Package csb :: Package statistics :: Package samplers :: Package mc :: Module multichain :: Class ReplicaHistory

Class ReplicaHistory

object --+
         |
        ReplicaHistory

Replica history object, works with both RE and RENS for the AlternatingAdjacentSwapScheme.

Instance Methods

__init__(self, samples, swap_interval, first_swap=None)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

list of ints

calculate_history(self, start_ensemble)
Calculates the replica history of the first state of ensemble #start_ensemble.

source code

list of Trajectory objects.

calculate_projected_trajectories(self, ensemble)
Calculates sequentially correlated trajectories projected on a specific ensemble.

source code

list of Trajectory objects.

calculate_trajectories(self)
Calculates sequentially correlated trajectories.

source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties
Inherited from `object`: `__class__`

Method Details

init(self, samples, swap_interval, first_swap=None)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

samples (list) - list holding ensemble states
swap_interval (int) - interval with which swaps were attempted, e.g., 5 means that every 5th regular MC step is replaced by a swap
first_swap (int) - sample index of the first sample generated by a swap attempt. If None, the first RE sampled is assumed to have sample index swap_interval. If specified, it has to be greater than zero

Overrides: object.__init__

(inherited documentation)

calculate_history(self, start_ensemble)

source code

Calculates the replica history of the first state of ensemble #start_ensemble.

Parameters:

start_ensemble (int) - index of the ensemble to start at, zero-indexed

Returns: list of ints

replica history as a list of ensemble indices

calculate_projected_trajectories(self, ensemble)

source code

Calculates sequentially correlated trajectories projected on a specific ensemble.

Parameters:

ensemble (int) - ensemble index of ensemble of interest, zero-indexed

Returns: list of Trajectory objects.

list of Trajectory objects containg sequentially correlated trajectories

calculate_trajectories(self)

source code

Calculates sequentially correlated trajectories.

Returns: list of Trajectory objects.: list of Trajectory objects containg sequentially correlated trajectories

Class ReplicaHistory

__init__(self, samples, swap_interval, first_swap=None) (Constructor)

calculate_history(self, start_ensemble)

calculate_projected_trajectories(self, ensemble)

calculate_trajectories(self)

init(self, samples, swap_interval, first_swap=None)
(Constructor)