MSE485/PHYS466/CSE485 :: MatSE Illinois :: University of Illinois at Urbana-Champaign

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i>clickers

We will be using i>clickers in every lecture. You can use either the older v1 or the newer v2 i>clickers. If you have not already done so, please register your clicker by visiting the MSE485 page in Compass. The navigation bar on the left should have an item "Register my i>clicker". The proven, educational benefit of using i>clickers depends on your active participation. Having another student answer questions using your clicker is considered cheating.

Online discussion forum

This class uses Piazza for announcements, updates, and all communication between the instructor, TAs, and students. Please visit this page to register.

Excused Absences

Excused absences may be requested by filling out the Excused Absences form. For more information, please read the course syllabus.

Schedule

All lectures will be recorded and the recordings will be posted under this link.

Date Reading Description Assignment due
M Aug 24 Orientation and Introduction
W Aug 26 Old lecture notes, Frenkel Smit (Chapter 4 and Appendix D), LeSar (Appendix G) Statistics and Errors I
F Aug 28 Old lecture notes, Frenkel Smit (Chapter 4 and Appendix D), LeSar (Appendix G) Statistics and Errors II
M Aug 31 Statistical Errors and Python Intro, iPython Notebook Statistics Errors,
W Sep 2 Old lecture notes, Frenkel Smit (Chapter 2), LeSar (Appendix D, G) Bias and Statistical Mechanics I
F Sep 4 Old lecture notes, Frenkel Smit (Chapter 2), LeSar (Appendix D, G) Statistical Mechanics II HW1 (IPYNB, PDF) due (upload here)
M Sep 7 Labor Day
W Sep 9 Molecular Dynamics (Overview)
F Sep 11 NO CLASS
M Sep 14 Old lecture notes 1, Old lecture notes 2, Frenkel Smit (Chapter 4), LeSar (Chapter 3) Molecular Dynamics: Boundary conditions and initial conditions
W Sep 16 Old lecture notes, Frenkel Smit (Appendix F), LeSar (Chapter 5) Molecular Dynamics: Forces and Integrators
F Sep 18 Old lecture notes, Frenkel Smit (Appendix F), LeSar (Chapter 5) Molecular Dynamics: Integrators, Code, Potentials I HW2 (IPYNB, PDF) due (upload here), solutions (PDF)
M Sep 21 Old lecture notes, Frenkel Smit (Chapter 4), LeSar (Chapter 5) Molecular Dynamics: Potentials II
W Sep 23 Old lecture notes, Frenkel Smit (Chapter 4), LeSar (Chapter 5) Molecular Dynamics: Potentials III
F Sep 25 Old lecture notes Potentials; Scalar Correlations
M Sep 28 Old lecture notes I, Old lecture notes II, Frenkel Smit (Chapter 6, Appendix B, C, E), LeSar (Chapter 6) Order parameters; Scalar Correlations
W Sep 30 Old lecture notes I, Old lecture notes II, Frenkel Smit (Chapter 6, Appendix B, C, E), LeSar (Chapter 6) Dynamical Correlations, Thermostats
F Oct 2 Thermostats and Quantum Mechanics HW3 (IPYNB, PDF) due (upload here), solutions
M Oct 5 Quantum Interactions and Density Functional Theory
W Oct 7 Random Numbers
F Oct 9 Random Number Generators
M Oct 12 Old lecture notes Tests for Random Number Generators
W Oct 14 Old lecture notes I, Old lecture notes II, Old lecture notes III, Frenkel Smit (Chapter 3), LeSar (Chapter 7) Non-uniform distribution, Variance reduction I
F Oct 16 Old lecture notes, Frenkel Smit (Chapter 3) Non-uniform distribution, Variance reduction II HW4 (IPYNB, PDF) due (upload here), solutions
M Oct 19 Old lecture notes, Frenkel Smit (Chapter 3) Markov Chains and Metropolis Monte Carlo
W Oct 21 Old lecture notes, Frenkel Smit (Chapter 13) Metropolis Monte Carlo II
F Oct 23 Old lecture notes, Frenkel Smit (Chapter 13, 17) Directed Monte-Carlo, Brownian Dynamics
M Oct 26 Old lecture notes, Frenkel Smit (Chapter 8), LeSar (Chapter 9) Brownian Dynamics, Kinetic Monte Carlo
W Oct 28 Kinetic Monte Carlo II
F Oct 30 Old lecture notes, Frenkel Smit (Chapter 7, 11) Free-energy methods I HW5 (IPYNB, PDF) due (upload here), solutions
M Nov 2 Old lecture notes, Frenkel Smit (Chapter 7, 11) Widom and Bennett method
W Nov 4 FS: Chapter 15 Constraints in MD
F Nov 6 Old lecture notes I, Article, LeSar (Chapter 7) Ising model I
M Nov 9 Constraints; Ising model II 1 slide proposals due (upload here)
W Nov 11 Project proposals I
F Nov 13 Project proposals II
M Nov 16 Polymers
W Nov 18 Old lecture notes Finite-Size Scaling
F Nov 20 Beyond Density Functional Theory HW6 (IPYNB, PDF) due (upload here)
M Nov 23 Thanksgiving Break
W Nov 25 Thanksgiving Break
F Nov 27 Thanksgiving Break
M Nov 30 Special 1: Crystal-Structure Prediction
W Dec 2 Quantum Monte Carlo I
F Dec 4 Quantum Monte Carlo II
M Dec 7 Special 2: Thermodynamics
W Dec 9 NO CLASS final reports due (upload here)
Thu Dec 17 FINAL: Presentations final presentations due (upload here)

Course Description

Scope

This class connects simulation results and properties of materials (structural or thermodynamic quantities), as well as numerical algorithms and systematic and statistical error estimations. Students will become familiar with molecular dynamics (integration algorithms, static and dynamic correlations functions and their connection to order and transport), Monte Carlo and Random Walks (variance reduction, Metropolis algorithms, Kinetic Monte Carlo, heat diffusion, Brownian motion), phase transitions (melting-freezing, calculating free energies), polymers (growth and equilibrium structure), quantum simulation (zero temperature and finite temperature methods), optimization techniques (e.g. simulated annealing).

Objectives

The objective is to learn and apply fundamental techniques used in (primarily classical) simulations in order to help understand and predict properties of microscopic systems in materials science, physics, chemistry, and biology. Students will work towards a final project, where they will define, model, implement, and study a particular problem using atomic-scale simulation techniques.

Course Grading

Grading

Your final grade for this class will be based upon your total score on all the components of the course. Please consult the course syllabus for details on particular components.

Course Component Percentage of total
Homework50
In-lecture i>clicker10
Project Proposal10
Final Presentation15
Final Report15

Final Grade

The following cutoff table will be used to calculate final scores.

Final Grade Minimum Points
A+ 97
A 93
A– 90
B+ 87
B 83
B– 80
C+ 77
C 73
C– 70
D+ 67
D 63
D– 60
F <60