def setup(self):
pes = paths.engines.toy.Gaussian(1, [1.0, 1.0], [0.0, 0.0])
integ = paths.engines.toy.LangevinBAOABIntegrator(0.01, 0.1, 2.5)
topology = paths.engines.toy.Topology(n_spatial=2,
n_atoms=1,
masses=[1.0],
pes=pes)
self.engine = paths.engines.toy.Engine(
options={
'n_frames_max': 1000,
'n_steps_per_frame': 10,
'integ': integ
},
topology=topology).named("engine")
self.other_engine = paths.engines.toy.Engine(options={
'n_frames_max': 5000,
'n_steps_per_frame': 1,
'integ': integ
},
topology=topology)
self.cv = paths.FunctionCV("x", lambda x: x.xyz[0][0])
self.state_A = paths.CVDefinedVolume(self.cv, float("-inf"),
0).named("A")
self.state_B = paths.CVDefinedVolume(self.cv, 10,
float("inf")).named("B")
self.network = paths.TPSNetwork(self.state_A,
self.state_B).named('network')
self.scheme = paths.OneWayShootingMoveScheme(
self.network, paths.UniformSelector(), self.engine).named("scheme")
self.other_scheme = paths.OneWayShootingMoveScheme(
self.network, paths.UniformSelector(), self.other_engine)
self.tempdir = tempfile.mkdtemp()
def make_mistis_network():
cvX = paths.FunctionCV(name="cvX", f=xval)
cvY = paths.FunctionCV(name="cvY", f=yval)
cvXprime = paths.FunctionCV(name="cvXprime", f=xprime)
x_under_min = paths.CVDefinedVolume(cvX, float("-inf"), -0.35)
x_over_max = paths.CVDefinedVolume(cvX, 0.35, float("inf"))
y_under_min = paths.CVDefinedVolume(cvY, float("-inf"), -0.35)
y_over_max = paths.CVDefinedVolume(cvY, 0.35, float("inf"))
stateA = (x_under_min & y_under_min).named("A")
stateB = (x_over_max & y_under_min).named("B")
stateC = (x_under_min & y_over_max).named("C")
interfacesAB = paths.VolumeInterfaceSet(
cvX, float("-inf"), [-0.35, -0.3, -0.27, -0.24, -0.2, -0.1]
)
interfacesAC = paths.VolumeInterfaceSet(
cvY, float("-inf"), [-0.35, -0.3, -0.27, -0.24, -0.2, -0.1, 0.0]
)
interfacesBA = paths.VolumeInterfaceSet(
cvXprime, float("-inf"), [-0.35, -0.3, -0.27, -0.24, -0.2, -0.1]
)
ms_outer = paths.MSOuterTISInterface.from_lambdas(
{iface: 0.0 for iface in [interfacesAB, interfacesBA]}
)
network = paths.MISTISNetwork(
[(stateA, interfacesAB, stateB),
(stateA, interfacesAC, stateC),
(stateB, interfacesBA, stateA)],
ms_outers=ms_outer,
strict_sampling=True
).named("mistis")
return network
def setup(self):
# set up the trajectory that we'll annotate in the tests
self.traj = make_1d_traj(
[-1, 1, 4, 3, 6, 11, 22, 33, 23, 101, 205, 35, 45])
# set up some states to test later
# this system is designed under the assumption that the "states" are
# defined by how many digits are in the x-coordinate (and I'll
# intentionally fail to identify some of them)
self.cv = paths.CoordinateFunctionCV("x", lambda s: s.xyz[0][0])
self.state_1 = paths.CVDefinedVolume(self.cv, 0, 9)
self.state_2 = paths.CVDefinedVolume(self.cv, 10, 99)
self.state_3 = paths.CVDefinedVolume(self.cv, 100, 999)
# create the annotations
self.annotation_1 = Annotation(state="1-digit", begin=1, end=4)
self.annotation_2 = Annotation(state="2-digit", begin=6, end=8)
self.annotation_3 = Annotation(state="3-digit", begin=10, end=10)
self.annotation_4 = Annotation(state="2-digit", begin=11, end=12)
self.states = {
"1-digit": self.state_1,
"2-digit": self.state_2,
"3-digit": self.state_3
}
self.annotated = AnnotatedTrajectory(self.traj)
self.annotations = [
self.annotation_1, self.annotation_2, self.annotation_3,
self.annotation_4
]
def setup(self):
self.cv = paths.FunctionCV("Id", lambda snap: snap.xyz[0][0])
cv_neg = paths.FunctionCV("Neg", lambda snap: -snap.xyz[0][0])
self.stateA = paths.CVDefinedVolume(self.cv, -1.0, 0.0)
self.stateB = paths.CVDefinedVolume(self.cv, 1.0, 2.0)
self.stateC = paths.CVDefinedVolume(self.cv, 3.0, 4.0)
interfacesAB = paths.VolumeInterfaceSet(
self.cv, -1.0, [0.0, 0.2, 0.4]
)
interfacesBC = paths.VolumeInterfaceSet(
self.cv, 1.0, [2.0, 2.2, 2.4]
)
interfacesBA = paths.VolumeInterfaceSet(
cv_neg, -1.0, [-1.0, -0.8, -0.6]
)
network = paths.MISTISNetwork([
(self.stateA, interfacesAB, self.stateB),
(self.stateB, interfacesBC, self.stateC),
(self.stateB, interfacesBA, self.stateA)
])
self.tisAB = network.input_transitions[(self.stateA, self.stateB)]
self.tisBC = network.input_transitions[(self.stateB, self.stateC)]
self.tisBA = network.input_transitions[(self.stateB, self.stateA)]
self.network = network
self.snapA = make_1d_traj([-0.5])[0]
self.noforbid_noextra_AB = paths.FullBootstrapping(
transition=self.tisAB,
snapshot=self.snapA
)
def setup(self):
paths.InterfaceSet._reset()
self.cv = paths.FunctionCV("x", lambda x: x.xyz[0][0])
self.state_A = paths.CVDefinedVolume(self.cv, float("-inf"), 0.0)
self.state_B = paths.CVDefinedVolume(self.cv, 1.0, float("inf"))
pes = paths.engines.toy.LinearSlope([0, 0, 0], 0)
integ = paths.engines.toy.LangevinBAOABIntegrator(0.01, 0.1, 2.5)
topology = paths.engines.toy.Topology(n_spatial=3,
masses=[1.0],
pes=pes)
self.engine = paths.engines.toy.Engine(options={'integ': integ},
topology=topology)
interfaces = paths.VolumeInterfaceSet(self.cv, float("-inf"),
[0.0, 0.1, 0.2])
network = paths.MISTISNetwork([(self.state_A, interfaces, self.state_B)
])
init_traj = make_1d_traj([-0.1, 0.2, 0.5, 0.8, 1.1])
scheme = paths.MoveScheme(network)
scheme.append([
paths.strategies.OneWayShootingStrategy(
selector=paths.UniformSelector(), engine=self.engine),
paths.strategies.PathReversalStrategy(),
paths.strategies.OrganizeByMoveGroupStrategy()
])
init_cond = scheme.initial_conditions_from_trajectories(init_traj)
self.sim = PathSampling(storage=None,
move_scheme=scheme,
sample_set=init_cond)
def setup(self):
pes = toys.HarmonicOscillator(A=[1.0], omega=[1.0], x0=[0.0])
topology = toys.Topology(n_spatial=1, masses=[1.0], pes=pes)
integrator = toys.LeapfrogVerletIntegrator(0.1)
options = {
'integ': integrator,
'n_frames_max': 100000,
'n_steps_per_frame': 2
}
self.engine = toys.Engine(options=options, topology=topology)
self.snap0 = toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[1.0]]),
engine=self.engine)
cv = paths.FunctionCV("Id", lambda snap : snap.coordinates[0][0])
self.cv = cv
self.center = paths.CVDefinedVolume(cv, -0.2, 0.2)
self.interface = paths.CVDefinedVolume(cv, -0.3, 0.3)
self.outside = paths.CVDefinedVolume(cv, 0.6, 0.9)
self.extra = paths.CVDefinedVolume(cv, -1.5, -0.9)
self.flux_pairs = [(self.center, self.interface)]
self.sim = DirectSimulation(storage=None,
engine=self.engine,
states=[self.center, self.outside],
flux_pairs=self.flux_pairs,
initial_snapshot=self.snap0)
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):
# As a test system, let's use 1D motion on a flat potential. If the
# velocity is positive, you right the state on the right. If it is
# negative, you hit the state on the left.
pes = toys.LinearSlope(m=[0.0], c=[0.0]) # flat line
topology = toys.Topology(n_spatial=1, masses=[1.0], pes=pes)
integrator = toys.LeapfrogVerletIntegrator(0.1)
options = {
'integ': integrator,
'n_frames_max': 100000,
'n_steps_per_frame': 5
}
self.engine = toys.Engine(options=options, topology=topology)
self.snap0 = toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[1.0]]),
engine=self.engine)
cv = paths.FunctionCV("Id", lambda snap : snap.coordinates[0][0])
self.left = paths.CVDefinedVolume(cv, float("-inf"), -1.0)
self.right = paths.CVDefinedVolume(cv, 1.0, float("inf"))
self.state_labels = {"Left" : self.left,
"Right" : self.right,
"None" : ~(self.left | self.right)}
randomizer = paths.NoModification()
self.filename = data_filename("committor_test.nc")
self.storage = paths.Storage(self.filename, mode="w")
self.storage.save(self.snap0)
self.simulation = CommittorSimulation(storage=self.storage,
engine=self.engine,
states=[self.left, self.right],
randomizer=randomizer,
initial_snapshots=self.snap0)
self.simulation.output_stream = open(os.devnull, 'w')
def test_fluxes(self):
left_interface = paths.CVDefinedVolume(self.cv, -0.3, float("inf"))
right_interface = paths.CVDefinedVolume(self.cv, float("-inf"), 0.3)
sim = DirectSimulation(storage=None,
engine=self.engine,
states=[self.center, self.outside],
flux_pairs=[(self.center, left_interface),
(self.center, right_interface)],
initial_snapshot=self.snap0)
fake_flux_events = {
(self.center, right_interface): [(15, 3), (23, 15), (48, 23)],
(self.center, left_interface): [(97, 34), (160, 97)]
}
sim.flux_events = fake_flux_events
n_flux_events = {
(self.center, right_interface): 3,
(self.center, left_interface): 2
}
assert_equal(sim.n_flux_events, n_flux_events)
expected_fluxes = {
(self.center, right_interface):
1.0 / (((15 - 3) + (23 - 15) + (48 - 23)) / 3.0),
(self.center, left_interface):
1.0 / (((97 - 34) + (160 - 97)) / 2.0)
}
for p in expected_fluxes:
assert_almost_equal(sim.fluxes[p], expected_fluxes[p])
def setup(self):
# PES is one-dimensional linear slope (y(x) = x)
pes = toys.LinearSlope(m=[-1.0], c=[0.0])
# one particle with mass 1.0
topology = toys.Topology(n_spatial=1, masses=[1.0], pes=pes)
integrator = toys.LeapfrogVerletIntegrator(0.02)
options = {
'integ': integrator,
'n_frames_max': 1000,
'n_steps_per_frame': 5
}
self.engine = toys.Engine(options=options, topology=topology)
# test uses three snapshots with different velocities
# 0: direction ok, velocity too low => falls back to dividing surface
# 1: wrong direction => backward shot towards B
# 2: direction ok, velocity high enough => successfull new trajectory
self.initial_snapshots = [
toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[1.0]]),
engine=self.engine),
toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[-1.0]]),
engine=self.engine),
toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[2.0]]),
engine=self.engine)
]
# reaction coordinate is just x coordinate
rc = paths.FunctionCV("Id", lambda snap: snap.coordinates[0][0])
# state A: [-inf, -1]
self.state_A = paths.CVDefinedVolume(rc, float("-inf"), -1.0)
# area between A and dividing surface: [-1, 0]
self.towards_A = paths.CVDefinedVolume(rc, -1.0, 0.0)
# state B: [1, inf]
self.state_B = paths.CVDefinedVolume(rc, 1.0, float("inf"))
# define state labels
self.state_labels = {
"A": self.state_A,
"B": self.state_B,
"ToA": self.towards_A,
"None": ~(self.state_A | self.state_B | self.towards_A)
}
# velocities are not randomized
randomizer = paths.NoModification()
self.filename = data_filename("rf_test.nc")
self.storage = paths.Storage(self.filename, mode="w")
self.storage.save(self.initial_snapshots)
self.simulation = ReactiveFluxSimulation(
storage=self.storage,
engine=self.engine,
states=[self.state_A, self.state_B],
randomizer=randomizer,
initial_snapshots=self.initial_snapshots,
rc=rc)
self.simulation.output_stream = open(os.devnull, 'w')
def setup(self):
# set up the trajectories, ensembles, etc. for this test
paths.InterfaceSet._reset()
cv_A = paths.FunctionCV('Id', lambda s: s.xyz[0][0])
cv_B = paths.FunctionCV('1-Id', lambda s: 1.0-s.xyz[0][0])
self.cv_x = cv_A
self.state_A = paths.CVDefinedVolume(cv_A,
float("-inf"), 0.0).named("A")
self.state_B = paths.CVDefinedVolume(cv_B,
float("-inf"), 0.0).named("B")
interfaces_AB = paths.VolumeInterfaceSet(cv_A, float("-inf"),
[0.0, 0.1, 0.2])
interfaces_BA = paths.VolumeInterfaceSet(cv_B, float("-inf"),
[0.0, 0.1, 0.2])
# trajectory that crosses each interface, one state-to-state
self.trajs_AB = [make_tis_traj_fixed_steps(i) for i in [0, 1, 2]]
self.trajs_AB += [make_1d_traj([(-0.5 + i) * 0.1
for i in range(12)])]
self.trajs_BA = [make_tis_traj_fixed_steps(i, reverse=True)
for i in [0, 1, 2]]
self.trajs_BA += [make_1d_traj([1.0 - (-0.5 + i) * 0.1
for i in range(12)])]
# set up mistis
self.mistis = paths.MISTISNetwork([
(self.state_A, interfaces_AB, self.state_B),
(self.state_B, interfaces_BA, self.state_A)
])
mover_stub_mistis = MoverWithSignature(self.mistis.all_ensembles,
self.mistis.all_ensembles)
mistis_ssets = self._make_fake_sampling_sets(self.mistis)
self.mistis_steps = self._make_fake_steps(mistis_ssets,
mover_stub_mistis)
self.mistis_weighted_trajectories = steps_to_weighted_trajectories(
self.mistis_steps,
self.mistis.sampling_ensembles
)
# TODO: set up mstis
self.mstis = paths.MSTISNetwork([
(self.state_A, interfaces_AB),
(self.state_B, interfaces_BA)
])
mover_stub_mstis = MoverWithSignature(self.mstis.all_ensembles,
self.mstis.all_ensembles)
mstis_ssets = self._make_fake_sampling_sets(self.mstis)
self.mstis_steps = self._make_fake_steps(mstis_ssets,
mover_stub_mstis)
self.mstis_weighted_trajectories = steps_to_weighted_trajectories(
self.mstis_steps,
self.mstis.sampling_ensembles
)
def setup(self):
op = paths.FunctionCV("Id", lambda snap: snap.coordinates[0][0])
vol1 = paths.CVDefinedVolume(op, 0.1, 0.5)
vol2 = paths.CVDefinedVolume(op, -0.1, 0.7)
vol3 = paths.CVDefinedVolume(op, 2.0, 2.5)
self.stateA = vol1
self.interstitial = vol2 & ~vol1
self.outInterface = ~vol2 & ~vol3
self.stateB = vol3
def test_flux_from_calvinist_dynamics(self):
# To check for the multiple interface set case, we need to have two
# dimensions. We can hack two "independent" dimensions from a one
# dimensional system by making the second CV non-monotonic with the
# first. For the full trajectory, we need snapshots `S` (in the
# state); `I` (interstitial: outside the state, but not outside
# either interface); `X_a` (outside interface alpha, not outside
# interface beta); `X_b` (outside interface beta, not outside
# interface alpha); and `X_ab` (outside interface alpha and beta).
cv1 = self.cv
cv2 = paths.FunctionCV("abs_sin",
lambda snap : np.abs(np.sin(snap.xyz[0][0])))
state = paths.CVDefinedVolume(cv1, -np.pi/8.0, np.pi/8.0)
other_state = paths.CVDefinedVolume(cv1, -5.0/8.0*np.pi, -3.0/8.0*np.pi)
alpha = paths.CVDefinedVolume(cv1, float("-inf"), 3.0/8.0*np.pi)
beta = paths.CVDefinedVolume(cv2, float("-inf"), np.sqrt(2)/2.0)
# approx alpha: x < 1.17 beta: abs(sin(x)) < 0.70
S = 0 # cv1 = 0.00; cv2 = 0.00
I = np.pi/5.0 # cv1 = 0.63; cv2 = 0.59
X_a = np.pi # cv1 = 3.14; cv2 = 0.00
X_b = -np.pi/3.0 # cv1 = -1.05; cv2 = 0.87
X_ab = np.pi/2.0 # cv1 = 1.57; cv2 = 1.00
other = -np.pi/2.0 # cv1 = -1.57; cv2 = 1.00
# That hack is utterly crazy, but I'm kinda proud of it!
predetermined = [S, S, I, X_a, # (2) first exit
S, X_a, # (4) cross A
S, X_ab, # (6) cross A & B
I, S, X_b, # (9) cross B
S, I, X_b, # (12) cross B
other, I, X_b, # (15) cross to other state
S, X_b, # (17) first cross B
S, X_a, # (19) first cross A
S, S, X_ab, # (22) cross A & B
I, X_ab, # (24) recrossing test
S, I, # (26) false crossing test
S, S]
engine = CalvinistDynamics(predetermined)
init = make_1d_traj([S])
sim = DirectSimulation(storage=None,
engine=engine,
states=[state, other_state],
flux_pairs=[(state, alpha), (state, beta)],
initial_snapshot=init[0])
sim.run(len(predetermined)-1)
# subtract 1 from the indices in `predetermined`, b/c 0 index of the
# traj comes after the found initial step
expected_flux_events = {
(state, alpha): [(4, 2), (6, 4), (22, 19)],
(state, beta): [(9, 6), (12, 9), (22, 17)]
}
assert_equal(len(sim.flux_events), 2)
assert_equal(sim.flux_events[(state, alpha)],
expected_flux_events[(state, alpha)])
assert_equal(sim.flux_events[(state, beta)],
expected_flux_events[(state, beta)])
def setup(self):
op = paths.FunctionCV("Id", lambda snap: snap.coordinates[0][0])
self.stateA = paths.CVDefinedVolume(op, 0.1, 0.5)
self.stateB = paths.CVDefinedVolume(op, 2.0, 2.5)
self.transition = paths.FixedLengthTPSTransition(self.stateA,
self.stateB,
length=4)
self.good_traj = self._make_traj("aixb")
self.short_traj = self._make_traj("axb")
self.long_traj = self._make_traj("aixbb")
self.bad_states_traj = self._make_traj("aixx")
def setup(self):
self.cv = paths.FunctionCV("x", lambda x: x.xyz[0][0])
vol_A = paths.CVDefinedVolume(self.cv, 0.0, 1.0).named("A")
vol_B = paths.CVDefinedVolume(self.cv, 2.0, 3.0).named("B")
vol_C = paths.CVDefinedVolume(self.cv, 4.0, 5.0).named("C")
vol_D = paths.CVDefinedVolume(self.cv, 6.0, 7.0).named("D")
self.states = [vol_A, vol_B, vol_C, vol_D]
self.ensemble = VisitAllStatesEnsemble(self.states, progress='silent')
sequence = [-0.5, 0.5, 1.5, 2.5, 3.5, 4.5, 5.5, 6.5, 7.5]
self.state_seq = [[], [vol_A], [], [vol_B], [], [vol_C], [], [vol_D],
[]]
self.traj = make_1d_traj(sequence)
def setup(self):
self.HAS_TQDM = paths.progress.HAS_TQDM
paths.progress.HAS_TQDM = False
paths.InterfaceSet._reset()
cvA = paths.FunctionCV(name="xA", f=lambda s: s.xyz[0][0])
cvB = paths.FunctionCV(name="xB", f=lambda s: -s.xyz[0][0])
state_A = paths.CVDefinedVolume(cvA, float("-inf"), -0.5).named("A")
state_B = paths.CVDefinedVolume(cvB, float("-inf"), -0.5).named("B")
interfaces_A = paths.VolumeInterfaceSet(cvA, float("-inf"),
[-0.5, -0.3])
network = paths.MISTISNetwork([(state_A, interfaces_A, state_B)])
self.scheme = MoveScheme(network)
self.scheme.append(OneWayShootingStrategy())
self.scheme.append(NearestNeighborRepExStrategy())
self.scheme.append(OrganizeByMoveGroupStrategy())
root_mover = self.scheme.move_decision_tree()
path_sim_mover = paths.PathSimulatorMover(root_mover, None)
null_mover = paths.IdentityPathMover(counts_as_trial=False)
ens_0 = network.sampling_ensembles[0]
ens_1 = network.sampling_ensembles[1]
# acc repex ens1-2
# acc fwd ens1
# acc bkwd ens2
# rej bkwd ens1
# rej repex ens1-2
step_info = [(1, True, path_sim_mover, 'repex', [ens_0, ens_1], None),
(2, True, path_sim_mover, 'shooting', [ens_0], 0),
(3, True, path_sim_mover, 'shooting', [ens_1], 1),
(4, False, path_sim_mover, 'shooting', [ens_0], 1),
(5, False, path_sim_mover, 'repex', [ens_0, ens_1], None)]
self.steps = [_make_acceptance_mock_step(*info) for info in step_info]
self.null_mover_6 = _make_null_mover_step(6, path_sim_mover,
null_mover)
self.null_mover_change_key = [(None, str([path_sim_mover, [None]]))]
acceptance_empty = MoveAcceptanceAnalysis(self.scheme)
acceptance = MoveAcceptanceAnalysis(self.scheme)
acceptance.add_steps(self.steps)
acceptance_null = MoveAcceptanceAnalysis(self.scheme)
acceptance_null.add_steps(self.steps + [self.null_mover_6])
self.analysis = {
'empty': acceptance_empty,
'normal': acceptance,
'with_null': acceptance_null
}
def unidirectional_tis_network():
r"""Fixture for unidirectional TIS with the default (RETIS) scheme.
This has states defined as initial state :math:`x < 0` and final state
:math:`x \ge 10`. The interfaces are at :math:`x=0`, :math:`x=3`, and
:math:`x=6`.
"""
paths.InterfaceSet._reset()
state_A = paths.CVDefinedVolume(DEFAULT_CV, float("-inf"), 0)
state_B = paths.CVDefinedVolume(DEFAULT_CV, 10, float("inf"))
interfaces = paths.VolumeInterfaceSet(DEFAULT_CV, float("-inf"), [0, 3, 6])
network = paths.MISTISNetwork([(state_A, interfaces, state_B)])
return network
def setup(self):
op = paths.FunctionCV("Id", lambda snap : snap.coordinates[0][0])
self.vol1 = paths.CVDefinedVolume(op, 0.1, 0.5)
self.vol3 = paths.CVDefinedVolume(op, 2.0, 2.5)
self.trajectory = make_1d_traj(coordinates=[0.2, 0.3, 0.6, 2.1, 2.2,
0.7, 0.4, 0.35, 2.4,
0.33, 0.32, 0.31],
velocities=[0.0]*12)
all_in_1 = paths.AllInXEnsemble(self.vol1)
self.segments = all_in_1.split(self.trajectory)
self.container = paths.TrajectorySegmentContainer(self.segments,
dt=0.5)
def setup(self):
xval = paths.CoordinateFunctionCV(name="xA", f=lambda s: s.xyz[0][0])
self.stateA = paths.CVDefinedVolume(xval, -1.0, -0.5).named("A")
self.stateB = paths.CVDefinedVolume(xval, 0.5, float("inf")).named("B")
self.ifacesA = paths.VolumeInterfaceSet(xval, -1.0,
[-0.5, -0.4, -0.3, -0.2])
self.ifacesB = paths.VolumeInterfaceSet(xval, [0.5, 0.4, 0.3, 0.2],
1.0)
self.tcp_A = paths.numerics.LookupFunction(
ordinate=[-0.5, -0.4, -0.3, -0.2, -0.1],
abscissa=[1.0, 0.5, 0.25, 0.125, 0.0625])
self.tcp_B = paths.numerics.LookupFunction(
ordinate=[0.5, 0.4, 0.3, 0.2, 0.1],
abscissa=[1.0, 0.2, 0.04, 0.008, 0.0016])
def _wc_hg_TPS_network(self, topology):
# separated for readability, not re-usability
d_WC = paths.MDTrajFunctionCV("d_WC", md.compute_distances,
topology, atom_pairs=[[275, 494]])
d_HG = paths.MDTrajFunctionCV("d_HG", md.compute_distances,
topology, atom_pairs=[[275, 488]])
d_bp = paths.MDTrajFunctionCV("d_bp", md.compute_distances,
topology, atom_pairs=[[274, 491]])
state_WC = (paths.CVDefinedVolume(d_WC, 0.0, 0.35) &
paths.CVDefinedVolume(d_bp, 0.0, 0.35)).named("WC")
state_HG = (paths.CVDefinedVolume(d_HG, 0.0, 0.35) &
paths.CVDefinedVolume(d_bp, 0.0, 0.35)).named("HG")
network = paths.TPSNetwork(state_WC, state_HG)
return network
def setup(self):
cvA = paths.FunctionCV(name="xA", f=lambda s: s.xyz[0][0])
cvB = paths.FunctionCV(name="xB", f=lambda s: -s.xyz[0][0])
self.stateA = paths.CVDefinedVolume(cvA, float("-inf"), -0.5)
self.stateB = paths.CVDefinedVolume(cvB, float("-inf"), -0.5)
interfacesA = paths.VolumeInterfaceSet(cvA, float("-inf"),
[-0.5, -0.3, -0.1])
interfacesB = paths.VolumeInterfaceSet(cvB, float("-inf"),
[-0.5, -0.3, -0.1])
self.network = paths.MSTISNetwork(
[(self.stateA, interfacesA), (self.stateB, interfacesB)],
ms_outers=paths.MSOuterTISInterface.from_lambdas({
interfacesA: 0.0,
interfacesB: 0.0
}))
def setup(self):
from .test_helpers import CallIdentity
xval = paths.FunctionCV("xval", lambda snap: snap.xyz[0][0])
self.stateA = paths.CVDefinedVolume(xval, float("-inf"), -0.5)
self.stateB = paths.CVDefinedVolume(xval, -0.1, 0.1)
self.stateC = paths.CVDefinedVolume(xval, 0.5, float("inf"))
self.states = [self.stateA, self.stateB, self.stateC]
self.traj = {}
self.traj['AA'] = make_1d_traj([-0.51, -0.49, -0.49, -0.52])
self.traj['AB'] = make_1d_traj([-0.51, -0.25, -0.25, 0.0])
self.traj['BA'] = make_1d_traj([0.0, -0.15, -0.35, -0.52])
self.traj['BB'] = make_1d_traj([0.0, -0.25, 0.25, 0.02])
self.traj['BC'] = make_1d_traj([0.01, 0.16, 0.25, 0.53])
self.traj['CC'] = make_1d_traj([0.51, 0.35, 0.36, 0.55])
self.traj['CA'] = make_1d_traj([0.52, 0.22, -0.22, -0.52])
def setup(self):
self.HAS_TQDM = paths.progress.HAS_TQDM
paths.progress.HAS_TQDM = False
# taken from the TestCommittorSimulation
import openpathsampling.engines.toy as toys
pes = toys.LinearSlope(m=[0.0], c=[0.0]) # flat line
topology = toys.Topology(n_spatial=1, masses=[1.0], pes=pes)
descriptor = peng.SnapshotDescriptor.construct(
toys.Snapshot,
{
'n_atoms': 1,
'n_spatial': 1
}
)
engine = peng.NoEngine(descriptor)
self.snap0 = toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[1.0]]),
engine=engine)
self.snap1 = toys.Snapshot(coordinates=np.array([[0.1]]),
velocities=np.array([[1.0]]),
engine=engine)
integrator = toys.LeapfrogVerletIntegrator(0.1)
options = {
'integ': integrator,
'n_frames_max': 10000,
'n_steps_per_frame': 5
}
self.engine = toys.Engine(options=options, topology=topology)
self.cv = paths.FunctionCV("Id", lambda snap: snap.coordinates[0][0])
self.left = paths.CVDefinedVolume(self.cv, float("-inf"), -1.0)
self.right = paths.CVDefinedVolume(self.cv, 1.0, float("inf"))
randomizer = paths.NoModification()
self.filename = data_filename("shooting_analysis.nc")
self.storage = paths.Storage(self.filename, mode="w")
self.simulation = paths.CommittorSimulation(
storage=self.storage,
engine=self.engine,
states=[self.left, self.right],
randomizer=randomizer,
initial_snapshots=[self.snap0, self.snap1]
)
self.simulation.output_stream = open(os.devnull, 'w')
self.simulation.run(20)
# set up the analysis object
self.analyzer = ShootingPointAnalysis(self.storage.steps,
[self.left, self.right])
def setup(self):
cv = paths.FunctionCV("Id", lambda snap: snap.xyz[0][0])
self.state_A = paths.CVDefinedVolume(cv, -0.1, 0.1)
self.state_B = ~paths.CVDefinedVolume(cv, -1.0, 1.0)
nml_increasing = paths.CVDefinedVolume(cv, 0.1, 1.0)
nml_decreasing = paths.CVDefinedVolume(cv, -1.0, -0.1)
increasing = paths.AllInXEnsemble(nml_increasing)
decreasing = paths.AllInXEnsemble(nml_decreasing)
self.ensemble = paths.SequentialEnsemble([
paths.LengthEnsemble(1) & paths.AllInXEnsemble(self.state_A),
paths.AllOutXEnsemble(self.state_A | self.state_B),
paths.LengthEnsemble(1) & paths.AllInXEnsemble(self.state_B)
])
self.incr_1 = self._make_active([0.0, 0.5, 1.1])
self.incr_2 = self._make_active([0.05, 0.6, 1.2])
self.decr_1 = self._make_active([0.0, -0.5, -1.1])
self.both_1 = self._make_active([0.0, 0.5, -0.5, 1.1])
self.both_2 = self._make_active([0.0, -0.4, 0.4, -1.1])
self.none_1 = self._make_active([0.0, 1.1])
self.none_2 = self._make_active([0.0, -1.1])
self.channels = {'incr': increasing, 'decr': decreasing}
# used in simplest tests of relabeling
self.toy_results = {
'a': [(0, 5), (8, 10)],
'b': [(3, 9)],
'c': [(7, 9)]
}
self.results_with_none = {
'a': [(0, 2), (6, 9)],
'b': [(5, 7), (9, 10)],
None: [(2, 5)]
}
self.set_a = frozenset(['a'])
self.set_b = frozenset(['b'])
self.set_c = frozenset(['c'])
self.toy_expanded_results = [(0, 5, self.set_a), (3, 9, self.set_b),
(7, 9, self.set_c), (8, 10, self.set_a)]
self.expanded_results_simultaneous_ending = [(0, 5, self.set_a),
(3, 9, self.set_b),
(7, 10, self.set_c),
(8, 10, self.set_a)]
self.expanded_oldest_skips_internal = [(0, 5, self.set_a),
(3, 9, self.set_b),
(7, 8, self.set_c),
(8, 10, self.set_a),
(10, 11, self.set_b)]
def test_load_results(self):
left_interface = paths.CVDefinedVolume(self.cv, -0.3, float("inf"))
right_interface = paths.CVDefinedVolume(self.cv, float("-inf"), 0.3)
fake_transition_count = [
(self.center, 1), (self.outside, 4), (self.center, 7),
(self.extra, 10), (self.center, 12), (self.outside, 14)
]
fake_flux_events = {(self.center, right_interface):
[(15, 3), (23, 15), (48, 23)],
(self.center, left_interface):
[(97, 34), (160, 97)]}
results = {'transition_count': fake_transition_count,
'flux_events': fake_flux_events}
self.sim.load_results(results)
assert_equal(self.sim.transition_count, fake_transition_count)
assert_equal(self.sim.flux_events, fake_flux_events)
def test_make_ensemble_with_forbidden(self):
forbidden = paths.CVDefinedVolume(self.cv_inc, 0.55, 0.65)
transitions = self.network.sampling_transitions
# TODO: switch once network is working
ensemble = self.post_network.make_ensemble(transitions, forbidden)
#ensemble = self.ms_outer.make_ensemble(transitions, forbidden)
test_AA = make_1d_traj([-0.1, 0.2, -0.2])
test_AXA = make_1d_traj([-0.1, 0.7, -0.2])
test_AFA = make_1d_traj([-0.1, 0.6, -0.2])
test_BB = make_1d_traj([1.1, 0.9, 1.2])
test_BXB = make_1d_traj([1.1, 0.5, 1.2])
test_BFB = make_1d_traj([1.1, 0.6, 1.2])
test_AXB = make_1d_traj([-0.1, 0.7, 1.1])
test_AFB = make_1d_traj([-0.1, 0.6, 1.1])
test_BXA = make_1d_traj([1.1, 0.5, -0.1])
test_BFA = make_1d_traj([1.1, 0.6, -0.1])
assert_equal(ensemble(test_AA), False)
assert_equal(ensemble(test_AXA), True)
assert_equal(ensemble(test_BB), False)
assert_equal(ensemble(test_BXB), True)
assert_equal(ensemble(test_BXA), True)
assert_equal(ensemble(test_AXB), True)
assert_equal(ensemble(test_AFA), False)
assert_equal(ensemble(test_BFB), False)
assert_equal(ensemble(test_AFB), False)
assert_equal(ensemble(test_BFA), False)
def setup(self):
# As a test system, let's use 1D motion on a flat potential. If the
# velocity is positive, you right the state on the right. If it is
# negative, you hit the state on the left.
pes = toys.LinearSlope(m=[0.0], c=[0.0]) # flat line
topology = toys.Topology(n_spatial=1, masses=[1.0], pes=pes)
integrator = toys.LeapfrogVerletIntegrator(0.1)
options = {
'integ': integrator,
'n_frames_max': 100000,
'n_steps_per_frame': 5
}
self.engine = toys.Engine(options=options, topology=topology)
self.snap0 = toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[1.0]]),
engine=self.engine)
cv = paths.FunctionCV("Id", lambda snap: snap.coordinates[0][0])
starting_volume = paths.CVDefinedVolume(cv, -0.01, 0.01)
forward_ensemble = paths.LengthEnsemble(5)
backward_ensemble = paths.LengthEnsemble(3)
randomizer = paths.NoModification()
self.filename = data_filename("shoot_from_snaps.nc")
self.storage = paths.Storage(self.filename, 'w')
self.simulation = ShootFromSnapshotsSimulation(
storage=self.storage,
engine=self.engine,
starting_volume=starting_volume,
forward_ensemble=forward_ensemble,
backward_ensemble=backward_ensemble,
randomizer=randomizer,
initial_snapshots=self.snap0)
self.simulation.output_stream = open(os.devnull, "w")
def setup(self):
op = paths.FunctionCV("Id", lambda snap: snap.coordinates[0][0])
vol1 = paths.CVDefinedVolume(op, 0.1, 0.5)
vol2 = paths.CVDefinedVolume(op, -0.1, 0.7)
vol3 = paths.CVDefinedVolume(op, 2.0, 2.5)
self.stateA = vol1
self.stateB = vol3
self.interfaceA0 = vol2
self.stateX = ~vol1 & ~vol3
transition = paths.TPSTransition(self.stateA, self.stateB)
self.analyzer = paths.TrajectoryTransitionAnalysis(transition, dt=0.1)
self.traj_str = "aaaxaxxbxaxababaxbbbbbxxxxxxa"
# frame numbers "0 5 0 5 0 5 8"
self.trajectory = self._make_traj(self.traj_str)
def from_dict(dct):
interface_set = VolumeInterfaceSet.__new__(VolumeInterfaceSet)
interface_set._load_from_dict(dct)
volume_func = lambda minv, maxv: paths.CVDefinedVolume(
interface_set.cv, minv, maxv)
super(InterfaceSet, interface_set).__init__()
interface_set._set_volume_func(volume_func)
return interface_set
def test_default_state_progress_report():
cv = paths.FunctionCV("x", lambda x: x.xyz[0][0])
vol_A = paths.CVDefinedVolume(cv, 0.0, 1.0).named("A")
vol_B = paths.CVDefinedVolume(cv, 2.0, 3.0).named("B")
vol_C = paths.CVDefinedVolume(cv, 4.0, 5.0).named("C")
vol_D = paths.CVDefinedVolume(cv, 6.0, 7.0).named("D")
n_steps = 100
found_vol = [vol_A, vol_B]
all_vol = [vol_A, vol_B, vol_C, vol_D]
tstep = 0.5
f = default_state_progress_report # keep on one line
assert f(n_steps, found_vol, all_vol) == \
"Ran 100 frames. Found states [A,B]. Looking for [C,D]."
assert f(n_steps, found_vol, all_vol, tstep) == \
"Ran 100 frames [50.0]. Found states [A,B]. Looking for [C,D]."
