def analyze_transition_duration(self, trajectory, stateA, stateB):
"""Analysis to obtain transition durations for given state.
Parameters
----------
trajectory : :class:`.Trajectory`
trajectory to analyze
stateA : :class:`.Volume`
initial state volume for the transition
stateB : :class:`.Volume`
final state volume for the transition
Returns
-------
:class:`.TrajectorySegmentContainer`
transitions from `stateA` to `stateB` within `trajectory`
"""
# we define the transitions ensemble just in case the transition is,
# e.g., fixed path length TPS. We want flexible path length ensemble
transition_ensemble = paths.SequentialEnsemble([
paths.AllInXEnsemble(stateA) & paths.LengthEnsemble(1),
paths.OptionalEnsemble( # optional to allow instantaneous hops
paths.AllOutXEnsemble(stateA) & paths.AllOutXEnsemble(stateB)
),
paths.AllInXEnsemble(stateB) & paths.LengthEnsemble(1)
])
segments = [seg[1:-1] for seg in transition_ensemble.split(trajectory)]
return TrajectorySegmentContainer(segments, self.dt)
def __init__(self, transition, snapshot, storage=None, engine=None,
extra_interfaces=None, forbidden_states=None):
super(FullBootstrapping, self).__init__(storage, engine)
if extra_interfaces is None:
extra_interfaces = list()
if forbidden_states is None:
forbidden_states = list()
interface0 = transition.interfaces[0]
ensemble0 = transition.ensembles[0]
state = transition.stateA
self.state = state
self.first_traj_ensemble = paths.SequentialEnsemble([
paths.OptionalEnsemble(paths.AllOutXEnsemble(state)),
paths.AllInXEnsemble(state),
paths.OptionalEnsemble(
paths.AllOutXEnsemble(state) & paths.AllInXEnsemble(interface0)
),
paths.OptionalEnsemble(paths.AllInXEnsemble(interface0)),
paths.AllOutXEnsemble(interface0),
paths.OptionalEnsemble(paths.AllOutXEnsemble(state)),
paths.SingleFrameEnsemble(paths.AllInXEnsemble(state))
]) & paths.AllOutXEnsemble(paths.join_volumes(forbidden_states))
self.extra_ensembles = [paths.TISEnsemble(transition.stateA,
transition.stateB, iface,
transition.orderparameter)
for iface in extra_interfaces
]
self.transition_shooters = [
paths.OneWayShootingMover(selector=paths.UniformSelector(),
ensemble=ens)
for ens in transition.ensembles
]
self.extra_shooters = [
paths.OneWayShootingMover(selector=paths.UniformSelector(),
ensemble=ens)
for ens in self.extra_ensembles
]
self.snapshot = snapshot.copy()
self.ensemble0 = ensemble0
self.all_ensembles = transition.ensembles + self.extra_ensembles
self.n_ensembles = len(self.all_ensembles)
self.error_max_rounds = True
def get_lifetime_segments(trajectory, from_vol, to_vol, forbidden=None,
padding=[0, -1]):
"""General script to get lifetimes.
Lifetimes for a transition between volumes are used in several other
calculations: obviously, the state lifetime, but also the flux
through an interface. This is a generic function to calculate that.
Parameters
----------
trajectory : :class:`.Trajectory`
trajectory to analyze
from_vol : :class:`.Volume`
the volume for which this represents the lifetime: the
trajectory segments returned are associated with the lifetime of
`from_vol`
to_vol : :class:`.Volume`
the volume which indicates the end of the lifetime: a frame in
this volume means the trajectory is no longer associated with
`from_vol`
forbidden : :class:`.Volume`
if a frame is in `forbidden`, it cannot be part of the lifetime
of `from_vol`. This isn't needed in 2-state lifetime
calculations; however, it is useful to exclude other states
from a flux calculation
padding : list
adjusts which frames are returned as list indices. That is, the
returned segments are `full_segment[padding[0]:padding[1]]`.
The `full_segment`s are the segments from (and including) each
first frame in `from_vol` (after a visit to `to_vol`) until (and
including) the first frame in `to_vol`. To get the full segment
as output, use `padding=[None, None]`. The default is to remove
the final frame (`padding=[0, -1]`) so that it doesn't include
the frame in `to_vol`.
Returns
-------
list of :class:`.Trajectory`
the frames from (and including) each first entry from `to_vol`
into `from_vol` until (and including) the next entry into
`to_vol`, with no frames in `forbidden`, and with frames removed
from the ends according to `padding`
"""
if forbidden is None:
forbidden = paths.EmptyVolume()
ensemble_BAB = paths.SequentialEnsemble([
paths.LengthEnsemble(1) & paths.AllInXEnsemble(to_vol),
paths.PartInXEnsemble(from_vol) & paths.AllOutXEnsemble(to_vol),
paths.LengthEnsemble(1) & paths.AllInXEnsemble(to_vol)
]) & paths.AllOutXEnsemble(forbidden)
ensemble_AB = paths.SequentialEnsemble([
paths.LengthEnsemble(1) & paths.AllInXEnsemble(from_vol),
paths.OptionalEnsemble(paths.AllOutXEnsemble(to_vol)),
paths.LengthEnsemble(1) & paths.AllInXEnsemble(to_vol)
])
BAB_split = ensemble_BAB.split(trajectory)
AB_split = [ensemble_AB.split(part)[0] for part in BAB_split]
return [subtraj[padding[0]:padding[1]] for subtraj in AB_split]