/usr/share/pyshared/ase/test/geometry.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 | "Test the ase.utils.geometry module"
import numpy as np
from ase.lattice.spacegroup import crystal
from ase.utils.geometry import get_layers, cut, stack
np.set_printoptions(suppress=True)
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)
ag111 = cut(ag, a=(4, -4, 0), b=(4, 4, -8), nlayers=5)
si111 = cut(si, a=(3, -3, 0), b=(3, 3, -6), nlayers=5)
#
#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]])
#
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