openpathsampling.engines.toy.LangevinBAOABIntegrator

class openpathsampling.engines.toy.LangevinBAOABIntegrator(dt, temperature, gamma)

Langevin integrator for simple toy models

Implementation of the BAOAB integrator of Leimkuhler and Matthews 1. In particular, see the appendix on p.54 of that reference, which is where we take our notation from.

Parameters

• dt (float) – time step

• temperature (float) –

• gamma (float) – friction constant for the Langevin equation

beta

inverse temperature

Type

float

c1

c1 parameter from Leimkuhler and Matthews

Type

float

c2

c2 parameter from Leimkuhler and Matthews

Type

float

c3

c3 parameter from Leimkuhler and Matthews

Type

float

References

1

B. Leimkuhler and C. Matthews. “Rational Construction of Stochastic Numerical Methods for Molecular Sampling.” Appl. Math. Res. Express, 2013, 34-56 (2013). doi:10.1093/amrx/abs010

__init__(dt, temperature, gamma)

Methods

__init__(dt, temperature, gamma)
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
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
step(sys)	Take an MD step.
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
beta
c1
c2
c3
cls	Return the class name as a string
dd
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