Written by Nathan M. Lui (2023)
With contributions from Dr. Ryan A. Woltornist (2021)
and many others; see the full list of contributors in the GitHub repo
The Short Course
The Short Course is designed as a primer for advanced undergraduates and beginning graduate students. It is intended to give the completely inexperienced reader a step-by-step guide to running electronic structure calculations on the AS-CHEM computing cluster at Cornell University, but it is our hope that these instructions are easily generalizable to other computing clusters. The Short Course’s main computational engine is Gaussian16 since it was originally designed for Collum group members, however a fully open-source edition (utilizing Psi4) is currently being written.
Software
Linux basics
My first script
SLURM basics
My first SLURM job
The Gaussian input file
My first Gaussian job
Understanding the Gaussian output file
Putting it all together: calculating cyclohexane A-values
The Long Course
The Long Course is a work in progress!
The Long Course is a set of more advanced topics in scripting and computational chemistry. It was written for those who have, or would like to, incorporate more advanced calculations/models into their research. The topics start by streamlining computational workflow (with bash scripting) and then progress towards the more under-the-hood options of computational engines.
Using bash to streamline computational workflow and data processing
So what exactly is an optimization?
Cost efficiency: Selecting basis sets and functionals without going overboard
Using custom basis sets and effective core potentials
What is a transition state?
The art of finding transition structures
The implicit/explicit solvation war
Electronic structure theory
Problems
My least favorite math teacher would always say that the only way to learn calculus is to solve lots of calculus problems. This is a collection of case studies and practice problems that you can use to try your own hand at computational chemistry. Let me know if there’s anything else you’d like to see here!
Cyclohexane A-values (from the Short Course)
The Smelly Dimer Problem
E-Z isomers of 3-(4-nitrophenyl)but-2-en-2-yl triflate
Resources
The Code Repo: Exercises and Problems
g16 “cheat codes” (routing line templates)
A collection of papers/resources I’ve amassed over the years.
Contributions and Corrections
This course is a living, breathing work-in-progress so if you spot any typos or if there are topics you’d like to add (to see added) to the course check out the GitHub repo or email me!
Supplemental Readings
The International Journal of Quantum Chemistry has published an excellent series of tutorial reviews for novices and professionals alike. I highly recommend looking through them. Below are a few you may find particularly helpful.
Fourteen Easy Lessons in Density Functional Theory
by John P. Perdew and Adrienn Ruzsinszky
Int. J. Quantum Chem. 2012, 110 (15), 2801
DFT in a nutshell
by Kieron Burke and Lucas O. Wagner
Int. J. Quantum Chem. 2013, 113 (2), 96
The devil in the details: A tutorial review on some undervalued aspects of density functional theory calculations by Pierpaolo Morgante and Roberto Peverati
Int. J. Quantum Chem. 2020, 120 (18), e26332