Simulation Methods in Physics II SS 2012

Overview

Type

Lecture (2 SWS) and Tutorials (2 SWS)

Lecturer

Prof. Dr. Christian Holm, (Lecture); Peter Košovan, Florian Dommert, Georg Rempfer, Tobias Richter (Tutorials)

Course language

English

Lectures

Time: Thursdays, 11:30 - 13:00, Room V 57.06

Tutorials

Time: Wednesday, 14:00-15.30, 2 hours, Room U 104

The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 104. 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 (preferably C or C++). 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 2011).

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.
  

Useful online resources

• E-book: D.P. Landau and K. Binder: A guide to Monte Carlo Simulations in Statistical Physics

• 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 (Often used by myself as a cheat sheet)

• 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

• 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.

Date	Subject	Ressources
12.04.2012	Ab initio methods, Quantum mechanics,Hartree-Fock, Density functional theory	Lecture Notes
19.04.2012	Classical force fields, Atomistic simulations, Biomolecules	Lecture Notes Graphic
26.04.2012	Water models, Born model of solvation	Lecture Notes
03.05.2012	Coarse-grained models, simulations of macromolecules and soft matter	Lecture Notes
10.05.2012	Long range interactions in periodic boundary conditions	Lecture Notes
17.05.2012	Holiday (Christi Himmelfahrt)
24.05.2012	Long range interactions in periodic boundary conditions,	Further reading
31.05.2012	Holiday (Pfingsten)
07.06.2012	Holiday (Fronleichnam)
14.06.2012	Poisson-Boltzmann theory, charged polymers	Lecture Notes Presentation slides
21.06.2012	Hydrodynamic methods: Lattice-Boltzmann, Brownian Dynamics, DPD, SRD	Lecture Notes
28.06.2012	Hydrodynamic methods II
05.07.2012	Advanced MC/MD methods	Lecture Notes
12.07.2012	Free energy methods I	Lecture Notes
19.07.2012	Free energy methods II	Lecture Notes

Tutorials

Scheduling of tutorials

New worksheets are handed out every two weeks (see the list below). 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 the tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.

Please send the report to the responsible person indicated with the given tutorial.

In general, it should be the same person who handed out the tutorial. The name and e-mail in the worksheet are those of the worksheet author, not the responsible tutor!

Tutorial 1 - Error analysis and correlations

• Handed out on 18.04.2012, continuead on 25.04.2012
• Send reports to Peter Košovan
• Worksheet (362 KB)
• Sourde Code (24 KB)

Tutorial 2 - GROMACS

• Handed out on 2.5.2012, continued on 9.5.2012
• Send reports to Florian Dommert
• Worksheet (246 KB)

Tutorial 3 - ESPResSo: Simulation of a coarse-grained polymer

• Handed out on 16.5.2012, continued on 23.5.2012
• Send reports to Peter Košovan
• Worksheet (321 KB)
• tutorial3.tcl (7 KB)
• Article of Kremer and Grest, 1986

Tutorial 4 - ESPResSo: Simulation of a charged rod with counterions

• Handed out on 6.6.2012, continued on 13.6.2012
• Send reports to Florian Dommert
• Worksheet for tutorial 4 (359 KB)
• tutorial4.tcl (7 KB)

Tutorial 5 - ESPResSo: Lattice-Boltzmann fluid

• Handed out on 20.6.2012, continued on 27.6.2012
• Send reports to Georg Rempfer
• Worksheet for tutorial 5 (399 KB) (Updated: Section about ssh tunnels)
• Additional material (3.05 MB)
• Demonstration Video

Tutorial 6 - Advanced MC/MD

• Handed out on 4.7.2012, continued on 11.7.2012
• Send reports to Tobias Richter

• Worksheet for tutorial 6 (362 KB)
• Source files tutorial 6 (430 KB)

Tutorial 7 - Closing ceremony

• 18.7.2011
• Discussion of the last tutorial
• Evaluation and discussion of the whole course
• In case of interest, we may go out together after the end of the tutorial

Tutorials in 2012 are mostly based on the ones from previous year. Updated worksheets will be made available online on the day when they should be handed out. If you want to take a look ahead and see what is coming, have a look at the worksheets from the previous year.

Obtaining extra points

The first person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. The same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints, but these are not awarded extra points.

Guidelines for submitting tutorial reports

Same as as in the previous semester.