Simulation Methods in Physics I WS 2017/2018

Overview

Type

Lecture (2 SWS) and Tutorials (2 SWS)

Lecturer

Prof. Dr. Christian Holm

Course language

English

Location and Time

Lecture: Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)

Tutorials: Wed, 15:45-17:15 (Tutor: David Sean) and Fri, 14:00-15:30 (Tutor: Michael Kuron); ICP, Allmandring 3, CIP-Pool (room 01.033)

Prerequisites

We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).

The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis. The tutorials build upon each other, therefore continuous attendance is expected.

Lecture

Scope

The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating a problem, hence we will not go too to deep into specific details but rather try to cover a broad range of methods. In more detail, the lecture will consist of:

Molecular Dynamics

The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.

The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.

Error Analysis

Autocorrelation, Jackknifing, Bootstrapping

Monte Carlo Simulations

Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.

Critical exponents

Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models

Course Material

Date	Subject	Resources	Remarks
2017-10-19	Course Content, Organization, Introduction	Slides
2017-10-26	MD: Integrators	Lecture Notes
2017-11-02	Basics of Statistical Mechanics	Lecture Notes
2017-11-09	Chaos, LJ-Potential, Units	Lecture Notes
2017-11-16	PBC, cell-lists, simple MD	Lecture Notes
2017-11-23	Observables, Brownian motion	Lecture Notes
2017-11-30	D, Green-Kubo, Langevin Dynamics	Lecture Notes
2017-12-07	Thermostats	Lecture Notes
2017-12-14	Thermostats, Barostats	Lecture Notes
2017-12-21	B.Sc. / M.Sc. thesis @ ICP: information & research topics	Slides
2018-01-11	Monte-Carlo Method	Lecture Notes
2018-01-18	Monte-Carlo and Critical Phenomena	Lecture Notes
2018-01-25	Critical Exponent	Lecture Notes
2018-02-01	Finite Size Scaling , Binder Parameters	Lecture Notes (3.71 MB)
2018-02-08	t.b.a.	Lecture Notes

Script

A preliminary version of the script can be downloaded here (929 kB).

If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to Johannes Zeman.

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

• Thermostats: Philippe H. Hünenberger, Thermostat Algorithms for Molecular Dynamics Simulations, Adv. Polym. Sci. (2005) 173:105–149.

• Error analysis: W. Janke, Statistical Analysis of Simulations:Data Correlations and Error Estimation, Quantum Simulations of Complex Many-Body Systems:

From Theory to Algorithms, Lecture Notes, (2002).

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

• 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.

Tutorials

Location and Time

• The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) on
  • Wednesdays, 15:45-17:15 (Tutor: David Sean)
  • Fridays 14:00-15:30 (Tutor: Michael Kuron)
• The tutorials on November 1st and 3rd are canceled due to a holiday.
• The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.
• The tutors are switched between the tutorials on December 13th and 15th.
• The Friday tutorial on December 22nd will be held by Florian Weik.
• The Wednesday tutorial on January 10th will be held by Michael Kuron. Please submit your reports to him.
• The Friday tutorial on February 8th will be held by David Sean. Please submit your reports to him.

Worksheets

Topic	Deadline	Worksheet	Further Resources
0. First steps with Linux, Python, and C	no submission required	Worksheet 0 (269 KB)	PythonTutorial.ipynb (33 KB) (nbviewer), NumPyTutorial.ipynb (120 KB) (nbviewer).
1. Integrators	2017-11-13 12:00	Worksheet 1 (287 KB)	solar_system.pkl.gz (496 bytes) cannonball_template.png (70 KB)
2. Statistical mechanics and Molecular Dynamics	2017-11-27 12:00	Worksheet 2 (332 KB)	Templates.tar.gz (6 KB) Cython Introduction (398 KB)
3. Molecular Dynamics and Observables	2017-12-11 12:00	Worksheet 3 (327 KB)	templates.tar.gz (4 KB)
4. Thermostats and Diffusion	2018-01-08 12:00 (both groups submit to Michael)	Worksheet 4 (241 KB)	templates.tar.gz (2 KB)
5. Monte-Carlo	2018-01-22 12:00	Worksheet 5 (248 KB)	janke02.pdf
6. Ising Model and Finite Size Scaling	2018-02-05 12:00 (both groups submit to David)	Worksheet 6 (225 KB)	templates.tar.gz (4 KB) remeber to use: python setup.py build_ext -fi

General Remarks

• For the tutorials, you will get a personal account for the ICP machines.
• For the reports, we have a nice latex-template.tex (7 KB).
• You can do the exercises in the CIP-Pool when it is not occupied by another course. The pool is accessible on all days, except weekends and late evenings.
• If you do the exercises in the CIP-Pool, all required software and tools are available.
• If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.
  • Python
  • The following Python packages:
    • IPython
    • NumPy
    • SciPy
    • matplotlib
  • A C compiler (e.g. GCC)
• We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.

Hand-in-exercises

• The worksheets are to be solved in groups of two or three people. We will not accept hand-in-exercises that only have a single name on it.
• A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.
• You have two weeks to prepare the report for each worksheet.
• The report has to be sent to your tutor via email.
• Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see Examination for details).

What happens in a tutorial

• The tutorials take place every week.
• The new worksheet will be available for download on the days before the tutorial.
• In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.
• In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.
• You will have to hand in the reports on Monday after the second tutorial.
• In the third tutorial after you received the worksheet, the solutions will be discussed:
  • The tutor will ask a team to present their solution.
  • The tutor will choose one of the members of the team to present each task.
  • This means that each team member should be able to present any task.
  • At the end of the term, everybody should have presented at least once.

Documentation

Linux

• Linux Cheat Sheet (2.27 MB) (source (42 KB)) - the most important linux commands on a single page

Python

• Use the existing documentation of Python itself! To get help on the command print, use

 pydoc print

• Or use the Web browser to read it. Start

 pydoc -p 4242

and visit the page http://localhost:4242

• http://python.org/doc/ - the official Python documentation (including tutorials etc.)
• Byte_of_Python.pdf (546 KB) - the free eBook "A byte of Python" [1], also available in German[2]

NumPy

• first of all, try to use

 pydoc numpy

• http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation
• Script of the lecture "Physik auf dem Computer" (German) (3.42 MB) - Numerics in Python using Numpy

LaTeX

• The Not So Short Introduction to LaTeX
• Documentation list of the LaTeX project

Running Python on your own computer

If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.

Debian und Ubuntu Linux

sudo apt-get update
sudo apt-get install python python-numpy python-scipy \
    python-matplotlib ipython ipython-notebook gcc g++ \
    cython
mkdir -p ~/.config/matplotlib
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc

OpenSUSE Linux

sudo zypper install python python-numpy python-scipy \
    python-matplotlib IPython gcc python-Cython
mkdir -p ~/.config/matplotlib
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc

Mac OS X

First, install the C compiler:

xcode-select --install
xcodebuild -license accept

Now download and install MacPorts. Next, you can install the Python packages.

sudo port selfupdate
sudo port install python27 py27-numpy py27-scipy \
    py27-matplotlib py27-ipython py27-jupyter py27-cython
sudo port select python python27
sudo port select ipython py27-ipython
sudo port select cython cython27

Windows

For Windows, we recommend Anaconda Python, an all-in-one package that includes all required Python modules.

For the worksheets that use Cython, you will also need to install a compatible C compiler. If you chose Python 2.7, that is Visual Studio 2008 Express Edition plus, if you are running 64-bit Windows, the Windows SDK 2008 (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers). If you chose Python 3.5 or 3.6, you need Visual Studio 2015 Community Edition (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).

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 hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)
• 60 min of oral examination (PL)
  • After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)
  • Contents: both lectures and the excercises of "Simulation Methods in Physics I"

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

• Obtain 50% of the possible points in the hand-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 I" (40520)

• Obtain 50% of the possible points in the hand-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 I" (35840)

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

C++ Course

The Computer Science department is offering a week-long C++ course at the end of this semester. We recommend all students that plan on participating the Advanced Simulation Methods lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP. Current bachelor students might be able to take this course as Schlüsselqualifikation -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as One Course (2 SWS) in an Application Field of Simulation Methods as part of the Fortgeschrittene Simulationsmethoden (Schwerpunkt) module, pending a change of the Modulhandbuch. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.