openpathsampling.ensemble.MinusInterfaceEnsemble

class openpathsampling.ensemble.MinusInterfaceEnsemble(state_vol, innermost_vols, n_l=2, forbidden=None, greedy=False)

This creates an ensemble for the minus interface.

The specific implementation allows us to use the multiple-segment minus ensemble described by Swenson and Bolhuis. The minus interface was originally developed by van Erp. For more details, see the section “Anatomy of a PathMover: the Minus Move” in the OpenPathSampling Documentation.

Parameters:

• state_vol (Volume) – The Volume which defines the state for this minus interface

• innermost_vols (list of Volume) – The Volume defining the innermost interface with which this minus interface does its replica exchange.

• n_l (integer (greater than one)) – The number of segments crossing innermost_vol for this interface.

References

T.S. van Erp. Phys. Rev. Lett.

D.W.H. Swenson and P.G. Bolhuis. J. Chem. Phys. 141, 044101 (2014). doi:10.1063/1.4890037

__init__(state_vol, innermost_vols, n_l=2, forbidden=None, greedy=False)

A path volume defines a set of paths.

Methods

__init__(state_vol, innermost_vols[, n_l, ...])	A path volume defines a set of paths.
args()	Return a list of args of the __init__ function of a class
base()	Return the most parent class actually derived from StorableObject
can_append(trajectory[, trusted])	Returns true, if the trajectory so far can still be in the ensemble if it is appended by a frame.
can_prepend(trajectory[, trusted])	Returns true, if the trajectory so far can still be in the ensemble if it is prepended by a frame.
check(trajectory)	Alias for __call__
check_reverse(trajectory[, trusted])	See __call__; same thing, but potentially in reverse frame order
count_weaks()	Return number of objects subclassed from StorableObject still in memory
descendants()	Return a list of all subclassed objects
extend_sample_from_trajectories(...[, ...])	Generate a sample in the ensemble by extending parts of trajectories
find_first_subtrajectory(trajectory)	Return the first sub-trajectory that matches the ensemble
find_last_subtrajectory(trajectory)	Return the last sub-trajectory that matches the ensemble
fix_name()	Set the objects name to be immutable.
from_dict(dct)	Reconstruct an object from a dictionary representaiton
get_sample_from_trajectories(trajectories[, ...])	Generate a sample in the ensemble by testing trajectories
get_uuid()
idx(store)	Return the index which is used for the object in the given store.
iter_extendable_slices(trajectory[, ...])	Return an iterator over maxiaml slices of extendable subtrajectories
iter_split(trajectory[, max_length, ...])	Return iterator over subtrajectories satisfying the given ensemble.
iter_valid_slices(trajectory[, max_length, ...])	Return an iterator over slices of subtrajectories matching the ensemble
named(name)	Name an unnamed object.
objects()	Returns a dictionary of all storable objects
reverse_uuid()
ruuid(uid)
set_observer(active)	(De-)Activate observing creation of storable objects
split(trajectory[, max_length, min_length, ...])	Return list of subtrajectories satisfying the given ensemble.
split_sample_from_trajectories(trajectories)	Generate a sample in the ensemble by searching for sub-parts
strict_can_append(trajectory[, trusted])	Returns true if the trajectory can be the beginning of a trajectory in the ensemble.
strict_can_prepend(trajectory[, trusted])	Returns true if the trajectory can be the end of a trajectory in the ensemble.
to_dict()	Convert object into a dictionary representation
trajectory_summary(trajectory)	Return dict with info on how this ensemble "sees" the trajectory.
trajectory_summary_str(trajectory)	Returns a string with the results of the trajectory_summary function.

Attributes

ACTIVE_LONG
CREATION_COUNT
INSTANCE_UUID
base_cls	Return the base class
base_cls_name	Return the name of the base class
cls	Return the class name as a string
default_name	Return the default name.
extendable_sub_ensembles
is_named	True if this object has a custom name.
name	Return the current name of the object.
observe_objects