University of Virginia, Department of Materials Science and Engineering Fall 2011, Tuesday and Thursday, 20:00 - 21:15 Thornton Hall A, Room 119
Click on pictures above to learn more about the corresponding projects	MSE 4270/6270: Introduction to Atomistic Simulations Instructor: Leonid V. Zhigilei Office: Wilsdorf Hall, Room 303D Office Hours: open Telephone: (434) 243 3582 E-mail: lz2n@virginia.edu Web: http://www.people.virginia.edu/~lz2n/mse627/ Class e-mail list: 11f-mse-4270-6270@collab.itc.virginia.edu

The emphasis of the course is on getting practical experience in designing and performing computer simulations. Pre-written codes implementing atomistic computational methods will be provided. Students will use and modify the pre-written codes and write their own simulation and data analysis codes while working on their homework assignments and term projects. A set of example problems for term project will be provided, although students are encouraged to choose a project relevant to their thesis research.

Recent research articles in the area of atomistic modeling will be discussed, with each student presenting one or two article. Students will learn to assess the quality and significance of published computational results.

Syllabus (pdf, 29 Kb)

Topics that will be covered include:

• Introduction      Handouts
  article by R. LeSar and D. C. Chrzan
  article by R. Gomperts, E. Renner, and M. Mehta
  article by U. Landman
  NSF White Paper on "Matter by design"
  NSF White Paper on "Computational Science"
  • Spatial and temporal hierarchy of microstructure and dynamics in materials
  • Types of models: quantum mechanical, atomistic, mesoscopic, continuum
  • Multiscale approaches
  
  
• Atomistic models: Molecular dynamics
  • Ordinary differential equations for particle dynamics    Handouts
  • The basics of classical molecular dynamics    Handouts,   Listing of MD code
    First MD papers by Gibson et al. (pdf, 4.4 MB) and Rahman (pdf, 1.1 MB)
    Recent papers on the quest for the record time (milliseconds) MD simulations Nature08 (pdf, 1 MB)
    and record length-scale (trillions of atoms) MD simulations IJMPC08 (pdf, 410 kB)
    
  • Initial conditions, creating lattice structures, introducing defects   Handouts
  • Defining and maintaining temperature and pressure   Handouts on pressure (pdf, 80 Kb)
  • Boundary conditions (free, periodic, stochastic, conducting, non-reflecting)   Handouts
  • Methods for constant temperature or/and pressure simulations   Handouts (pdf, 210 Kb)
  • Tricks of the trade (neighbor lists, force/energy tables, potential cutoffs, etc.)
    Article on tabulated potentials by Wolff and Rudd (pdf, 178 Kb)
    Article on cell-linked neighbor list method by Mattson and Rice (pdf, 480 Kb)
  
  
• Monte Carlo methods   Handouts
  • The basics of Monte Carlo
  • Monte Carlo integration, thermodynamic averages
  • Importance sampling, Metropolis scheme
  • Lattice Monte Carlo, Ising model
  • Multi-state Potts models (grain coarsening, recrystallization)
  • Kinetic Monte Carlo (surface processes, thin film growth)   Handouts
  • Lecture on Direct Simulation Monte Carlo by Alexey Volkov   Handouts
  
  
• Interatomic potentials     Handouts
  Handouts on EAM and Tersoff potentials by Prof. Robert A. Johnson
  • Introduction, Born-Oppenheimer approximation
  • Pair potentials and their limitations
  • Calculation of elastic constants from potential function
  • Potentials for ionic systems, ceramics
  • Many-body potentials for metallic systems
  • Many-body potentials for covalently bounded systems
  • Forces from "first principles" (time permitting)
  
  
• Analysis of the simulation results
  • Equilibrium properties (energy, temperature, pressure, velocity distributions)   Handouts
  • Structural properties (geometrical tessellation, pair correlation functions, atomic-level stresses)
    Handouts on correlation functions
  • Dynamic properties (diffusion, time correlation functions)   Handouts on diffusion
  
  
• Mesoscopic methods (time permitting)    
  • Discrete dislocation dynamics
    • Strain and stress fields for edge and screw dislocations in an isotropic medium
    • The equation of motion in Newtonian Dislocation Dynamics
    • Examples from 2D and 3D simulations
    • Current problems
  • Coarse-grained models for organic materials
  
  
• Bridging the scale gaps between different simulation levels
  • Simultaneous integration of the models
  • Sequential integration of the models (hierarchical approach)
  • Examples of combined methods (MD-FEM, MD-MC, etc.)
  
  
• Computer use
  • Introduction to UNIX, Networking, and visualization
    Unix help and a simple Fortran code,   Introduction to GNUPLOT by Eduardo Bringa
  • Visualization (VRML, Java-applets, animated gifs, animations with Tecplot)  
  
  
• Codes to be provided
  • MSE627-MD code for MD/MC simulation
  • MSE627-CG crystal generator (FCC, BCC, diamond)
  • MSE627-MC Ising model for binary alloys

Term project

Objective: To get experience in designing and performing computer simulations.

Parts of the project:

1. Design (or adapt an idea from literature) a simulation that is of scientific or computational interest to you
2. Choose and justify a computational approach appropriate for the problem of interest
3. Write the code (or parts of the code that have not been supplied)
4. Run simulations and analyze the results
5. Prepare a report; include electronic copies of your code
6. Make a short presentation to the class (mini-symposium)

Tentative program of the mini-symposium can be found here

A set of example problems for term projects can be found here.

Projects: A problem chosen for the term project should have some science content and be doable in the timeframe of one semester. Students are encouraged to choose a project relevant to their thesis research. If the intention is to continue computational work in the future, the term project may be a well-defined part of a larger research project.

Discussion of published research articles

Each student will lead at least two discussions of a recent research paper in the area of atomistic simulations (~10-15 min). Although a few papers will be proposed by instructor, students are encouraged to propose papers that are interesting or relevant to their research work (but not to the term project). Papers will be distributed at least one week before the discussion.

Examples of research articles (from past discussions)

Title	Author(s)	Source	Discussion Leader	Day
Multiple shear banding in a computational amorphous alloy model	M. Wakeda, Y. Shibutani, S. Ogata, J. Park	Appl. Phys. A 91, 281 (2008), PDF (400 kB)	Cheng-Yu Shih	Tuesday, October 18
Molecular dynamics simulations of arbon nanotubes in water	J. H. Walther, R. Jaffe, T. Halicioglu, P. Koumoutsakos	Center for Turbulence Research, Proceedings of the Summer Program, pp. 5-20 (2010), PDF (402 kB)	Karen Long	Thursday, October 27
Locally activated Monte Carlo method for long-time-scale simulations	M. Kaukonen, J. Peräjoki and R. M. Nieminen	Phys. Rev. B 61, 980 (2000), PDF (94 kB)	Xuhui Feng	Thursday, October 27
Hierarchical models of plasticity: dislocation nucleation and interaction	R. Phillips, D. Rodney, V. Shenoy, E. Tadmor and M. Ortiz	Modelling Simul. Mater. Sci. Eng. 7, 769 (1999), PDF (990 kB)	Brad Richards	Thursday, October 27
Molecular dynamics simulation of the contact angle of liquids on solid surfaces	B. Shi, V. K. Dhir	J. Chem. Phys. 130, 034705 (2009), PDF (268 kB)	Jayaprakash Srinivasan	Tuesday, November 1
A molecular dynamics study of the graphitization ability of transition metals for catalysis of carbon nanotube growth via chemical vapor deposition	Y. Shibuta, J.A. Elliott	Chem. Phys. Lett. 472, 200 (2009), PDF (2.2 MB)	Brandon McClimon	Thursday, November 3
Actuation of a suspended nano-graphene sheet by impact with an argon cluster	N. Inui, K. Mochiji, K. Moritani	Nanotechnology 19, 505501 (2008), PDF (820 kB)	Rebecca Conti	Monday, November 7
Molecular dynamics simulations of carbon nanotube-based gears	J. Han, A. Globus, R. Jaffe, G. Deardorff	Nanotechnology 8, 95 (1997), PDF (816 kB)	Bernard Wittmaack	Monday, November 7
Photodesorption of water ice: A molecular dynamics study	S. Andersson, E.F. van Dishoeck	Astronomy and Astrophysics 491, 907 (2008), PDF (580 kB)	Micah Schaible	Monday, November 7
Gallium-induced milling of silicon: A computational investigation of focused ion beams	M.F. Russo,Jr., M. Maazouz, L.A. Giannuzzi, C. Chandler, M. Utlaut, B.J. Garrison	Microsc. Microanal. 14, 315 (2008), PDF (390 kB)	Christopher Duska	Monday, November 7
Molecular dynamics study of self-diffusion in bcc Fe	M. I. Mendelev, Y. Mishin	Phys. Rev. B 80, 144111 (2009), PDF (578 kB)	Thomas Lawlor	Monday, November 7
Thermal transport in graphene and effects of vacancy defects	H. Zhang, G. Lee, K. Cho	Phys. Rev. B 84, 115460 (2011), PDF (660 kB)	Nam Le	Monday, November 7
Pillared graphene: A new 3-D network nanostructure for enhanced hydrogen storage	G.K. Dimitrakakis, E. Tylianakis, G. E. Froudakis	Nano Lett. 8, 3166 (2008), PDF (2.1 MB)	Chris Baker	Monday, November 7
Atomic-level characterization of the structural dynamics of proteins	D.E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R.O. Dror, M.P. Eastwood, J.A. Bank, J.M. Jumper, J.K. Salmon, Y. Shan, W. Wriggers	Science 330, 341 (2010), PDF (2.6 MB)	Christoph Klein	Monday, November 7
Simulation of the formation and morphology of ice mantles on interstellar grains	H.M. Cuppen, E. Herbst	Astrophys. J. 668, 294 (2007), PDF (700 kB)	Herbert Ryan	Monday, November 7
Epitaxial growth of Si1-xGex on Si(100)2x1: A molecular-dynamics study	S. Ethier, L. J. Lewis	J. Mater. Res. 7, 2817 (1992), PDF (1.0 MB)	Gopalakrishnan Ramalingam	Thursday, November 10
Molecular dynamics simulation of ice nucleation and growth process leading to water freezing	M. Matsumoto, S. Saito, I. Ohmine	Nature 416, 409 (2002), PDF (573 kB)	Kevin Duvall	Thursday, November 10
Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals	M. S. Daw, M. I. Baskes	Phys. Rev. B 29, 6443-6453 (1984), PDF (1.2 MB)	Jayendran Srinivasan	Tuesday, November 29
Brine rejection from freezing salt solutions: A molecular dynamics study	L. Vrbka, P. Jungwirth	Phys. Rev. Lett. 95, 148501 (2005), PDF (1.2 Mb)	Tyler Owens	Thursday, December 1
Molecular dynamics simulations of stress-induced phase transformations and grain nucleation at crack tips in Fe	A. Latapie and D. Farkas	Modelling Simul. Mater. Sci. Eng. 11, 745-753 (2003), PDF (1.2 Mb)	Jishnu Bhattacharyya	Thursday, December 1
Extended Finnis-Sinclair potential for bcc and fcc metals and alloys	X.D. Dai, Y. Kong, J.H. Li, B.X. Liu	J. Phys.: Condens. Matter 18, 4527 (2006), PDF (740 kB)	Max Lupton	Thursday, December 1
Interfacil thermal conductance between silicon and a vertical carbon nanotube	M. Hu., P. Keblinski, J.-S. Wang, N. Raravikar	J. Appl. Phys. 104, 083503 (2008), PDF (465 kB)	Justin Smoyer	Thursday, December 1

"It is also a good rule not to put overmuch confidence in the observational results that are put forward until they are confirmed by theory."
        Sir Arthur Stanley Eddington

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lz2n@virginia.edu     Computational Materials Group     Materials Science & Engineering