openpathsampling.snapshot_modifier.RandomVelocities

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

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 openmm 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 openmm.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)

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
probability_ratio(old_snapshot, new_snapshot)	Only here for backwards compatability, will raise in the future
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