openpathsampling.DirectSimulation

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

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)[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)

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