openpathsampling.shooting.GaussianBiasSelector

class openpathsampling.shooting.GaussianBiasSelector(collectivevariable, alpha=1.0, l_0=0.5)

A selector that biases according to a Gaussian along specified CollectiveVariable, with mean l_0 and width parameter alpha. That is, for snapshot \(x\) and CV \(\lambda\), the selection probability for each frame is weighted according to the function

\[P_\text{sel}(x) \propto \exp(-\alpha (\lambda(x) - l_0)^2)\]

Note that normalization here depends on the trajectory that the snapshot is a part of: the sum of the probabilities for all frames is 1, which gives a different normalization constant than the standard Gaussian distribution normalization, and exact probabilities for selecting a given snapshot will change depending on the trajectory it is a part of.

Parameters:

• collectivevariable (CollectiveVariable) – the axis to use for the Gaussian

• alpha (float) – the width of the Gaussian

• l_0 (float) – the center of the Gaussian

__init__(collectivevariable, alpha=1.0, l_0=0.5)

Methods

__init__(collectivevariable[, alpha, l_0])
args()	Return a list of args of the __init__ function of a class
base()	Return the most parent class actually derived from StorableObject
count_weaks()	Return number of objects subclassed from StorableObject still in memory
descendants()	Return a list of all subclassed objects
f(snapshot, trajectory)	Returns the unnormalized proposal probability of a snapshot
fix_name()	Set the objects name to be immutable.
from_dict(dct)	Reconstruct an object from a dictionary representaiton
get_uuid()
idx(store)	Return the index which is used for the object in the given store.
named(name)	Name an unnamed object.
objects()	Returns a dictionary of all storable objects
pick(trajectory)	Returns the index of the chosen snapshot within trajectory
probability(snapshot, trajectory)
probability_ratio(snapshot, old_trajectory, ...)
reverse_uuid()
ruuid(uid)
set_observer(active)	(De-)Activate observing creation of storable objects
sum_bias(trajectory)	Returns the unnormalized probability probability of a trajectory.
to_dict()	Convert object into a dictionary representation

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.
is_named	True if this object has a custom name.
name	Return the current name of the object.
observe_objects