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import pytest
from ase import Atom, Atoms
from ase.io import Trajectory, read
from ase.constraints import FixBondLength
from ase.calculators.calculator import PropertyNotImplementedError
@pytest.fixture
def co():
return Atoms([Atom('C', (0, 0, 0)),
Atom('O', (0, 0, 1.2))])
@pytest.fixture
def trajfile_and_images(co):
fname = '1.traj'
co = co.copy()
with Trajectory(fname, 'w', co) as traj:
written = []
for i in range(5):
co.positions[:, 2] += 0.1
traj.write()
written.append(co.copy())
with Trajectory('1.traj', 'a') as traj:
co = read('1.traj')
print(co.positions)
co.positions[:] += 1
traj.write(co)
written.append(co.copy())
with Trajectory('1.traj') as traj:
for a in traj:
print(1, a.positions[-1, 2])
co.positions[:] += 1
with Trajectory('1.traj', 'a') as traj:
traj.write(co)
written.append(co.copy())
assert len(traj) == 7
co[0].number = 1
traj.write(co)
written.append(co.copy())
co[0].number = 6
co.pbc = True
traj.write(co)
written.append(co.copy())
co.pbc = False
o = co.pop(1)
traj.write(co)
written.append(co.copy())
co.append(o)
traj.write(co)
written.append(co.copy())
return fname, written
@pytest.fixture
def trajfile(trajfile_and_images):
return trajfile_and_images[0]
@pytest.fixture
def images(trajfile_and_images):
return trajfile_and_images[1]
def test_trajectory(trajfile, images):
imgs = read(trajfile, index=':')
assert len(imgs) == len(images)
for img1, img2 in zip(imgs, images):
assert img1 == img2
# Verify slicing works.
with Trajectory(trajfile, 'r') as read_traj:
sliced_traj = read_traj[3:8]
assert len(sliced_traj) == 5
sliced_again = sliced_traj[1:-1]
assert len(sliced_again) == 3
assert sliced_traj[1] == sliced_again[0]
def test_append_nonexistent_file(co):
fname = '2.traj'
with Trajectory(fname, 'a', co) as t:
pass
with Trajectory('empty.traj', 'w') as t:
pass
with Trajectory('empty.traj', 'r') as t:
assert len(t) == 0
def test_only_energy():
with Trajectory('fake.traj', 'w') as t:
t.write(Atoms('H'), energy=-42.0, forces=[[1, 2, 3]])
a = read('fake.traj')
with Trajectory('only-energy.traj', 'w', properties=['energy']) as t:
t.write(a)
b = read('only-energy.traj')
e = b.get_potential_energy()
assert e + 42 == 0
with pytest.raises(PropertyNotImplementedError):
b.get_forces()
def test_constraint_and_momenta():
a = Atoms('H2',
positions=[(0, 0, 0), (0, 0, 1)],
momenta=[(1, 0, 0), (0, 0, 0)])
a.constraints = [FixBondLength(0, 1)]
with Trajectory('constraint.traj', 'w', a) as t:
t.write()
b = read('constraint.traj')
assert not (b.get_momenta() - a.get_momenta()).any()
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