- class openpathsampling.FullBootstrapping(transition, snapshot, storage=None, engine=None, extra_interfaces=None, extra_ensembles=None, forbidden_states=None, initial_max_length=None)
Takes a snapshot as input; gives you back a sampleset with trajectories for every ensemble in the transition.
TISTransition) – the TIS transition to fill by bootstrapping
Snapshot) – the initial snapshot
Storage) – storage file to record the steps (optional)
DynamicsEngine) – MD engine to use for dynamics
extra_interfaces (list of
Volume) – additional interfaces to make into TIS ensembles (beyond those in the transition)
extra_ensembles (list of
Ensemble) – additional ensembles to sample after the TIS ensembles
forbidden_states (list of
Volume) – regions that are disallowed during the initial trajectory. Note that these region are allowed during the interface sampling
initial_max_length (int) – maximum length of the initial A->A trajectory
- __init__(transition, snapshot, storage=None, engine=None, extra_interfaces=None, extra_ensembles=None, forbidden_states=None, initial_max_length=None)
__init__(transition, snapshot[, storage, ...])
Return a list of args of the __init__ function of a class
Attach a hook class or method to this simulation.
Return the most parent class actually derived from StorableObject
Return number of objects subclassed from StorableObject still in memory
Return a list of all subclassed objects
Return a hook dictionary with no hooks.
Set the objects name to be immutable.
Reconstruct an object from a dictionary representaiton
Return the index which is used for the object in the given store.
Name an unnamed object.
Returns a dictionary of all storable objects
Run the simulator for a number of steps
Run the hooks for the given
Save the initial state as an MCStep to the storage
(De-)Activate observing creation of storable objects
Will sync all collective variables and the storage to disk
Convert object into a dictionary representation
Return the base class
Return the name of the base class
Return the class name as a string
Return the default name.
True if this object has a custom name.
Return the current name of the object.