Difference between revisions of "Simulation Methods in Physics I WS 2013"

Revision as of 16:42, 15 January 2014

The lecture on Thu 05.12.2013 is shifted to Mo 2.12.2014 at 09:00-10:30.

Overview

Type: Lecture (2 SWS) and Tutorials (2 SWS)
Lecturer: JP Dr. Maria Fyta (Lecture); Dr. Olaf Lenz, Bibek Adhikari, Elena Minina (Tutorials)
Course language: English
Location and Time: Lecture: Thu, 11:30 - 13:00 (Seminar room ICP, Allmandring 3); Tutorials: Wed, 15:45-17:15 (Bibek), Fri, 15:45-17:15 (Elena) (CIP-Pool ICP, Allmandring 3)
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 or C).

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 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 lecture should introduce different approaches to simulate a physical systems. In this respect, rather a broad range of methods will be outlined than an exhaustive presentation of specific computational methods. Roughly, the lecture will consist of:

General overview: The first 2-3 weeks will be dedicated on the general common aspects of computer simulations, elements of statistical ensemble theory and elements of elasticity theory, which are essential in understanding and performing simulations.

Quantum Mechanics: An extensive presentation of quantum mechanical simulations will be given in the second part of this course. Here, a general overview of the ideas behind these kinds of simulations will be given.

Molecular Dynamics: A more extensive investigation of classical Molecular Dynamics (MD) simulations is planned. This includes the algorithm, the integrators, the thermostats, to name a few necessary to perform MD simulations.; In terms of the respective tutorials, the goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.

Monte Carlo Simulations: A part of the lecture will be dedicated on Monte Carlo (MC) methods and their algorithms. Specific examples, such as the Ising model will be studied.

Error Analysis: The way errors come into the simulations and how to estimate these will be outlined.<-!!Autocorrelation, Jackknifing, Bootstrapping-->

Potentials: An important component of molecular simulations are the potentials or force fields chosen to model the interactions within the simulated system. The efficiency of the simulations is stongly dependent on this choice. To this purpose, various methods can be applied for obtaining efficient potentials for different methods. Here, representative examples will be outlined.

Simulation of liquids: Methods such as the lattice Boltzmann method and specific details on simulating liquids will be briefly given.

Advanced simulation techniques: In the end of the course, a short overview of other more advanced methods than the ones studied here will be presented. Examples include MC beyond the Metropolis algorithm, metadynamics or rare events sampling.

Prerequisites

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

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.

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)

University of Virginia, Introduction to atomistic simulations

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.

Course Material

Date	Subject	Resources
17.10.2013	Course Content, Introduction	Lecture Notes (2.54 MB)
24.10.2013	Molecular Dynamics (Introduction, integrators)	Lecture Notes (4.59 MB)
31.10.2013	Energy minimization, common features in computer simulations of particles	Lecture Notes (8.91 MB)
07.11.2013	Basics of Stat Mech, ensembles, observables	Lecture Notes (6.53 MB)
14.11.2013	More on StatMech, MD (thermostats/barostats;intro)	Lecture Notes (4.94 MB)
21.11.2013	MD (thermostats)	Lecture Notes (6.35 MB)
28.11.2013	MD (barostats), error analysis	Lecture Notes (4.32 MB)
05.12.2013	Error analysis (cont.) (binning, jackknife analysis)	Lecture Notes (2.63 MB)
12.12.2013	Introduction to Monte Carlo (MC)	Lecture Notes (8.43 MB)
19.12.2013	MC (Metropolis algorithm), Introducing thesis projects @ ICP	Lecture Notes (1.68 MB)
09.01.2014	MC (Ising model), phase transitions & critical phenomena	Lecture Notes (6.04 MB)
16.01.2014	Langevin dynamics, Brownian dynamics
23.01.2014	Interactions, long-range interactions, building potentials
30.01.2014	Elements of elasticity theory
06.02.2014	Introduction to quantum-mechanical methods

Tutorials

Location and Time

Wednesday, 15:45-17:15 (Bibek Adhikari)
Friday, 15:45-17:15 (Elena Minina)

Worksheets

Worksheet 6: Ising Model and Finite Size Scaling

Deadline: Wednesday, 29 January 2014, 10:00
Worksheet 6 (file does not exist!)
templates.tar.gz (file does not exist!) - Archive that contains the files required for this worksheet.

Worksheet 5: Monte-Carlo

Deadline: Wednesday, 15 January 2014, 10:00
Worksheet 5 (217 KB)

Worksheet 4: Error Analysis and Langevin Thermostat

Deadline: Monday, 16 December 2013, 10:00
Worksheet 4 (233 KB)
templates.tar.gz (8.43 MB) - Archive that contains the files required in some tasks

Worksheet 3: Molecular Dynamics 2 and Observables

Deadline: Monday, 2 December 2013, 10:00
Worksheet 3 (319 KB)
templates.tar.gz (4 KB) - Archive that contains the files required in some tasks

Worksheet 2: Statistical Mechanics and Molecular Dynamics

Deadline: Monday, 18 November 2013, 10:00
Worksheet 2 (331 KB)
templates.tar.gz (6 KB) - Archive that contains the files required in some tasks
latex-template.tex (7 KB) - LaTeX-template for the report

Worksheet 1: Integrators

Deadline: Monday, 4th November 2013, 10:00
Worksheet 1 (288 KB)
solar_system.pkl.gz (496 bytes) - Archive that contains the files required in some tasks
cannonball_template.png (114 KB) - Python program template as an image

General Remarks

The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 1.033, Allmandring 3).
For the tutorials, you will get a personal account for the ICP machines.
All material required for the tutorials can also be found on the ICP computers in the directory /group/sm/2013.
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 to use LaTeX to prepare the report.
You have two weeks to prepare the report for each worksheet.
The report has to be sent to the 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.
You will receive the new worksheet 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 for the tutor.
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
A good and freely available book about using Linux: Introduction to Linux by M. Garrels
Short introduction to shell scripting (bash)
A more detailed introduction to bash scripting

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) (3.24 MB) - Numerics in Python, using Numpy

LaTeX

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 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 2013)
- Contents: both lectures and the tutorials 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 tutorials of this lecture as a prerequisite for the examination
30 min of oral examination (PL) about the lecture and the tutorials

BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech I" (40520)

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 tutorials

MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker I" (35840)

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

@@ Line 140: / Line 140: @@
 === Worksheets ===
+==== Worksheet 6: Ising Model and Finite Size Scaling  ====
+* Deadline: '''Wednesday, 29 January 2014, 10:00'''
+* {{Download|WS_201e_SM1_worksheet6.pdf|Worksheet 6}}
+* {{Download|WS_201e_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}} - Archive that contains the files required for this worksheet.
 ==== Worksheet 5: Monte-Carlo  ====