OPS Channel Analysis¶

Purpose of Module
Background Information
Testing
Examples
Source Code

In many cases, more than one channel is available to a system – either because there are multiple channels between two states, or because there are multiple states, and transitions between each pair is a different channel. This module provides tools to identify which paths are in each channel, and to study the statistical behavior of the switching between channels.

Purpose of Module ¶

In practical examples, more than one channel (i.e., mechanism) can occur during a path sampling simulation. This is inherently the case if you have multiple stable states, since the transition between each pair of states will be of separate interest. It can also be the case when you have a single pair of states, but multiple channels that connect the states.

This module uses the OPS Ensemble.split function to study how a simulation samples these channels. The user must provide a list of possible channels, described as OPS Ensemble objects. From this, each path is analyzed, and various statistical behavior about the sampling process can be determined.

The main object added in this module is the ChannelAnalysis object, which performs this analysis and stores the results. Once the analysis has been performed, several properties can be extracted, including:

switching_matrix: how many times a switch from one channel to another occurred
residence_times: the number of MC steps spent with the path in each channel (returns the entire list so the user can calculate distribution properties with, e.g., numpy)
total_time: total number of MC steps spent in each channel
status(step_num): the channel the simulation was in for a given step number

In principle, a path might satsify the requirement for more than one channel at a time. This analysis class allows for that, and gives the user the option of setting its treat_multiples attribute:

newest: use the most recent channel entered
oldest: use the least recent channel entered
multiple: treat multiple channels as a new type of channel, e.g., ‘a’ and ‘b’ because ‘a,b’
all: treat each channel individually, despite overlaps. For status this is the same as ‘multiple’

Background Information ¶

This module builds on OpenPathSampling, a Python package for path sampling simulations. To learn more about OpenPathSampling, you might be interested in reading:

OPS documentation: http://openpathsampling.org
OPS source code: http://github.com/openpathsampling/openpathsampling

Testing ¶

Tests in OpenPathSampling use the nose package.

This module has been included in the OpenPathSampling core. Its tests can be run by setting up a developer install of OpenPathSampling and running the command nosetests from the root directory of the repository.