2006 Summer School on Computational Materials Science

Ab Initio Molecular Dynamics Simulation Methods in Chemistry

2006 Icon 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 wavefunction-based 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 31-August 11, 2006 at the University of Illinois at Urbana-Champaign 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 hands-on introduction to the Quantum-ESPRESSO 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: Key-Ideas
  • 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]
  • Density-functional pertubation theory [pdf]
  • Molecular structure and dynamics with DFT [pdf]
  • Computer simulation of thermally activated processes [pdf]
Guido Fratesi University of Milan
  • Density-functional 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
  • Car-Parrinello and Born-Oppenheimer molecular dynamics:
  • Ab Initio Molecular Dynamics: Part One (Mazari) [Google video]
  • Ab Initio Molecular Dynamics: Part Two (Mazari) [Google video]
  • Introduction to Car-Parrinello 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 Hartree-Fock-Equations [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: Multi-reference [pdf, doc]
Glenn Martyna IBM
  • Introduction to Car-Parrinello Ab Initio MD [pdf]
  • Equations of Motion and Numerical Integration [pdf]
  • Equilibrium Statistical Mechanics [pdf]

Victor Batista Yale University
  • Grid-Based Wavepacket Propagation [Google video]
  • Matching Pursuit Wavepacket and Density Matrix Methods [Google video]
  • Lecture Notes: Introduction to AIMD Simulations [pdf]
  • Lecture Notes: Solutions to Problems [pdf]

Srinivasan Iyengar Indiana University
  • Atom Centered Density Matrix Propagation [Google video]
  • Quantum Wavepacket Ab Initio Molecular Dynamics [Google video]
Todd Martinez UIUC
  • Ab Initio Multiple Spawning Dynamics [pdf]
  • Ab Initio Quantum Molecular Dynamics [pdf]
  • Insights for Light-Driven Molecular Devices from Ab Initio Multiple Spawning Excited-State 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, Nano-scale modeling with Undergraduates at Prairie View A&M University [pdf]
  • Bothina Hamad, University of Jordan, Education and research in Jordan, challenges and outlooks [ppt]


  • 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)
  • High-Performance Computing: J. Kim (UIUC)


The Summer School is held at University of Illinois at Urbana-Champaign campus and is sponsored in part by: