University of Virginia, Department of Materials Science and Engineering Fall 2009, Tuesday and Thursday, 12:30-13:45 Wilsdorf Hall, Room 101
Click on pictures above to learn more about the corresponding projects	MSE 4592/6270: 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: 09f-mse-4592-6270@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 (pdf, 2.1 Mb)
  article by R. LeSar and D. C. Chrzan, (pdf, 312 kB)
  article by R. Gomperts, E. Renner, and M. Mehta, (pdf, 394 kB)
  article by U. Landman, (pdf, 779 kB)
  • 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 (pdf, 106 Kb)
  • The basics of classical molecular dynamics    Handouts (pdf, 1.1 Mb),  Listing of MD code (pdf, 72 Kb)
    First MD papers by Gibson et al. (pdf, 4.4 MB) and Rahman (pdf, 1.1 MB)
    A recent paper on the quest for the record time (milliseconds) MD simulations Nature08 (pdf, 1 MB)
    
  • Initial conditions, creating lattice structures, introducing defects   Handouts (pdf, 165 Kb)
  • Defining and maintaining temperature and pressure   Handouts on pressure (pdf, 80 Kb)
  • Boundary conditions (free, periodic, stochastic, conducting, non-reflecting)   Handouts (pdf, 970 Kb)
  • 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 (pdf, 246 Kb)
  • 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 (pdf, 1.6 Mb)
  • Lecture on Direct Simulation Monte Carlo by Alexey Volkov   Handouts (pdf, 660 Kb)
  
  
• Interatomic potentials     Handouts (pdf, 300 Kb)
  Handouts on EAM and Tersoff potentials by Prof. Robert A. Johnson (pdf, 5 Mb)
  • 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 (pdf, 1 Mb)
  • Structural properties (geometrical tessellation, pair correlation functions, atomic-level stresses)
    
  • Dynamic properties (diffusion, time correlation functions)   Handouts on diffusion (pdf, 259 Kb)
  
  
• 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
  • An example VRML code for visualization of an atomic structure (requires a VRML plugin)

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)

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 for discussion

Title	Author(s)	Source	Discussion Leader	Day
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)	Bing Hao	October 29
Diffusion of nanoclusters	P. Jensen, A. Clement, L. J. Lewis	Computational Materials Science 30, 137-142 (2004), PDF (422 Kb)	Qiang Qian	November 10
Atomistic simulation of an f.c.c./b.c.c. interface in Ni-Cr alloys	J. K. Chen, D. Farkas and W. T. Reynolds Jr	Acta Materialia 45, 4415 (1998), PDF (515 Kb)	Xiaowei Liu	November 12
Amorphization and Fracture in Silicon Diselenide Nanowires: A Molecular Dynamics Study	W. Li, R. K. Kalia, P. Vashishta	Phys. Rev. Lett. 77, 2241 (1996), PDF (228 kB)	Wenjing Yin	November 17
Microscopic view of structural phase transitions induced by shock waves	K. Kadau, T. C. Germann, P. S. Lomdahl, B. L. Holian	Science 296, 1681 (2002), PDF (994 kB)	Harmonie Sahalov	November 19
Calculations of the thermal conductivities of ionic materials by simulation with polarizable interaction potentials	N. Ohtori, M. Salanne, P. A Madden	J. Chem. Phys. 130, 104507 (2009), PDF (334 kB)	Theron Rodgers	November 24
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)	Hui Xu	November 24
Multiscale modeling approach for calculating grain-boundary energies from first principles	O. A. Shenderova, D. W. Brenner, A. A. Nazarov, A. E. Romanov, L. H. Yang	Phys. Rev. B 57, R3181 (1998), PDF (110 kB)	Priya Ghatwai	December 1
Molecular dynamics study of self-diffusion in bcc Fe	M. I. Mendelev, Y. Mishin	Phys. Rev. B 80, 144111 (2009), PDF (578 kB)	Chengping Wu	December 1
Drag on a nanotube in uniform liquid argon flow	W. Tang and S. G. Advani	J. Chem. Phys. 125, 174706 (2006), PDF (751 Kb)	David Nicholson	December 3
Brine rejection from freezing salt solutions: A molecular dynamics study	L. Vrbka, P. Jungwirth	Phys. Rev. Lett. 95, 148501 (2005), PDF (1.2 Mb)	Jukka-Pekka Kaikkonen	December 3
Molecular dynamics simulation of the thin film deposition of Co/Cu(111) with Pb surfactant	B.-H. Kim and Y.-C. Chung	J. Appl. Phys. 106, 044304 (2009), PDF (355 Kb)	Qiaohua Tan	December 8
Connecting atomistic and mesoscale simulations of crystal plasticity	V. Bulatov, F. F. Abraham, L. Kubin, B. Devincre, S. Yip	Nature 391, 669 (1998), PDF (429 Kb)
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)
Low-speed fracture instabilities in a brittle crystal	J. R. Kermode, T. Albaret, D. Sherman, N. Bernstein, P. Gumbsch, M. C. Payne, G. Csanyi, A. De Vita	Nature 455, 1224 (2008), PDF (713 Kb)
Interfacial thermal conductance between silicon and a vertical carbon nanotube	M. Hu, P. Keblinski, J.-S. Wang, and N. Raravikar	J. Appl. Phys. 104, 083503 (2008), PDF (458 kB)
Microscopic insights into the sputtering of thin organic films on Ag{111} induced by C60 and Ga bombardment	Z. Postawa, B. Czerwinski, N. Winograd, and B. J. Garrison	J. Phys. Chem. B 109, 11973 (2005), PDF (983 kB)
How Fast Can Cracks Propagate?	F. F. Abraham & H. Gao	Phys. Rev. Lett. 84, 3113 (2000), PDF (144 kB)
Dynamics of nanoscale jet formation and impingement on flat surfaces	S. Murad and I. K. Puri	Physics of Fluids 19, 128102 (2007), PDF (697 kB)
Molecular dynamics study of martensitic transformations in sintered Fe-Ni nanoparticles	K. Kadau, P. Entel, and P. S. Lomdahl	Comp. Phys. Commun. 147, 126-129 (2002), PDF (715 Kb)
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)
Molecular dynamics study of solid thin-film thermal conductivity	J. R. Lukes, D. Y. Li, X.-G. Liang, C.-L. Tien	Journal of Heat Transfer 122, 536-543 (2000), PDF (624 Kb)
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing	V. S. Pande, I. Baker, J. Chapman, S. P. Elmer, S. Khaliq, S. M. Larson, Y. M. Rhee, M. R. Shirts, C. D. Snow, E. J. Sorin, B. Zagrovic	Biopolymers 68, 91-109 (2003), PDF (746 Kb) Also see this link
Changing Shapes in the Nanoworld	N. Combe, P. Jensen and A. Pimpinelli	Phys. Rev. Lett. 85, 110-113 (2000), PDF (260 kB)
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)
Experiment and simulation of cluster emission from 5 keV Ar ­> Cu	T. J. Colla, H. M. Urbassek, A. Wucher, C. Staudt, R. Heinrich, B. J. Garrison, C. Dandachi und G. Betz	Nucl. Instrum. Meth. B 143, 284-297 (1998), PDF (1 Mb)
Plastic flow localization in irradiated materials: a multiscale modeling approach	T. Diaz de la Rubia, H. M. Zbib, T. A. Khraishi, B. D. Wirth, M. Victoria, M. J. Caturla	Nature 406, 871 (2000), PDF (413 Kb)
Test of the Universal Scaling Law for the Diffusion Coefficient in Liquid Metals	J. J. Hoyt, M. Asta, B. Sadigh	Phys. Rev. Lett. 85, 594 (2000), PDF (85 kB)
A simple model for the growth of polycrystalline Si using the kinetic Monte Carlo simulation	S. W. Levine and P. Clancy	Modelling Simul. Mater. Sci. Eng. 8, 751 (2000), PDF (631 kB)
Diffusion limited biofilm growth	P. Gonpot, R. Smith and A. Richter	Modelling Simul. Mater. Sci. Eng. 8, 707 (2000), PDF (1 MB)
Mesoscopic scale simulation of dislocation dynamics in fcc metals: Principles and applications	M Verdier, M Fivel and I Groma	Modelling Simul. Mater. Sci. Eng. 6, 755 (1998), PDF (486 kB)
Multi-lattice Monte Carlo model of thin films	H. Huang and G.H. Gilmer	Journal of Computer-Aided Materials Design 6, 117 (1999), PDF (635 kB)

"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