Python Interface

class ndsimulator.engines.Committor(n_basins, criteria, engine_method, engine_method_kwargs={}, diffusion_time=0, emin: float = - 1.2, run: Optional[ndsimulator.data.AllData] = None)

Committor simulation. MD engine that stops at basin or when it hits maximum steps.

Parameters

  • n_basins (int) – Number of basins

  • criteria (list) – Commit criteria. [[[x1_min, x1_max], [x2_min, x2_max], …, [xn_min, xn_max]], [2nd basin], …]

  • diffusion_time (int, optional) – . Defaults to 0.

  • run (AllData, optional) – Pointers for AllData. Defaults to None.

begin()

trigger initialization

commit(nostop, kBT, colv, criteria, pe, emin)

determine whether the current state atoms.colv meet the commit criteria. This function can be reloaded for more complex senario.

Parameters

nostop (boolean) – True for not committed

initialize(run)

initialization. For finite temperature, set up MD engine. For 0 K, set up minimization

update(step, time)

normal integration step or minimization step but condition the stopping criteria with committing criteria

Parameters

  • step (int) – current time step

  • time (float) – current time