2. Introduction to Manipulating Atoms in Python

2.1. Introduction

This section introduces several tools that have become “industry standards” for computational chemistry, most notably the Atomic Simulation Environment (A-S-E). These tools are under active development and open source, meaning they may break or behave unexpectedly. Our group has also developed software to interface with these tools, namely the sparc-dft-api. This is a “bleeding edge” code also under active development (by primarily non-computer scientists). This introduction is designed to orient you towards the more robust portions of the codes, but keep in mind that you may encounter bugs or unexpected behavior. If you do, we strongly encourage you to attempt to fix them yourself and submit pull requests for review. At a minimum, you should raise an issue on the appropriate repository.

This section may appear a bit overwhelming if you have not had a Materials Science course before, or are unfamiliar with conceptrs from heterogeneous catalysis. We remind the stduent to take a deep breath and remember that every expert practictioner was once a beginner. Reminder The grad students are available and happy to answer any questions you may have. The grad students should be used as a resource to address conceptual and technical questions to. The nitty-gritty details of debugging code we leave to you as an exercise. If for any reason you get stuck and cannot figure out a path forward, then please do reach out to a grad-student.