def setup(self):
cv = paths.CoordinateFunctionCV('x', lambda x: x.xyz[0][0])
vol_A = paths.CVDefinedVolume(cv, float("-inf"), 0.0)
vol_B = paths.CVDefinedVolume(cv, 1.0, float("inf"))
ensembles = [
paths.LengthEnsemble(1).named("len1"),
paths.LengthEnsemble(3).named("len3"),
paths.SequentialEnsemble([
paths.LengthEnsemble(1) & paths.AllInXEnsemble(vol_A),
paths.AllOutXEnsemble(vol_A | vol_B),
paths.LengthEnsemble(1) & paths.AllInXEnsemble(vol_A)
]).named('return'),
paths.SequentialEnsemble([
paths.LengthEnsemble(1) & paths.AllInXEnsemble(vol_A),
paths.AllOutXEnsemble(vol_A | vol_B),
paths.LengthEnsemble(1) & paths.AllInXEnsemble(vol_B)
]).named('transition'),
]
self.ensembles = {ens.name: ens for ens in ensembles}
self.traj_vals = [-0.1, 1.1, 0.5, -0.2, 0.1, -0.3, 0.4, 1.4, -1.0]
self.trajectory = make_1d_traj(self.traj_vals)
self.engine = CalvinistDynamics(self.traj_vals)
self.satisfied_when_traj_len = {
"len1": 1,
"len3": 3,
"return": 6,
"transition": 8,
}
self.conditions = EnsembleSatisfiedContinueConditions(ensembles)
def setup(self):
self.mytraj = make_1d_traj(coordinates=[-0.5, 0.1, 0.2, 0.3, 0.5],
velocities=[1.0, 1.0, 1.0, 1.0, 1.0])
self.dyn = CalvinistDynamics(
[-0.5, -0.4, -0.3, -0.2, -0.1, 0.1, 0.2, 0.3, 0.4, 0.5])
self.dyn.initialized = True
self.ens = LengthEnsemble(5)
self.gs = SampleSet(
Sample(replica=0, trajectory=self.mytraj, ensemble=self.ens))
class TestEnsembleSatisfiedContinueConditions(object):
def setup(self):
cv = paths.CoordinateFunctionCV('x', lambda x: x.xyz[0][0])
vol_A = paths.CVDefinedVolume(cv, float("-inf"), 0.0)
vol_B = paths.CVDefinedVolume(cv, 1.0, float("inf"))
ensembles = [
paths.LengthEnsemble(1).named("len1"),
paths.LengthEnsemble(3).named("len3"),
paths.SequentialEnsemble([
paths.LengthEnsemble(1) & paths.AllInXEnsemble(vol_A),
paths.AllOutXEnsemble(vol_A | vol_B),
paths.LengthEnsemble(1) & paths.AllInXEnsemble(vol_A)
]).named('return'),
paths.SequentialEnsemble([
paths.LengthEnsemble(1) & paths.AllInXEnsemble(vol_A),
paths.AllOutXEnsemble(vol_A | vol_B),
paths.LengthEnsemble(1) & paths.AllInXEnsemble(vol_B)
]).named('transition'),
]
self.ensembles = {ens.name: ens for ens in ensembles}
self.traj_vals = [-0.1, 1.1, 0.5, -0.2, 0.1, -0.3, 0.4, 1.4, -1.0]
self.trajectory = make_1d_traj(self.traj_vals)
self.engine = CalvinistDynamics(self.traj_vals)
self.satisfied_when_traj_len = {
"len1": 1,
"len3": 3,
"return": 6,
"transition": 8,
}
self.conditions = EnsembleSatisfiedContinueConditions(ensembles)
@pytest.mark.parametrize('trusted', [True, False])
@pytest.mark.parametrize(
'traj_len,expected',
[
# expected = (num_calls, num_satisfied)
(0, (1, 0)),
(1, (2, 1)),
(2, (3, 1)),
(3, (3, 2)),
(5, (2, 2)),
(6, (3, 3)),
(7, (1, 3)),
(8, (3, 4)),
])
def test_call(self, traj_len, expected, trusted):
if trusted:
already_satisfied = [
self.ensembles[key]
for key, val in self.satisfied_when_traj_len.items()
if traj_len > val
]
for ens in already_satisfied:
self.conditions.satisfied[ens] = True
traj = self.trajectory[:traj_len]
mock = Mock(wraps=self.conditions._check_previous_frame)
self.conditions._check_previous_frame = mock
expected_calls, expected_satisfied = expected
result = self.conditions(traj, trusted)
assert result == (expected_satisfied != 4)
assert sum(self.conditions.satisfied.values()) == expected_satisfied
if trusted:
# only test call count if we're trusted
assert mock.call_count == expected_calls
def test_long_traj_untrusted(self):
traj = make_1d_traj(self.traj_vals + [1.0, 1.2, 1.3, 1.4])
assert self.conditions(traj) is False
def test_generate(self):
init_snap = self.trajectory[0]
traj = self.engine.generate(init_snap, self.conditions)
assert len(traj) == 8