2006 Summer School on Computational Materials Science
Ab Initio Molecular Dynamics Simulation Methods in Chemistry
July 31August 11, 2006 · University of Illinois at UrbanaChampaign
This summer school provides an overview of advanced
electronic structure and molecular dynamics methods and
their interplay in ab initio molecular dynamics (AIMD)
simulations. Theory and practical applications of both
density functional theory and wavefunctionbased electronic
structure methods are included, as well as classical and
quantum molecular dynamics. The goal of the school is to provide students with the
background necessary to understand and to use AIMD
simulation techniques. The school was July 31August 11,
2006 at the University of Illinois at UrbanaChampaign campus. The summer school lectures are held in the NCSA Building, 1205 W. Clark Street, Urbana.
AIMD School Program
The AIMD summer school includes focused sessions on the use and programming of high performance computing, and a handson introduction to the QuantumESPRESSO codes for electronic structure calculations, structural optimization, and ab initio molecular dynamics.
Participants should have some previous familiarity with either electronic structure theory or molecular dynamics techniques.
Lecture videos and presentation files on Ab Initio Molecular Dynamics
The presentation and lab files are available singly, or as one ZIP archive. The videos are available on Google video.
Topics and presenters, in chronological order
Videos 
Presentation and lab files 
Dave Ennis Ohio Supercomputer Center 

 Supercomputing History: KeyIdeas
 Parallel Programming with MPI

Stefano Baroni Sissa Trieste and DEMOCRITOS 
 General introduction to total energy and forces in DFT, and path finding methods
 Lecture 1 [Currently not available]
 Lecture 2 [Google video]
 Lecture 3 [Google video]

 Densityfunctional pertubation theory [pdf]
 Molecular structure and dynamics with DFT [pdf]
 Computer simulation of thermally activated processes [pdf]

Guido Fratesi University of Milan 
 Densityfunctional perturbation theory

 Structural Optimization [pdf]
 PWSCF First Examples [pdf]
 Rare Events [pdf]

Nicola Marzari MIT
Paolo Giannozzi Scuola Normale Superiore and DEMOCRITOS
Axel Kohlmeyer University of Pennsylvania 
 CarParrinello and BornOppenheimer molecular dynamics:
 Ab Initio Molecular Dynamics: Part One (Mazari) [Google video]
 Ab Initio Molecular Dynamics: Part Two (Mazari) [Google video]
 Introduction to CarParrinello Ab Initio MD (Giannozzi) [Google video]

 Ab Initio Molecular Dynamics: Part One [pdf]
 Ab Initio Molecular Dynamics: Part Two [pdf]

Week Two:
Topics and presenters, in chronological order
Videos 
Presentation and lab files 
Thom Dunning UIUC 
 Convergence in Electronic Structure Methods [Google video]
 Construction and Assessment of Basis Sets for Electronic Structure [Google video]

 Solution of the Electronic Schroedinger Equation
 Using Basis Sets to Solve the HartreeFockEquations [pdf]
 Using Basis Sets to Solve the Electronic Schrodinger Equation with Electron Correlation [pdf]
 Exercise: Systematic Improvement of Basic Sets [pdf]

Brett Bode Iowa State University 

 Lab: Quantum Chemistry with GAMESS [pdf]
 GAMESS and MACMOLPLT [pdf ,ppt]
 Lab: macmolplt.tar.gz [.gz]
 Lab: README.MacMolPlt [txt]

Marcus Elstner University of Heidelberg 
 Theory, Performance and Applications of DFTB [Google video]
 Theory and Implementation of QM/MM Schemes [Google video]
 Semiempirical Methods for Excited States and Dispersion [Google video]

 Introduction into DFTB: July 25, 2006 [pdf]
 Introduction into DFTB: July 28, 2006 [pdf]
 Introduction into DFTB: August 7, 2006 [pdf]
 Approximate methods for large molecular systems [ppt]
 DFT and VdV interactions [ppt]
 QM/MM Calculations and Applications to Biophysics [ppt]

Lubos Mitas North Carolina State University 
 Fundamentals of Quantum Monte Carlo [Google video]
 Applications of and Advances in QMC [Currently not available]

 Quantum Monte Carlo Methods [pdf]
 Quantum Monte Carlo Methods: recent developments and applications [pdf]
 Quantum Monte Carlo lab notes [pdf]

Spiridoula Matsika Temple University 
 Electronic Structure for Excited States (Multiconfigurational Methods) [Google video]
 Conical Intersections [Google video]

 Conical Intersections [pdf, ppt]
 Electronic Structure for Excited States [pdf, ppt]
 Lab: Multireference [pdf, doc]

Glenn Martyna IBM 

 Introduction to CarParrinello Ab Initio MD [pdf]
 Equations of Motion and Numerical Integration [pdf]
 Equilibrium Statistical Mechanics [pdf]

Victor Batista Yale University 

 Lecture Notes: Introduction to AIMD Simulations [pdf]
 Lecture Notes: Solutions to Problems [pdf]

Srinivasan Iyengar Indiana University 
 
Todd Martinez UIUC 

 Ab Initio Multiple Spawning Dynamics [pdf]
 Ab Initio Quantum Molecular Dynamics [pdf]
 Insights for LightDriven Molecular Devices from Ab Initio Multiple Spawning ExcitedState Dynamics of Organic and Biological Chromophores [pdf]
 Introduction to Full Multiple Spawning using MOPAC [pdf]

Jason Quenneville Los Alamos National Laboratory 

 Reactive Empirical Force Fields [pdf, ppt]

Alejandro Strachan Purdue University 
 Molecular Dynamics Modeling of Thermal and Mechanical Properties [Google video]

 Lab: deformation of nanoscale materials [pdf]
 Molecular dynamics modeling of thermal and mechanical properties [pdf, ppt]
 Exercise for Empirical Reactive Force Fields Shock compression of RDX [pdf]

Faculty presentations
Two faculty participants of the summer school gave presentations about their research and institutions, during the school.
 Huajun Fan, Prarie View A&M University, Nanoscale modeling with Undergraduates at Prairie View A&M University [pdf]
 Bothina Hamad, University of Jordan, Education and research in Jordan, challenges and outlooks [ppt]
Organizers
 AIMD: T. Martínez, D. Ceperley, R. Martin, and D. Johnson (UIUC)
 Quantum–ESPRESSO: N. Marzari (MIT) and P. Giannozzi (Scuola Normale Superiore, Pisa, and DEMOCRITOS, Trieste)
 HighPerformance Computing: J. Kim (UIUC)
Sponsors
The Summer School is held at University of Illinois at UrbanaChampaign campus and is sponsored in part by: