openpathsampling.engines.toy.LangevinBAOABIntegrator

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

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)[source]

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