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# fmt: off
"""
This is testing NEB in general, though at the moment focusing on the shared
calculator implementation that is replacing
the SingleCalculatorNEB class.
Intending to be a *true* unittest, by testing small things
"""
from pytest import mark, raises, warns
from ase import Atoms
from ase.calculators.emt import EMT
from ase.calculators.singlepoint import SinglePointCalculator
from ase.mep import neb
pytestmark = mark.optimize
def test_get_neb_method():
neb_dummy = neb.NEB([])
assert isinstance(neb.get_neb_method(neb_dummy, "eb"), neb.FullSpringMethod)
assert isinstance(neb.get_neb_method(neb_dummy, "aseneb"), neb.ASENEBMethod)
assert isinstance(neb.get_neb_method(neb_dummy, "improvedtangent"),
neb.ImprovedTangentMethod)
assert isinstance(neb.get_neb_method(neb_dummy, "spline"),
neb.SplineMethod)
assert isinstance(neb.get_neb_method(neb_dummy, "string"),
neb.StringMethod)
with raises(ValueError, match=r".*some_random_string.*"):
_ = neb.get_neb_method(neb_dummy, "some_random_string")
class TestNEB:
@classmethod
def setup_class(cls):
cls.h_atom = Atoms("H", positions=[[0., 0., 0.]], cell=[10., 10., 10.])
cls.h2_molecule = Atoms("H2", positions=[[0., 0., 0.], [0., 1., 0.]])
cls.images_dummy = [cls.h_atom.copy(), cls.h_atom.copy(),
cls.h_atom.copy()]
def test_deprecations(self, testdir):
# future warning on deprecated class
with warns(FutureWarning, match=r".*Please use.*"):
deprecated_neb = neb.SingleCalculatorNEB(self.images_dummy)
assert deprecated_neb.allow_shared_calculator
neb_dummy = neb.NEB(self.images_dummy)
with warns(FutureWarning, match=r".*Please use.*idpp_interpolate.*"):
neb_dummy.idpp_interpolate(steps=1)
def test_neb_default(self):
# default should be allow_shared_calculator=False
neb_dummy = neb.NEB(self.images_dummy)
assert not neb_dummy.allow_shared_calculator
def test_raising_parallel_errors(self):
# error is calculators are shared in parallel run
with raises(RuntimeError, match=r".*Cannot use shared calculators.*"):
_ = neb.NEB(self.images_dummy, allow_shared_calculator=True,
parallel=True)
def test_no_shared_calc(self):
images_shared_calc = [self.h_atom.copy(), self.h_atom.copy(),
self.h_atom.copy()]
shared_calc = EMT()
for at in images_shared_calc:
at.calc = shared_calc
neb_not_allow = neb.NEB(images_shared_calc,
allow_shared_calculator=False)
# error if calculators are shared but not allowed to be
with raises(ValueError, match=r".*NEB images share the same.*"):
neb_not_allow.get_forces()
# raise if calc cannot be shared
with raises(RuntimeError, match=r".*Cannot set shared calculator.*"):
neb_not_allow.set_calculators(EMT())
# same calculators
new_calculators = [EMT() for _ in range(neb_not_allow.nimages)]
neb_not_allow.set_calculators(new_calculators)
for i in range(neb_not_allow.nimages):
assert new_calculators[i] == neb_not_allow.images[i].calc
# just for the intermediate images
neb_not_allow.set_calculators(new_calculators[1:-1])
for i in range(1, neb_not_allow.nimages - 1):
assert new_calculators[i] == neb_not_allow.images[i].calc
# nimages-1 calculator is not allowed
with raises(RuntimeError, match=r".*does not fit to len.*"):
neb_not_allow.set_calculators(new_calculators[:-1])
def test_init_checks(self):
mismatch_len = [self.h_atom.copy(), self.h2_molecule.copy()]
with raises(ValueError, match=r".*different numbers of atoms.*"):
_ = neb.NEB(mismatch_len)
mismatch_pbc = [self.h_atom.copy(), self.h_atom.copy()]
mismatch_pbc[-1].set_pbc(True)
with raises(ValueError, match=r".*different boundary conditions.*"):
_ = neb.NEB(mismatch_pbc)
mismatch_numbers = [
self.h_atom.copy(),
Atoms("C", positions=[[0., 0., 0.]], cell=[10., 10., 10.])]
with raises(ValueError, match=r".*atoms in different orders.*"):
_ = neb.NEB(mismatch_numbers)
h_atom = self.h_atom.copy()
h_atom.set_pbc(True)
mismatch_cell = [h_atom.copy(), h_atom.copy()]
mismatch_cell[-1].set_cell(mismatch_cell[-1].get_cell() + 0.00001)
with raises(NotImplementedError, match=r".*Variable cell.*"):
_ = neb.NEB(mismatch_cell)
def test_freeze_method(self):
at = self.h_atom.copy()
at.calc = EMT()
at.get_forces()
results = dict(**at.calc.results)
neb.NEB.freeze_results_on_image(at, **results)
assert isinstance(at.calc, SinglePointCalculator)
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