openpathsampling.ReactiveFluxSimulation

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

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)[source]

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)

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