [0, 2, 0], [0.5, 0, 3]], 'ORCC')
checkcell([[1, 0, 0], [0, 2, 0], [0.501, 0, 3]], 'MCL')
checkcell([[1, 0, 0], [0.5, 3**0.5 / 2, 0], [0, 0, 3]], 'HEX')
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