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
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
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