openpathsampling.snapshot_modifier.SingleAtomVelocityDirectionModifier

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

Change a single atom according to the delta_v.

Note that even though this only uses the delta_v to change one atom, the velocities of other atoms will also be changed in order to preserve the initial kinetic energy and possibly also to remove linear momenta.

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
`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`