openpathsampling.shooting.GaussianBiasSelector

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

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)[source]

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