CH121a Atomic Level Simulations of Materials and Molecules

Instructor: Prof. William A. Goddard III

TA: Jin Qian, 056 BI,

TA: Daniel Brooks, 432 BI,

Course website:

Hours: MWF 2:00-3:00pm. Units: 3-0-6, Spring 2017

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

Generally: 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 6 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 4 weeks. The homework for the last 3 weeks is to turn in a one page progress report each week. The final is a research report describing the calculations and conclusions.


Methods to be covered in the lectures include:

Hartree Fock and Density Function methods of Quantum Mechanics

Force Fields appropriate for organic, biological, inorganic, semiconductor, metallic systems, reactions

Molecular Dynamics (structure optimization, vibrations, phonons, elastic moduli)

Molecular Dynamics (Verlet, microcanonical, Nose, Gibbs)

Monte Carlo, Statistical thermodynamics (Kubo relations, correlation functions)

Coarse grain approaches (solvation, diffusion, psuedoatoms, dislocations)

Applications will include prototype examples involving such materials as:

Organic molecules (structures and reactions)

Biochemical (amino acids, proteins, carbohydrates, nucleic acids, Protein ligand complexes, DNA-ligand complexes)

Polymers (amorphous, crystalline, RIS theory, block)

Semiconductors (bulk, impurity sites, surface reconstruction, chemisorption)

Ceramics (metal oxides, zeolites)

Metal alloys (crystalline, amorphous, plasticity)

Catalysis (homogeneous and heterogeneous)

Grading Policy:

Weekly problem set for the first 6 weeks 60%

Midterm proposal + progress report for the last 3 weeks + final report 40%

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.

The computer operator system is Unix system. If you are not familiar with that, please check out the brief introduction below:

Unix Tutorial

Please do not be afraid to ask questions about the computers, the software, or any part of the lab. The TAs are here to help, it is our job. During this course we will be using Unix interface so if you are unfamiliar with Unix, plan extra time for learning that as well

Cheat Sheets:

    Unix Cheat Sheet
    VI Cheat Sheet

Lecture notes (from 2016) :

    1/4/2016 Lectures 1 2016
    1/6/2016 Lectures 2 2016
    1/8/2016 Lectures 3 2016
    1/11/2016 Lectures 4 2016
    1/13/2016 Lectures 5 2016
    1/20/2016 Lectures 6 2016
    1/22/2016 Lectures 7 2016
    1/27/2016 Lectures 8 2016
    1/29/2016 Lectures 9 2016
    2/12/2016 Lectures 10/11 2016

Homework (2017):

    Problem Set 1 docx
    Problem Set 2 pdf
    Problem Set 3 pdf
    Problem Set 4 pdf
    Problem Set 5 pdf   modules   2pt guide

Homework (2016):

    Problem Set 1 pdf
    Problem Set 2 pdf
    Problem Set 3 pdf
    Problem Set 4 pdf

Homework (2015):

    Problem Set 1 pdf
    Problem Set 2 pdf
    Problem Set 3 pdf
    Problem Set 4 pdf in- and output input files tarball

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