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# fmt: off
from dataclasses import dataclass
from itertools import product
from pathlib import Path
import numpy as np
import pytest
from ase.io import read
from ase.spacegroup.symmetrize import (
IntermediateDatasetError,
check_symmetry,
get_symmetrized_atoms,
)
spglib = pytest.importorskip('spglib')
@dataclass
class Mineral:
name: str
spacegroup: int
cod_id: str # Crystallographic Open Database entry
@property
def datafile(self):
return Path(f'minerals/cod_{self.cod_id}.cif')
# Named minerals in testdata
named_minerals = [
# Centrosymmetric triclinic
Mineral(name='artroeite', spacegroup=2, cod_id='9001665'),
# Enantiomorphic (chiral) polar monoclinic
Mineral(name='alloclasite', spacegroup=4, cod_id='9004112'),
# Polar orthorhombic
Mineral(name='cobaltite', spacegroup=29, cod_id='9004218'),
# Enantiomorphic (chiral) tetragonal
Mineral(name='cristobalite', spacegroup=92, cod_id='9017338'),
# Enantiomorphic (chiral) trigonal
Mineral(name='heazlewoodite', spacegroup=155, cod_id='9007640'),
# Polar trigonal
Mineral(name='molybdenite 3R', spacegroup=160, cod_id='9007661'),
# Centrosymmetric hexagonal
Mineral(name='breithauptite', spacegroup=194, cod_id='1010930'),
# Cubic
Mineral(name='moissanite 3C', spacegroup=216, cod_id='1010995'),
]
@pytest.mark.parametrize('mineral', list(named_minerals))
def test_mineral_spacegroups(datadir, mineral):
atoms = read(datadir / mineral.datafile)
dataset = check_symmetry(atoms)
assert dataset.number == mineral.spacegroup
@pytest.mark.parametrize('mineral,rngseed', product(
list(named_minerals), [13, 42, 93]))
def test_mineral_symmetrization(datadir, mineral, rngseed):
atoms = read(datadir / mineral.datafile)
assert mineral.spacegroup > 1 # some symmetry
# Break the symmetry
rng = np.random.default_rng(rngseed)
cell = atoms.get_cell()
atoms.set_cell(cell.array + rng.normal(scale=0.01, size=(3, 3)))
atoms.rattle(0.01, rng=rng)
rattled_dataset = check_symmetry(atoms)
assert rattled_dataset.number == 1
# Find a symmetry precision that recovers the original symmetry
symprec = 1e-5
_symatoms, dataset = get_symmetrized_atoms(atoms, symprec=symprec)
while dataset.number != mineral.spacegroup:
if symprec > 0.5:
raise ValueError('Could not recover original symmetry of the'
f'mineral {mineral.name}')
symprec *= 1.2
try:
_symatoms, dataset = get_symmetrized_atoms(
atoms, symprec=symprec, final_symprec=1e-5)
except IntermediateDatasetError:
continue
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