Simulationsmethoden in der Physik 2 / Simulation methods in physics 2 (SS 2011)

Overview

Type

Lecture (2 SWS) and Tutorials (1 SWS)

Lecturer

Prof. Dr. Christian Holm, JP Dr. Axel Arnold, Dr. Marcello Sega (Lecture); Olaf Lenz and Peter Košovan (Tutorials)

Course language

Deutsch oder Englisch, wie gewünscht - German or English, by vote

Lectures

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

Tutorials

Time: Friday, 14:00-15.30, 2 hours/(every other week), 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 108. 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.

Note: students from the COMMAS master will have to attend tutorials every week, and one extra tutorial is expected. Course can count then as 2SWS plus 2SWS tutorials

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).

NOTE: students from the COMMAS master will have to present, at the end of the course, a supplementary project (topic to be discussed with tutors).

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

• 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

Date	Subject
28.04.2011	Ab initio methods, Quantum mechanics
05.05.2011	Hartree-Fock, Density functional theory, Carr-Parinello MD
12.05.2011	Classical force fields, Atomistic simulations, Biomolecules
19.05.2011	Water models, Born model of solvation
26.05.2011	Coarse-grained models, simulations of macromolecules and soft matter
02.06.2011	Holiday (Christi Himmelfahrt)
09.06.2011	Long range interactions in periodic boundary conditions
16.06.2011	Holiday (Pfingsten)
23.06.2011	Holiday (Fronleichnam)
30.06.2011	Hydrodynamic methods: Lattice-Boltzmann, Brownian Dynamics, DPD, SRD
01.07.2011	Hydrodynamic methods II Extra lecture in tutorial time
07.07.2011	Poisson-Boltzmann theory
14.07.2011	Advanced MC/MD methods
21.07.2011	Free energy methods I
28.07.2011	Free energy methods II

Tutorials

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.

Scheduling of tutorials

Tutorials are scheduled every two weeks (see table below). In the week between the tutorials, the tutors will be available to help the you with any problems. Since participation is optional, it is recommended that you notify the tutors that you are intending to come and seek their assistance.

Tutorial 1 - Error analysis

• Tutorial on 6.5.2011 (Peter Košovan)
• Worksheet for tutorial 1 (311 KB)
• Code for tutorial 1 (20 KB).

Tutorial 2 - GROMACS

• Tutorial on 13.5.2011 (Peter Košovan)
• Optional tutorial on 20.5.2011 (Peter Košovan)
• Worksheet for tutorial 2 (356 KB)
• Code for tutorial 2 (1.71 MB)

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

• Tutorial on 27.5.2011 (Olaf Lenz)
• No optional tutorial on 3.6.2011 (almost holiday)
• Worksheet for tutorial 3 (349 KB)
• tutorial3.tcl (7 KB)
• Article of Kremer and Grest, 1986 (710 KB)

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

• Tutorial on 10.6.2011 (Olaf Lenz)
• No optional tutorial on 17.6.2011 (holiday)
• Hand in report until 22.6.2011
• Worksheet for tutorial 4 (343 KB)
• tutorial4.tcl (7 KB)
• Article of Deserno, 2000 ()

Tutorial 5 - ESPResSo: Lattice-Boltzmann fluid

• Tutorial on 24.6.2011 (Olaf Lenz)
• no tutorial on 1.7.2011: replacement lecture Poisson-Boltzmann
• Optional tutorial on 8.7.2011 (Olaf Lenz)
• Try to hand in the report until 13.7.2011
• Worksheet for tutorial 5 (336 KB)
• tutorial5-1.tcl (2 KB)
• tutorial5-2.tcl (2 KB)
• msd.pl (926 bytes)

Tutorial 6 - Advanced MC/MD

• Tutorial on 15.7.2011 (Peter Košovan)
• Optional tutorial on 22.7.2011 (Peter Košovan)
• Worksheet for tutorial 6 (318 KB)
• tutorial6.tgz (31 KB)

Tutorial 7 - Closing ceremony

• Might involve experiments of the effect of dilute aqueous solutions of ethanol on the human body
• Tutorial on 29.7.2011 (Peter Košovan, Olaf Lenz)

Guidelines for submitting tutorial reports

Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a single pdf document or alternatively as a paper printout. Handwritten reports will also be accepted. Source code should always be sent via e-mail. If the code concerns only a few lines, it may be included in the text of the report. Reports clearly not meeting these requirements may be rejected without evaluation.

Identical pieces of reports annihilate when submitted by different people producing anti-points for both. The amount of anti-points grows exponentially with the similarity. It is fine if you help each other and discuss your results, but each part of the report has to be an original, not a copy from your neighbour.

If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." cannot be awarded any points.

Deadline

Approximately 10 days after the tutorial, but no later than Wednesday 8:00 of the week when the next worksheet is going to be handed out. Reports on paper can be handed in personally until lunch break on the same day.

In case of special circumstances (illness, accident, ...) contact the tutor immediately via e-mail to agree on an alternative deadline.

Text of the report

Has to contain author name, student ID and date.

Should be subdivided into sections, each section being clearly related to one task of the homework.

Must be written in sentences, not points like in a presentation.

All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.

For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.

Figures and plots

Each figure has to have a number and a caption or title saying what is in the figure.

In text, refer to figures by the number or title, so that it is clear which figure you are referring to.

Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.

Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.

All figures have to be included in the report. Figures sent as separate files will not be considered.

You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.

Source files

Remember that someone has to read your code, understand it and check that it is correct.

Provide all files in which you made changes!

Use variables with intuitively understandable names. If not, at least put a comment saying what it means.

If the code is more complex, add comments to it. Especially to parts which may not be straightforward to understand.

We recommend that you indent your code for better readability.