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
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
|
# fmt: off
import numpy as np
import pytest
from ase.atoms import Atoms
from ase.build import bulk
from ase.calculators.calculator import all_changes
from ase.calculators.lj import LennardJones
from ase.constraints import FixSymmetry
from ase.filters import FrechetCellFilter, UnitCellFilter
from ase.md.verlet import VelocityVerlet
from ase.optimize.precon.lbfgs import PreconLBFGS
from ase.spacegroup.symmetrize import check_symmetry, is_subgroup
spglib = pytest.importorskip('spglib')
pytestmark = pytest.mark.optimize
class NoisyLennardJones(LennardJones):
def __init__(self, *args, rng=None, **kwargs):
self.rng = rng
LennardJones.__init__(self, *args, **kwargs)
def calculate(self, atoms=None, properties=['energy'],
system_changes=all_changes):
LennardJones.calculate(self, atoms, properties, system_changes)
if 'forces' in self.results:
self.results['forces'] += 1e-4 * self.rng.normal(
size=self.results['forces'].shape, )
if 'stress' in self.results:
self.results['stress'] += 1e-4 * self.rng.normal(
size=self.results['stress'].shape, )
def setup_cell():
# setup an bcc Al cell
at_init = bulk('Al', 'bcc', a=2 / np.sqrt(3), cubic=True)
F = np.eye(3)
for k in range(3):
L = list(range(3))
L.remove(k)
(i, j) = L
R = np.eye(3)
theta = 0.1 * (k + 1)
R[i, i] = np.cos(theta)
R[j, j] = np.cos(theta)
R[i, j] = np.sin(theta)
R[j, i] = -np.sin(theta)
F = np.dot(F, R)
at_rot = at_init.copy()
at_rot.set_cell(at_rot.cell @ F, True)
return at_init, at_rot
def symmetrized_optimisation(at_init, filter):
rng = np.random.RandomState(1)
at = at_init.copy()
at.calc = NoisyLennardJones(rng=rng)
at_cell = filter(at)
print("Initial Energy", at.get_potential_energy(), at.get_volume())
with PreconLBFGS(at_cell, precon=None) as dyn:
dyn.run(steps=300, fmax=0.001)
print("n_steps", dyn.get_number_of_steps())
print("Final Energy", at.get_potential_energy(), at.get_volume())
print("Final forces\n", at.get_forces())
print("Final stress\n", at.get_stress())
print("initial symmetry at 1e-6")
di = check_symmetry(at_init, 1.0e-6, verbose=True)
print("final symmetry at 1e-6")
df = check_symmetry(at, 1.0e-6, verbose=True)
return di, df
def test_as_dict():
atoms = bulk("Cu")
atoms.set_constraint(FixSymmetry(atoms))
assert atoms.constraints[0].todict() == {
'name': 'FixSymmetry',
'kwargs': {
'atoms': bulk('Cu'),
'symprec': 0.01,
'adjust_positions': True,
'adjust_cell': True,
'verbose': False,
},
}
def test_fail_md():
atoms = bulk("Cu")
atoms.set_constraint(FixSymmetry(atoms))
atoms.calc = LennardJones()
# This will not fail if the user has no logfile specified
# a little bit weird...
with pytest.raises(NotImplementedError):
dyn = VelocityVerlet(atoms, timestep=1.0, logfile="-")
dyn.run(5)
@pytest.fixture(params=[UnitCellFilter, FrechetCellFilter])
def filter(request):
return request.param
@pytest.mark.filterwarnings('ignore:ASE Atoms-like input is deprecated')
@pytest.mark.filterwarnings('ignore:Armijo linesearch failed')
def test_no_symmetrization(filter):
at_init, _at_rot = setup_cell()
at_unsym = at_init.copy()
di, df = symmetrized_optimisation(at_unsym, filter)
assert di.number == 229 and not is_subgroup(sub_data=di, sup_data=df)
@pytest.mark.filterwarnings('ignore:ASE Atoms-like input is deprecated')
@pytest.mark.filterwarnings('ignore:Armijo linesearch failed')
def test_no_sym_rotated(filter):
_at_init, at_rot = setup_cell()
at_unsym_rot = at_rot.copy()
di, df = symmetrized_optimisation(at_unsym_rot, filter)
assert di.number == 229 and not is_subgroup(sub_data=di, sup_data=df)
@pytest.mark.filterwarnings('ignore:ASE Atoms-like input is deprecated')
@pytest.mark.filterwarnings('ignore:Armijo linesearch failed')
def test_sym_adj_cell(filter):
at_init, _at_rot = setup_cell()
at_sym_3 = at_init.copy()
at_sym_3.set_constraint(
FixSymmetry(at_sym_3, adjust_positions=True, adjust_cell=True))
di, df = symmetrized_optimisation(at_sym_3, filter)
assert di.number == 229 and is_subgroup(sub_data=di, sup_data=df)
@pytest.mark.filterwarnings('ignore:ASE Atoms-like input is deprecated')
@pytest.mark.filterwarnings('ignore:Armijo linesearch failed')
def test_sym_rot_adj_cell(filter):
at_init, _at_rot = setup_cell()
at_sym_3_rot = at_init.copy()
at_sym_3_rot.set_constraint(
FixSymmetry(at_sym_3_rot, adjust_positions=True, adjust_cell=True))
di, df = symmetrized_optimisation(at_sym_3_rot, filter)
assert di.number == 229 and is_subgroup(sub_data=di, sup_data=df)
@pytest.mark.filterwarnings('ignore:ASE Atoms-like input is deprecated')
def test_fix_symmetry_shuffle_indices():
atoms = Atoms(
'AlFeAl6', cell=[6] * 3,
positions=[[0, 0, 0], [2.9, 2.9, 2.9], [0, 0, 3], [0, 3, 0],
[0, 3, 3], [3, 0, 0], [3, 0, 3], [3, 3, 0]], pbc=True)
atoms.set_constraint(FixSymmetry(atoms))
at_permut = atoms[[0, 2, 3, 4, 5, 6, 7, 1]]
pos0 = atoms.get_positions()
def perturb(atoms, pos0, at_i, dpos):
positions = pos0.copy()
positions[at_i] += dpos
atoms.set_positions(positions)
new_p = atoms.get_positions()
return pos0[at_i] - new_p[at_i]
dp1 = perturb(atoms, pos0, 1, (0.0, 0.1, -0.1))
dp2 = perturb(atoms, pos0, 2, (0.0, 0.1, -0.1))
pos0 = at_permut.get_positions()
permut_dp1 = perturb(at_permut, pos0, 7, (0.0, 0.1, -0.1))
permut_dp2 = perturb(at_permut, pos0, 1, (0.0, 0.1, -0.1))
assert np.max(np.abs(dp1 - permut_dp1)) < 1.0e-10
assert np.max(np.abs(dp2 - permut_dp2)) < 1.0e-10
|
