Atomic Scale Simulations @ UFABC


When: May 15 – May 26, 2017
Where: Universidade Federal do ABC, Santo André - SP, Brazil
Location lectures, morning (10-12): Auditorium A-111 Santo André
Location hands-on session, afternoon (14-16): Computer rooms L504B and L505B

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What To Expect:

This 2-week intensive course aims at senior undergraduate, graduate, and postdoctoral scholars. Attendees will be introduced to:

  • the theoretical background of powerful modern molecular dynamics and Monte-Carlo schemes,
  • predictive quantum-mechanical approaches such as density functional theory,
  • hands-on experience with Python coding, visualization, and running own simulations using freely available open-source software packages.


Morning lectures provide theoretical background and afternoons are for hands-on practice and implementation in computer labs. This combination conveys good understanding of all theoretical approaches. Attendees will develop their own ideas for a toy problem, implement small parts of code if necessary, run simulations, and write a short report on results and obstacles encountered.

Course Description:

This class covers computational techniques for microscopic systems ranging from a few up to millions of atoms. Molecular dynamics provides exciting insight into the dynamic aspect of thermodynamic phase-space averages. Important concepts, such as potential-energy surfaces, classical potentials, and their quantum-mechanical foundation will be outlined. Connections to accurate, computationally expensive methods, e.g.  those based on density functional theory will be pointed out. Furthermore, this class covers probabilistic Monte-Carlo techniques, that differ conceptually: The idea of probabilistic integration, Markov-Chain approaches, and Metropolis Monte-Carlo will be presented. Examples for practical applications of the different techniques are discussed throughout.


Monday, May 15:

Morning, 10-12 (Lecture): "Statistical Mechanics Review"
Afternoon, 14-16 (Hands-on): "Python and Visualization"

Tuesday, May 16:

Morning, 10-12 (Lecture): "Molecular Dynamics"
Afternoon, 14-16 (Hands-on): "Statistical Data Analysis"

Wednesday, May 17:

Morning, 10-12 (Lecture): "Potentials in Molecular Dynamics"
Afternoon, 14-16 (Hands-on): "Lennard-Jones Molecular Dynamics "

Thursday, May 18:

Morning, 10-12 (Lecture): "Correlations and Thermostats"
Afternoon, 14-16 (Hands-on): "Temperature and Structure Factor in Molecular Dynamics"

Friday, May 19:

Morning, 10-12 (Lecture): "Quantum Simulations"
Afternoon, 14-16 (Hands-on): "Running LAMMPS (an open-source molecular dynamics package)"

Monday, May 22:

Morning, 10-12 (Lecture): "Probability Tools and Random Number Generators"
Afternoon, 14-16 (Hands-on): "Implementing and characterizing a random number generator"

Tuesday, May 23:

Morning, 10-12 (Lecture): "Markov Chains and Metropolis Monte Carlo I" and "Markov Chains and Metropolis Monte Carlo II"
Afternoon, 14-16 (Hands-on): "Writing a Monte-Carlo Code"

Wednesday, May 24:

Work on project

Thursday, May 25:

Morning, 10-12 (Lecture): "Directed Monte-Carlo, Kinetic Monte Carlo"
Afternoon, 14-16 (Hands-on): Develop and work on project

Friday, May 26:

Morning, 10-12 (Lecture): "Ising Model, Crystal structure search, Free energy"
Afternoon, 14-16 (Hands-on): Project presentations/discussions


Please contact André Schleife ( or Cedric Rocha Leao (!