CMGDB

Conley Morse Graph Database

Overview

This project uses combinatorial and topological methods to compute dynamics of discrete dynamical systems.

Dependencies and Installation

The dependencies and install instructions on a Mac using Homebrew are listed below.

Boost and GMP

Install Boost and GMP

brew install boost
brew install gmp

SDSL

Install the Succinct Data Structure Library (SDSL)

git clone https://github.com/simongog/sdsl-lite.git
cd sdsl-lite
./install.sh /usr/local/

It is also possible to intall the sdsl-lite library with Homebrew using this repository with the commands

brew tap Brewsci/bio
brew install sdsl-lite

Eigen3

Install Eigen3

brew install eigen

graphviz

Install graphviz

brew install graphviz

CMake

Install CMake

brew install cmake

jupyter and graphviz

Install the jupyter and graphviz Python packages

python -m pip install jupyter graphviz

Install CMGDB

git clone https://github.com/marciogameiro/CMGDB.git
cd CMGDB
./install.sh

Documentation and Examples

To get started on how to run the code see the examples in the Jupyter notebooks in the examples folder.

In particular the notebooks Examples.ipynb, Gaussian_Process_Example.ipynb, and Conley_Index_Examples.ipynb present basic examples on how to run the code and are a good starting point.

Here is an old survey and a talk that might be useful.