Getting Started

Introduction

The goal of McCode Academy (and this whole website honestly) is to get people comfortable with the ways that math, code, and chemical intuition intersect. In order to do that, we (originally the McCoy Group circa 2020) are documenting some of the most important things and most common stumbling blocks we found while getting started ourselves. We hope that in this way, we can help you avoid some headaches and feel more confident diving into your first research project.

Through these pages, we have attempted to hit the highlights and lay a nice ground work for using Python in a quantum chemistry setting. You will find lists of helpful functions, common issues we’ve faced (and solutions to them), and some guiding exercises for applying these tools.

If you are feeling a little overwhelmed by all of this we recommend starting with either (or both!) of these MolSSI (the Molecular Sciences Software Institute) tutorials:

• Getting Started in Computational Chemistry
• Python Scripting for Computational Molecular Science

NOTE: You will see these tutorials and others from MolSSI referenced throughout this resource, and they are all complementary to what we are trying to do here.

The biggest hurdle to overcome when starting out isn’t the kind of abstract thinking coding requires, nor is it needing to understand the syntax of the language, and it’s definitely not needing to know how computers do what they do–very few programmers actually know that. Instead, it’s literally just getting everything installed and playing nicely together. So we’re gonna walk through the basics of what’ll be needed to get through this tutorial.

Let’s start with…

• Linux Terminal Tutorial: A brief introduction to the Linux Command Line.
• An Introduction to Python/Anaconda: You can find download instructions here too!
• Interactive Python: An Introduction to using python through the command line.
• What is an IDE?: An Introduction to Integrated Development Environments and why we like them!

Then, Walk through Code Structures

• Your “First” Python Script
• How to Write a Function
• From Functions to Classes
• An Extended Class Example

Next, Look at How to

• Use NumPy
• Manage Data
• Plot Results

Or get some practice in with some Exercises

Already know about some of this? Prefer to work through it in a different order? All good by us. Do what’s best for you.

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