Advanced Uses of OPS Ensembles
One of the novelties of OpenPathSampling is the new set-theoretic treatment of path ensembles. The second paper on OPS contains more details. This section will illustrate a few uses of that approach.
Visit all states
We want a path which contains at least one frame in each state. The question is, what ensemble can we use to create such a trajectory?
The first obvious thought would be:
goal_ensemble = PartInXEnsemble(A) & PartInXEnsemble(B)
(which can, of course, be further generalized to more states). However,
while that is the ensemble we want to eventually satisfy, we can’t use its
can_append to create it, because its
can_append always returns
True: the trajectory will go on forever!
But we can use a trick: since what we want is the first trajectory that
goal_ensemble, we know that every shorter trajectory will not
satisfy it. This means that the shorter trajectories must satisfy the
goal_ensemble, and the trajectory we want will be the
first trajectory that does not satisfy the complement!
So the trick we’ll use is to build the trajectory by using the fact that the
shorter trajectories are in the complement of
goal_ensemble, which is
complement = AllOutXEnsemble(A) | AllOutXEnsemble(B)
generate function will stop when that is no longer true, giving us the
trajectory we want. This can be directly generalized to more states.
Here we’re not even using the
can_append function. That happens to be
the same as the ensemble itself for this particular ensemble, but
conceptually, we’re actually using the test of whether a trajectory is in
the ensemble at all.
init_traj_ensemble = paths.AllOutXEnsemble(A) | paths.AllOutXEnsemble(B) trajectory = engine.generate(engine.current_snapshot, [init_traj_ensemble])
Those two lines are the entirety of what you need to do to generate a trajectory that visits both states.
Note that this functionality has been implemented in OPS as the
VisitAllStatesEnsemble. When using that, you should use the
can_append method. That ensemble adds progress reporting functionality
to show how many frames have been run and what states have been found so
far, so it is more pleasant to use. However, this idea is what underlies its