CH121a Atomic Level Simulations of Materials and Molecules

Instructor: Prof. William A. Goddard III

TA: Yalu Chen, B207 A,

Course website:

Hours: MWF 2:00-3:00pm

Units: 3-0-6

Term:Winter 2020

TA Office Hours: TBD

Location: 115 Beckman Institute (on the south side of BI patio)

Prerequisites: some knowledge of quantum mechanics, classical mechanics, thermodynamics, chemistry, Unix. It is sufficient to have learned the material in Ma 2, Ph 2, Ch 1, but nice to have had some exposure to material covered in courses such as Ph12, Ch 21, Ch 41, ChE 63, APh 25, Bi 8, MS 15, and ME 18


Ch121a uses a practical hands-on approach to learning the tools of modern computational chemistry and computational materials science relevant to atomistic descriptions of the structures and properties of chemical, biological, and materials systems. This course is aimed at experimentalists (and theorists) in chemistry, materials science, chemical engineering, applied physics, biochemistry, physics, geophysics, and mechanical engineering with an interest in characterizing and designing molecules, drugs, and materials. Thus the lectures cover the basics of the quantum mechanics, force fields, molecular dynamics, Monte Carlo, statistical mechanics, etc. required to understand the theoretical basis for the simulations while the homework applies these principles to practical problems. The homework in the first 5 weeks involves using available computer softwares, aimed at exposing the students to understand how to use atomistic simulations to solve problems, how to make decisions on specific approaches and relevent parameters, and how to analyze the results. The midterm requires each student to submit a proposal for a project using the methods of Ch121a to solve a research problem that can be completed in 5 weeks. The homework for the last 5 weeks is to turn in a one page progress report each week. The final is a research report describing the calculations and conclusions.

Grading Policy:

Weekly problem set for the first 5 weeks 50%. Midterm proposal + progress report + final report 50%. No credit will be given for late assignments.

If necessary, please contact Prof. Goddard to request an extension.

General Lab Instructions:

All homework in this course will focus on using the computers and software programs within the Goddard group to solve chemical problems. To prepare for each lab, please read over the homework handout before arriving in the computer lab. The labs will be held in 115 Beckman Institute on Friday. Since you have a limited time in lab, please be familiar with your homework problem set before your arrival.

Lecture Slides:


Problem Sets and Lab Sessions:

    Problem Set 1 (Lab Session 01/10/2020)
    Problem Set 2 (Lab Session 01/17/2020)
    Problem Set 3 (Lab Session 01/22/2020)
    Problem Set 4 (Lab Session 01/31/2020)
    Problem Set 5 (Lab Session 02/07/2020)

Additional Resourses:

    Unix Cheat Sheet
    VI Cheat Sheet
    2pt user guide for PS5

Lecture Slides from Previous Year:


Questions? Comments? Send mail to Prof. Goddard or the TAs.