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Allow n_rounds to be passed to stability_oracle_factory #5

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Allow n_rounds to be passed to stability_oracle_factory #5

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7 changes: 5 additions & 2 deletions thresholds/stability.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ def check_stability(simulation, n_steps=1000, n_rounds=10, potential_energy_thre


def stability_oracle_factory(simulation, set_initial_conditions,
n_steps=1000, potential_energy_threshold=1000 * unit.kilojoule_per_mole):
n_steps=1000, n_rounds=10, potential_energy_threshold=1000 * unit.kilojoule_per_mole):
"""Construct a stochastic function that accepts a scalar (timestep, in femtoseconds)
and checks whether integration at that timestep appears stable.

Expand All @@ -41,6 +41,9 @@ def stability_oracle_factory(simulation, set_initial_conditions,
may set state to a sample from equilibrium, or from some other interesting ensemble of initial conditions.
n_steps : int
how many timesteps to simulate
n_rounds : int, default 10
how many rounds to use to run n_steps
e.g. if n_steps is 1000, specifying n_rounds as 10 will run 10 rounds of 100 steps
potential_energy_threshold : simtk.unit (energy)
if the potential energy of the simulation exceeds this threshold, NaNs are nigh

Expand All @@ -61,7 +64,7 @@ def stability_oracle(dt):

set_initial_conditions(simulation)

return check_stability(simulation, n_steps, potential_energy_threshold)
return check_stability(simulation, n_steps=n_steps, n_rounds=n_rounds, potential_energy_threshold=potential_energy_threshold)

def iterated_stability_oracle(dt, n_iterations=10):
"""Return True if stability_oracle is True n_iterations times, terminating early when possible.
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