Simulation Methods in Physics I 11 12
- Lecture (2 SWS) and Tutorials (2 SWS)
- Prof. Dr. Christian Holm (Lecture); Marcello Sega and Peter Košovan (Tutorials)
- Course language
- Deutsch oder Englisch, wie gewünscht - German or English, by vote
- Time: Thursdays, 11:30 - 13:00, Room V 57.06
- Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.00, Room V27.U104
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.
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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++).
Prerequisites for the examination
- Attendance of the exercise classes
- Obtaining 50% of the possible marks in the hand-in exercises
(In German: USL -V )
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II. The grade will be determined in the following way : There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.
People taking other modules where this course is part of should contact the lecturer for optional other examinations.
|Date||Topics (subject may change during the course)||Downloads|
|20.10.2011||Course Content, Organisation,Introduction||Lecture Notes 20.10.2011|
|27.10.2011||Equation of Motion and simple Integrators for Classical MD||Lecture Notes 27.10.2011|
|03.11.2011||Integrators cont., simple Potentials for Liquids, LJ Units||Lecture Notes 03.11.2011|
|10.11.2011||Stat Mech in a Nutshell, efficiency considerations, Simple MD Program||Lecture Notes 10.11.2011|
|17.11.2011||Observables in MD||Lecture Notes 17.11.2011|
|24.11.2011||Diffusion, Brownian motion, RDF||Lecture Notes 24.11.2011|
|01.12.2011||Green-Kubo relations, temperature fluctuations in NVE ensemble||Lecture Notes 01.12.2011 Presentation 01.12.2011|
|08.12.2011||Thermostats and different ensembles||Lecture Notes 08.12.2011|
|15.12.2011||Finite differencing techniques, solving PDEs||Lecture Notes 15.12.2011|
|22.12.2011||Overview over research topics at the ICP||Lecture Notes 22.12.2011|
|12.01.2012||Introduction to Monte Carlo Methods, Metropolis Alg.||Lecture Notes 12.01.2012|
|19.01.2012||Phase transitions, critical phenomena||Lecture Notes 19.01.2012|
|26.01.2012||Finite Size Scaling||Lecture Notes 26.01.2012|
|09.02.2012||Single particle Quantum Mechanics||Lecture Notes 09.02.2012 Euclidian Lattice Theory|
Tutorials (U 104)
- Scheduling of tutorials
- First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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.
|Week||Date||Topic and files to download||Responsible tutor|
|1.||26.10.2011||T0: First steps with Linux and C
|2.||2.11.2011||Discussion of T0
T1: Equations of motion and integrators
|3.||9.11.2011||Working on problems from T1||Peter Košovan|
|4.||16.11.2011||Discussion of T1
T2: Molecular Dynamics: Lennard-Jones liquid
|5.||23.11.2011||Working on problems from T2||Peter Košovan|
|6.||30.11.2011||Discussion of T2
T3: MD in NVE and NVT ensembles; implementing different thermostats
|7.||7.12.2011||Working on problems from T3||Peter Košovan|
|8.||14.12.2011||Discussion of T3
T4: The finite Difference and Finite element methods
|9.||21.12.2011||Working on problems from T4||Marcello Sega|
|10.||11.1.2012||Discussion of T4
T5: Simple and importance sampling. Random walks.
|11.||18.1.2012||Working on problems from T5||Marcello Sega|
|12.||25.1.2012||Discussion of T5
T6: Monte Carlo-Ising model
|13.||1.2.2012||Working on problems from T6||Peter Košovan|
|14.||8.2.2012||Discussion of T6, end of the tutorials||Peter Košovan|
Assessment of the tutorials
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.
- Obtaining extra points
- Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.
- 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. 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.
- If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.
Guidelines for submitting the 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. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.
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.
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.
In your communications by email, always send the message to both tutors.
- Every other Monday morning, that is, two days before the next task is handed out.
- A delayed submission is penalized -1 point for each day of the delay.
- The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.
- In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual 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.
- Should be written in sentences, not points like in a presentation.
- Should not repeat the introduction from the worksheet.
- 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.
- There is no upper or lower size limit on the report. Use common sense.
- 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 easy to read.
- We recommend that you indent your code for better readability.
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.
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.
Cambridge University Press, 2004. ISBN: 9780511816581.
D. P. Landau, K. Binder.
A guide to Monte Carlo Simulations in Statistical Physics.
Edition second edition.
M. E. J. Newman, G. T. Barkema.
Monte Carlo Methods in Statistical Physics.
Edition 2002 edition.
Oxford University Press, 1999.
Useful online resources
- Linux cheat sheet here (53 KB)
- E-book: D.P. Landau and K. Binder: A guide to Monte Carlo Simulations in Statistical Physics
- 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)
- Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.