Tools for analyzing Markov models using statistical physics and graph theory
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README.md
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README.md

Introduction

Tools for conducting simulations of Markov processes on various various graph structures, with particular attention given to calculation of thermodynamic quantities like entropy production rate.

Transition matrix generators for common graph types (Cayley tree, stochastic "small world")

Tools for working with transition matrices (reordering states, renormalizing, biasing)

Tools for generating and sampling trajectories in a Markov chain and quantifying thermodynamic quantities like mutual information and heat generation.

Tools for visualizing Markov matrices using the NetworkX python graph theory library

Dependencies

networkx

numpy

matplotlib

Examples