openpathsampling.PathSampling

class openpathsampling.PathSampling(storage, move_scheme=None, sample_set=None, initialize=True)

General path sampling code.

Takes a single move_scheme and generates samples from that, keeping one per replica after each move.

__init__(storage, move_scheme=None, sample_set=None, initialize=True)

Parameters:

• storage (openpathsampling.storage.Storage) – the storage where all results should be stored in

• move_scheme (openpathsampling.MoveScheme) – the move scheme used for the pathsampling cycle

• sample_set (openpathsampling.SampleSet) – the initial SampleSet for the Simulator

• initialize (bool) – if False the new PathSimulator will continue at the step and not create a new SampleSet object to cut the connection to previous steps

Methods

__init__(storage[, move_scheme, sample_set, ...])	param storage: the storage where all results should be stored in
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
from_step(storage, step[, initialize])	param storage: the storage to be used to hold the simulation results
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
restart_at_step(step[, storage])	Continue with a loaded pathsampling at a given step
reverse_uuid()
run(n_steps)	Run the simulator for a number of steps
run_hooks(hook_name, **kwargs)	Run the hooks for the given hook_name
run_one_step(step_info[, hook_state])
run_until(n_steps)
run_until_decorrelated([time_reversal])	Run until all trajectories are decorrelated.
run_until_n_accepted(n_accepted)
ruuid(uid)
save_current_step()	Save the current step to the storage.
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
current_step
default_name	Return the default name.
hook_names
is_named	True if this object has a custom name.
live_visualizer
name	Return the current name of the object.
observe_objects