openpathsampling.DirectSimulation

class openpathsampling.DirectSimulation(storage=None, engine=None, states=None, flux_pairs=None, initial_snapshot=None)

Direct simulation to calculate rates and fluxes.

In practice, this is primarily used to calculate the flux if you want to do so without saving the entire trajectory. However, it will also save the trajectory, if you want it to.

Parameters:

• storage (Storage) – file to store the trajectory in. Default is None, meaning that the trajectory isn’t stored (also faster)

• engine (DynamicsEngine) – the engine for the molecular dynamics

• states (list of Volume) – states to look for transitions between

• flux_pairs (list of 2-tuples of (state, interface)) – fluxes will calculate the flux out of state and through interface for each pair in this list

• initial_snapshot (Snapshot) – initial snapshot for the MD

transitions

for each pair of states (from_state, to_state) as a key, gives the number of frames for each transition from the entry into from_state to entry into to_state

Type:

dict with keys 2-tuple of paths.Volume, values list of int

rate_matrix

calculates the rate matrix, in units of per-frames

Type:

pd.DataFrame

fluxes

flux out of state and through interface for each (state, interface) key pair

Type:

dict with keys 2-tuple of paths.Volume, values float

n_transitions

number of transition events for each pair of states

Type:

dict with keys 2-tuple of paths.Volume, values int

n_flux_events

number of flux events for each (state, interface) pair

Type:

dict with keys 2-tuple of paths.Volume, values int

__init__(storage=None, engine=None, states=None, flux_pairs=None, initial_snapshot=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.
load_results(results)
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.
fluxes
hook_names
is_named	True if this object has a custom name.
n_flux_events
n_transitions
name	Return the current name of the object.
observe_objects
rate_matrix
results
transitions