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# fmt: off
import numpy as np
import pytest
from ase.build import bulk, molecule
from ase.calculators.emt import EMT
from ase.filters import (
ExpCellFilter,
Filter,
FrechetCellFilter,
StrainFilter,
UnitCellFilter,
)
from ase.optimize import QuasiNewton
from ase.stress import full_3x3_to_voigt_6_strain, voigt_6_to_full_3x3_strain
@pytest.mark.optimize()
def test_filter(testdir):
"""Test that the filter and trajectories are playing well together."""
atoms = molecule('CO2')
atoms.calc = EMT()
filter = Filter(atoms, indices=[1, 2])
with QuasiNewton(filter, trajectory='filter-test.traj',
logfile='filter-test.log') as opt:
opt.run()
# No assertions=??
@pytest.mark.optimize()
@pytest.mark.filterwarnings("ignore:Use FrechetCellFilter")
@pytest.mark.parametrize(
'filterclass', [StrainFilter,
UnitCellFilter,
FrechetCellFilter,
ExpCellFilter])
@pytest.mark.parametrize(
'mask', [[1, 1, 0, 0, 0, 1],
[1, 0, 0, 0, 0, 0],
[1, 0, 1, 1, 0, 0],
[0, 1, 0, 0, 1, 1]]
)
def test_apply_strain_to_mask(filterclass, mask):
cu = bulk('Cu', a=3.14) * (6, 3, 1)
orig_cell = cu.cell.copy()
rng = np.random.RandomState(69)
# Create extreme deformation
deformation_vv = np.eye(3) + 1e2 * rng.randn(3, 3)
filter = filterclass(cu, mask=mask)
if filterclass is not StrainFilter:
pos_and_deform = \
np.concatenate((cu.get_positions(),
deformation_vv), axis=0)
else:
pos_and_deform = full_3x3_to_voigt_6_strain(deformation_vv)
# Apply the deformation to the filter, which should then apply it
# with a mask.
filter.set_positions(pos_and_deform)
full_mask = voigt_6_to_full_3x3_strain(mask) != 0
# Ensure the mask is respected to a very tight numerical tolerance
assert np.linalg.solve(orig_cell, cu.cell)[~full_mask] == \
pytest.approx(np.eye(3)[~full_mask], abs=1e-12)
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