Physics 466/MSE485/CSE485: Atomic Scale Simulation 

This course is designed to teach you the algorithms and approach for doing simulations at the atomic level.


Lectures: MWF 3:00-3:50 136 Loomis Laboratory

Instructor: Bryan Clark
Office Hours: Tuesday 4:00 to 5:00 pm, ESB 3rd floor common area
email: bkclark_at_illinois_dot_edu
Office: 2111 Engineering Science Building (ESB)

TA: Xiongjie Yu
Office Hours: Friday 4:00 to 5:00 pm, ESB 3rd floor common area



The key to this class will be the homework.  This is the aspect of the course you will learn the most from.  It will often involve programing and will be difficult but is designed to teach you the important concepts in atomic simulations.   There will four types of homework in this class (and no exam!). The first is the standard homework. There are six of these and you must complete and submit them on your own (although you may discuss with other people).     The second is the mini-project.  There will be a list of possible mini-projects.  You need only do one (if you want to do another, I'd be happy to replace one of your standard homework grades with the grade from the mini-project).   The mini-project is due by the middle of the semester and can be done in groups of (up to) 3.   You only need to do the mini-project if you are taking the class for four credits. We will give less "help" on the mini-projects; you will be expected to really take the initiative here.    Everyone will be assigned a paper (and a class)  to give a two minute summary.  Finally, there will be a final project.  The final project can be anything of your choosing (approved by me) and can be done in groups (up to) 3.  We will have a list of possible final projects.  

If you are taking the class for four credits your grade will be based on

If you are taking the class for three credits your grade will be based on

A comment about partial credit.  There will not be significant partial credit for code that doesn't produce the correct answer (although the homeworks are structured to be able to get credit for intermediate results).  There are a million ways a code can be incorrect and it's very hard to evaluate how close you were to the correct answer.  On the other hand, we will give you guideposts to help you learn to tell if your code is correct before submitting.  It should be rare that you will submit broken code and not know it. 

In addition, there will be occassionally ways to earn extra credit.  For example, if you want to do an additional mini-project, one standard homework grade can be swapped out. Also, we will post the "best" (fastest, clearest, written well in a different language, etc.) assignments on the website.   If yours happens to be selected, you will get +5 points on that homework. Which assignments count as "best" is up to the discretion of the course staff.

All homework sets and information related to homework (requirements, computer help, software help, teams, etc) will be posted on this CITES wiki page.


Course Material:

Course Texts: Understanding Molecular Simulations, D. Frenkel and B. Smit, 2nd Edition ("FS") -Note, although this is the best reference text it will not be carefully followed
Text Source Code:  here 
Supplementary Text: Computer Simulations of Liquids, M.P. Allen and D.J. Tidesley (Oxford Univ. Press), 1997 (Reprinted)
Computer Help and software help: Please check out this CITES wiki page.
Standard Homework: Please check out this CITES wiki page.
Mini-Projects: To be added
Project Information: To be added
Piazza discussion board: You must sign up for this (just search the course name on Piazza). Important information will be posted here and you will be able to communicate with us through it
Class Schedule: here