openpathsampling.snapshot_modifier.VelocityDirectionModifier

class openpathsampling.snapshot_modifier.VelocityDirectionModifier(delta_v, subset_mask=None, remove_linear_momentum=True, engine=None)[source]

Randomly change all the velocities (in the subset masked, at least) according to the given delta_v.

Parameters
  • delta_v (float or array-like of float) – velocity change parameter, as the width of a Gaussian from which each degree of freedom’s velocity change is chosen. Can be a list with length n_atoms (mapping to each atom); length equal to the subset mask (mapping to each element of the subset mask); or a float (mapping the same value to all atoms).

  • subset_mask (list of int or None) – the subset to use (default None, meaning use all). The values select along the first axis of the input array. For example, in a typical shape=(n_atoms, 3) array, this will pick the atoms.

  • rescale_linear_momenta (bool) – whether the total linear momentum should be removed from the system, default is True

__init__(delta_v, subset_mask=None, remove_linear_momentum=True, engine=None)

Methods

__init__(delta_v[, subset_mask, …])

apply_to_subset(full_array, modified[, …])

Replaces elements of full_array according to the subset mask

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

extract_subset(full_array[, subset])

Extracts elements from full_array according to self.subset_mask

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

reverse_uuid()

ruuid(uid)

set_observer(active)

(De-)Activate observing creation of storable objects

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