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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.spacegroup.symmetrize import FixSymmetry, check_symmetry, is_subgroup
from ase.optimize.precon.lbfgs import PreconLBFGS
from ase.constraints import UnitCellFilter, ExpCellFilter
spglib = pytest.importorskip('spglib')
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)
dyn = PreconLBFGS(at_cell, precon=None)
print("Initial Energy", at.get_potential_energy(), at.get_volume())
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
@pytest.fixture(params=[UnitCellFilter, ExpCellFilter])
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):
print("NO SYM")
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):
print("NO SYM ROT")
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):
print("SYM POS+CELL")
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):
print("SYM POS+CELL ROT")
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
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