openpathsampling.ReactiveFluxSimulation

class openpathsampling.ReactiveFluxSimulation(storage, engine=None, states=None, randomizer=None, initial_snapshots=None, rc=None)

Reactive Flux simulations (effective positive flux).

Parameters:

• storage (Storage) – the file to store simulations in

• engine (DynamicsEngine) – the dynamics engine to use to run the simulation

• states (list of Volume) – the volumes representing the stable states, first state A then state B

• randomizer (SnapshotModifier) – the method used to modify the input snapshot before each shot

• initial_snapshots (list of Snapshot) – initial snapshots to use

• rc (CollectiveVariable) – reaction coordinate

__init__(storage, engine=None, states=None, randomizer=None, initial_snapshots=None, rc=None)

Methods

__init__(storage[, engine, states, ...])
args()	Return a list of args of the __init__ function of a class
attach_default_hooks()
attach_hook(hook[, hook_for])	Attach a hook class or method to this simulation.
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
empty_hooks()	Return a hook dictionary with no hooks.
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()
run(n_per_snapshot[, as_chain])	Run the simulation.
run_hooks(hook_name, **kwargs)	Run the hooks for the given hook_name
ruuid(uid)
save_initial_step()	Save the initial state as an MCStep to the storage
set_observer(active)	(De-)Activate observing creation of storable objects
sync_storage()	Will sync all collective variables and the storage to disk
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
calc_name
cls	Return the class name as a string
default_name	Return the default name.
hook_names
is_named	True if this object has a custom name.
name	Return the current name of the object.
observe_objects