def from_state_pairs(cls, state_pairs):
sampling = []
transitions = {}
for (initial, final) in state_pairs:
if len(sampling) == 1:
sampling[0].add_transition(initial, final)
elif len(sampling) == 0:
sampling = [paths.TPSTransition(initial, final)]
else:
raise RuntimeError(
"More than one sampling transition for TPS?")
transitions[(initial, final)] = paths.TPSTransition(initial, final)
network = cls.__new__(cls)
super(cls, network).__init__()
network._sampling_transitions = sampling
network.transitions = transitions
return network
def __init__(self, initial_states, final_states):
super(TPSNetwork, self).__init__()
try:
iter(initial_states)
except TypeError:
initial_states = [initial_states]
try:
iter(final_states)
except TypeError:
final_states = [final_states]
all_initial = paths.join_volumes(initial_states)
all_initial.name = "|".join([v.name for v in initial_states])
all_final = paths.join_volumes(final_states)
all_final.name = "|".join([v.name for v in final_states])
self._sampling_transitions = [
paths.TPSTransition(all_initial, all_final)
]
self.transitions = {
(initial, final): paths.TPSTransition(initial, final)
for (initial,
final) in itertools.product(initial_states, final_states)
if initial != final
}
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)