Welcome to the Otago Research Genetic Algorithm for Nanoclusters, Including Structural Methods and Similatity (Organisms) documentation!

Citation Python Version GitHub release (latest by date) PyPI Conda Binder Licence

Section author: Dr. Anna Garden <anna.garden@otago.ac.nz>

Section author: Geoffrey Weal <geoffrey.weal@gmail.com>

Group page: https://blogs.otago.ac.nz/annagarden/

Page to cite with work from: Development of a Structural Comparison Method to Promote Exploration of the Potential Energy Surface in the Global Optimisation of Nanoclusters; Geoffrey R. Weal, Samantha M. McIntyre, and Anna L. Garden; JCIM; in submission stage.

What is this Documentation about?

This documentation is designed to guide the user to use the Otago Research Genetic Algorithm for Nanoclusters, Including Structural Methods and Similatity (Organisms) program.

What is Organisms

The Otago Research Genetic Algorithm for Nanoclusters, Including Structural Methods and Similarity (Organisms) program is designed to perform a genetic algorithm global optimisation for nanoclusters. It has been designed with inspiration from the Birmingham Cluster Genetic Algorithm and the Birmingham Parallel Genetic Algorithm from the Roy Johnston Group (see J. B. A. Davis, A. Shayeghi, S. L. Horswell, R. L. Johnston, Nanoscale, 2015,7, 14032 (https://doi.org/10.1039/C5NR03774C or link to Davis pdf here) and R. L. Johnston, Dalton Trans., 2003, 4193–4207 (https://doi.org/10.1039/B305686D or link to Johnston pdf here).

This algorithm is designed to explore the potential energy surface of a cluster system, using the genetic algorithm, and to local the putative globally lowest energetic cluster. It was designed for obtaining low energy structures of clusters that could be catalytically interesting. The algorithm was designed by Dr Anna Garden and the Garden group at the University of Otago, Dunedin, New Zealand. See for more information about what the group does at blogs.otago.ac.nz/annagarden. The Github page for this program can be found at github.com/GardenGroupUO/Organisms.

The genetic algorithm uses the ideas of Darwin’s theory of evolution to locate the global minimum.

Try Organisms before you Clone/Pip/Conda (on Binder/Jupter Notebooks)!

If you are new to the Organisms program, it is recommended try it out by running Organisms live on our interactive Jupyter+Binder page before you download it. On Jupyter+Binder, you can play around with the Organisms program on the web. You do not need to install anything to try Organisms out on Jupyter+Binder.

Click the Binder button below to try Organisms out on the web! (The Binder page may load quickly or may take 1 or 2 minutes to load)

Binder

Installation

It is recommended to read the installation page before using the Organisms program. See Installation: Setting Up the Organisms Program and Pre-Requisites Packages for more information. Note that you can install Organisms through pip3 and conda.

Table of Contents

Indices and tables