openpathsampling.PathSimulator

class openpathsampling.PathSimulator(storage)

Abstract class for the “main” function of a simulation.

Parameters:

storage (Storage) – Storage file for results

save_frequency

Results should be sync’d (saved to disk) after every save_frequency steps. Note: subclasses must directly implement this, the attribute is just a placeholder.

Type:

int

output_stream

Subclasses should write output to this, allowing a standard way to redirect any output.

Type:

file

allow_refresh

Whether to allow the output to refresh an ipynb cell; default True. This is likely to be overridden when a pathsimulator is wrapped in another simulation.

Type:

bool

__init__(storage)

Methods

__init__(storage)
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_steps)	Run the simulator for a number of steps
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