openpathsampling.snapshot_modifier.RandomVelocities

class openpathsampling.snapshot_modifier.RandomVelocities(beta=None, engine=None, subset_mask=None)[source]

Randomize velocities according to the Boltzmann distribution.

Notes

This modifier will only work with snapshots that have the velocities feature and the masses feature. Furthermore, the units have to be such that the input beta and the features masses and velocities are all in the same unit system. In particular, 1.0 / beta * masses must be in units of velocity**2.

For the OpenMMEngine, for example (after from simtk import unit as u), the beta parameter for 300 K would be created with

beta = 1.0 / (300.0 * u.kelvin * u.BOLTZMANN_CONSTANT_kB)
Parameters
  • beta (float or simtk.unit.Quantity) – inverse temperature (including kB) for the distribution

  • engine (DynamicsEngine or None) – engine to be used for constraints; if None, use the snapshot’s engine

  • 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.

__init__(beta=None, engine=None, subset_mask=None)[source]

Methods

__init__([beta, engine, 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