Simulation Methods in Physics II SS 2013

Exams

The following dates and times have been scheduled for the oral exams.Please send an e-mail (Maria Fyta, Jens Smiatek) noting your preference. We will send an e-mail back confirming (or not) the date.

Thu. Sep 19: 10:00, 11:00, 13:00, and 14:00

Overview

Type

Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)

Lecturer

JP. Dr. Maria Fyta, (Lecture); Dr. Jens Smiatek(Tutorials)

Course language

English

NO lecture on 11.07.The lecture on 18.07 will start earlier at 11am.

Lectures

Time: Thursdays, 11:30 - 13:00, ICP, Allmandring 3, Seminarroom 1

Exception: the lecture of 02.05 will NOT take place that day, but on 30.04 at 08:30-10:00.

Tutorials

Time: Tuesdays, 08:00-10:00, ICP, Allmandring 3, CIP-Pool

The tutorials have their own title "Simulationsmethoden in der Praxis", as they can be attended independently of the lecture and are in fact part part of the Physics MSc module "Fortgeschrittene Simulationsmethoden" and not of the module that contains the lecture "Simulation Methods in Physics II".

The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis. The tutorials build on each other, therefore continuous attendance is expected.

Scope

The course intends to give an overview about modern simulation methods used in physics today. The stress of the lecture will be to introduce different approaches to simulate a problem, hence we will not go too to deep into specific details but rather try to cover a broad range of methods. For an idea about the content look at the lecture schedule.

Prerequisites

We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations, as well as knowledge of a programming language. The knowledge of the previous course Simulation Methods I is expected.

Certificate Requirements

1. Attendance of the exercise classes

2. Obtaining 50% of the possible marks in the hand-in exercises

There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II) determined at the end of lecture Simulation Methods II.

The final grade will be determined in the following way: There will be an oral examination performed at (or after) the end of the course Simulation Methods II (SS 2012).

Recommended literature

• Daan Frenkel, Berend Smit.
  Understanding Molecular Simulation: From Algorithms to Applications.
  Part of Computational Science, volume 1. Edition 2.
  Academic Press, San Diego, 2002. ISBN: 978-0-12-267351-1.
  [DOI]
• Mike P. Allen, Dominik J. Tildesley.
  Computer Simulation of Liquids.
  Part of Oxford Science Publications. Edition 1.
  Clarendon Press, Oxford, 1987.
  
• D. C. Rapaport.
  The Art of Molecular Dynamics Simulation.
  Edition 2.
  Cambridge University Press, 2004. ISBN: 9780511816581.
  [DOI]
• D. P. Landau, K. Binder.
  A guide to Monte Carlo Simulations in Statistical Physics.
  Edition second edition.
  Cambridge, 2005.
  
• M. E. J. Newman, G. T. Barkema.
  Monte Carlo Methods in Statistical Physics.
  Edition 2002 edition.
  Oxford University Press, 1999.
  
• Sauro Succi.
  The lattice Boltzmann equation for fluid dynamics and beyond.
  Oxford University Press, New York, USA, 2001. ISBN: 9780198503989.
  [PDF] (13 MB)
• M. E. Tuckermann.
  Statistical Mechanics: Theory and Molecular Simulation.
  Oxfor University Press Oxford Graduate Texts, Oxford, 2010.
  
• Martin O. Steinhauser, Kai Grass, Elmar Strassburger, Alexander Blumen.
  Impact failure of granular materials – Non-equilibrium multiscale simulations and high-speed experiments.
  International Journal of Plasticity XXX:XXX, 2008.
  [PDF] (5.2 MB)
• F. Martin, H. Zipse.
  Charge Distribution in the Water Molecule - A Comparison of Methods.
  Journal of Computational Chemistry 26(1):97–105, 2004.
  
• E. Kaxiras.
  Atomic and electronic structure of solids.
  apud Cambridge, Cambridge, 2003.
  
• Andrew Leach.
  Molecular Modelling: Principles and Applications.
  apud Pearson Education Ltd., 2001. ISBN: 978-0582382107.
  

Useful online resources

• Roethlisberger, Tavernarelli, EPFL, Lausanne, 2011: Introduction to electronic structure methods.

• E-Book: Kieron Burke et al.,University of California, 2007: E-Book: The ABC of DFT.

• Linux cheat sheet here (53 KB).

• A good and freely available book about using Linux: Introduction to Linux by M. Garrels

• Not so frequently asked questions about GNUPLOT

• Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)

• Short introduction to shell scripting (bash)

• A more detailed introduction to bash scripting

• MIT Opencourseware "Reactive potentials and applications"

• University of Virginia, Introduction to atomistic simulations

• Principles of Multiscale Modeling, Weinan E (2011)

• Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.

Lecture

To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.

A script on the course material is now available, thanks to Larissa Dill Script (670 KB).

Date	Subject	Resources
11.04.2013	Introduction, electronic stucture	Lecture Notes (3.19 MB)
18.04.2013	Elements of quantum mechanics, Hartree and Hartree-Fock approximations	Lecture Notes (3.22 MB)
25.04.2013	Density functional theory (DFT), functionals, pseudopotentials, elements of solid state physics	Lecture Notes (5.51 MB)
30.04.2013	Time-dependent density functional theory, post-Hartree-Fock methods	Lecture Notes (5.12 MB)
09.05.2013	Holiday (Christi Himmelfahrt)
16.05.2013	QM forces, energy minimization, CPMD, quantum Monte Carlo, QM/MM, tight-binding	Lecture Notes (7.41 MB)
23.05.2013	Holiday (Pfingsten)
30.05.2013	Holiday (Fronleichnam)
06.06.2013	Classical force fields, explicit water models	Lecture Notes 1 (3.1 MB), Lecture Notes 2 (2.11 MB)
13.06.2013	Implicit solvent models	Lecture Notes (4.71 MB)
20.06.2013	MD simulations of biomolecules, force fields	Lecture Notes (5.91 MB)
27.06.2013	Hydrodynamic methods: Brownian Dynamics, DPD, Lattice-Boltzmann	Lecture Notes (4.66 MB)
04.07.2013	Interatomic potentials	Lecture Notes (4 MB)
11.07.2013	Cancelled	[]
18.07.2013	EAM, coarse-graining and nuggets on multiscale simulations	Lecture Notes 1 (2.04 MB), Lecture Notes 2 (5.96 MB)

Tutorials

• The tutorials will take place on Tuesdays between 8-10 am in the ICP CIP-Pool.

• New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 18.04. The following week is dedicated to working on problems related to the last worksheet. Homework in the form of a report should be sent to Jens Smiatek before the next worksheet will be handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.

Work sheets

• Worksheet 1 (zip-File with SIESTA input files and attachments) Quantum mechanical approaches - Hückel approximation and DFT methods
  • Worksheet 1 (the work sheet as a single PDF file)
  • SIESTA Download
  • SIESTA Installation Guide
  • Hands-on-tutorial for SIESTA, Lyon 2007

• Worksheet 2 (zip-File with si.fdf) Properties of fermions and Density functional theory

• Worksheet 3 (zip-File with water topology and input files for GROMACS) Diffusion processes and atomistic water model properties
  • Worksheet 3 (the work sheet as a single PDF file)
  • GROMACS Download

• Worksheet 4 (zip-File with input files) All-atom Molecular Dynamics simulations of the alanine dipeptide
  • Worksheet 4 (the work sheet as a single PDF file)
  • GROMACS Download
  • GROMACS Manual
  • Example: How to set up a GROMACS simulation
  • How to visualize GROMACS trajectories with VMD

• Worksheet 5 (zip-File with script files for ESPResSo) Coarse-grained simulations with ESPResSo
  • Worksheet 5 (the work sheet as a single PDF file)
  • ESPResSo-Homepage
  • ESPResSo-Download
  • ESPResSo-Manual

Examination

Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:

BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP

• Obtain 50% of the possible points in the hands-in excercises of this lecture as well as for the first part of the lecture as a prerequisite for the examination (USL-V)
• 60 min of oral examination (PL)
  • After the lecture (i.e. Summer 2013)
  • Contents: both lectures and the excercises of "Simulation Methods in Physics I"

International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005)

• Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination
• 30 min of oral examination (PL) about the lecture and the excercises

BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????)

• Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)
• 40 min of oral examination (PL) about the lecture and the excercises

MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????)

• The marks for the module are the marks obtained in the excercises (BSL)