Simulation Methods in Physics II SS 2016

Exam dates: Mo 19.9.2016 between 10am-14pm and Wed 12.10.2016 between 10am-12pm and 14-15pm. Please, send an e-mail to Christian Holm with your preferred date and time.

Overview

Type

Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)

Lecturer

Prof. Dr. Christian Holm, JP Dr. Maria Fyta

Course language

English

Location and Time

Lecture: Thu, 11:30 - 13:00; ICP, Allmandring 3-->, Seminar Room (room 01.079)

Tutorials: Thu, 14:00 - 15:30 (Tutors: Dr. Frank Uhlig, Johannes Zeman; ICP, Allmandring 3, CIP-Pool (room 01.033)

The tutorials have their own title "Simulationsmethoden in der Praxis", as they can be attended independently of the lecture and are in fact part part of the Physics MSc module "Fortgeschrittene Simulationsmethoden" and not of the module containing the lecture "Simulation Methods in Physics II".

These hands-on-tutorials 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 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. 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 each worksheet

The final grade will be determined from the final oral examination.

Oral Examination

Please email to Christian Holm or Maria Fyta in order to arrange a date in September or october for the oral examination.

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.
  
• Michael Rubinstein, Ralph H. Colby.
  Polymer Physics.
  Oxford University Press, Oxford, UK, 2003.
  
• M. E. J. Newman, G. T. Barkema.
  Monte Carlo Methods in Statistical Physics.
  Edition 2002 edition.
  Oxford University Press, 1999.
  
• Sauro Succi.
  The lattice Boltzmann equation for fluid dynamics and beyond.
  Oxford University Press, New York, USA, 2001. ISBN: 9780198503989.
  [PDF] (13 MB)
• M. E. Tuckermann.
  Statistical Mechanics: Theory and Molecular Simulation.
  Oxfor University Press Oxford Graduate Texts, Oxford, 2010.
  
• F. Martin, H. Zipse.
  Charge Distribution in the Water Molecule - A Comparison of Methods.
  Journal of Computational Chemistry 26(1):97–105, 2004.
  
• E. Kaxiras.
  Atomic and electronic structure of solids.
  apud Cambridge, Cambridge, 2003.
  
• Andrew Leach.
  Molecular Modelling: Principles and Applications.
  apud Pearson Education Ltd., 2001. ISBN: 978-0582382107.
  

Useful online resources

• Roethlisberger, Tavernarelli, EPFL, Lausanne, 2011: Introduction to electronic structure methods.

• E-Book: Kieron Burke et al.,University of California, 2007: E-Book: The ABC of DFT.

• 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

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

• A more detailed introduction to bash scripting

• Principles of Multiscale Modeling, Weinan E (2011)

• 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	Resources
07.04.2016	Introduction, Ab initio methods, Quantum mechanics, Hartree-Fock	Lecture Notes (2.7 MB) Lecture Notes (3.11 MB)
14.04.2016	Density functional theory, Car-Parrinello MD	Lecture Notes (2.99 MB)
21.04.2016	ab initio MD, post Hartree-Fock methods	Lecture Notes (5.59 MB)
28.04.2016	Classical force fields, Atomistic simulations, Biomolecules, Water models	Lecture Notes (1.37 MB) Lecture Notes (3.81 MB)
05.05.2016	Holiday (Christi Himmelfahrt)
12.05.2016	Coarse-grained models, simulations of macromolecules and soft matter	Lecture Notes (4.25 MB)
19.05.2016	Holiday (Pfingsten)
26.05.2016	Holiday (Fronleichnam)
02.06.2016	Poisson-Boltzmann theory, charged polymers	Slides (6.94 MB)
09.06.2016	Poisson-Boltzmann theory, charged polymers cont.	Lecture Notes (171 kB)
16.06.2016	Long range interactions in periodic boundary conditions	Lecture Notes (4.01 MB)
23.06.2016	Hydrodynamic methods I Stokesian and Brownian Dynamics	Lecture Notes (2 MB) Lecture Notes (3.84 MB)
30.06.2016	Hydrodynamic methods II Lattice-Boltzmann, DPD, MPCD	Lecture Notes (2.63 MB)
07.07.2016	Free energy methods	Lecture Notes (6.13 MB)
14.07.2016	Advanced MC/MD methods	Lecture Notes (3.17 MB)

Tutorials

Location and Time

• The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), time Thu 14:00-15:30 (Tutors: Frank Uhlig / Johannes Zeman )

Worksheets

Worksheet 6: Advanced MD/MC: The Widom insertion method

• Available online: June 27, 2016
• Deadline: July 11, 2016
• Worksheet 6 (283 KB)
• template.tcl (14 KB) - ESPResSo sample script

Worksheet 5: Hydrodynamics and the Lattice-Boltzmann method

• Deadline: June 27, 2016
• Worksheet 5 (507 KB)
• template.tcl (1 KB) - ESPResSo sample script
• Sample videos:

Worksheet 4: Charge distribution around a charged rod

• Available online: May 30, 2016
• Deadline: June 13, 2016
• Worksheet 4 (287 KB)
• template.tcl (7 KB) - ESPResSo sample script
• Solution (410 KB) - Sample solution

Worksheet 3: Coarse-grained polymers and their properties

• Deadline: May 30, 2016
• Worksheet 3 (246 KB)
• template.tcl (8 KB) - ESPResSo sample script
• Solution (286 KB) - Sample solution

Worksheet 2: Diffusion processes and properties of atomistic water models

• Deadline: May 9, 2016
• Worksheet 2 (266 KB)
• templates.tar.gz (12 KB) - Archive containing GROMACS input files
• Solution (447 KB) - Sample solution

Worksheet 1: Quantum mechanical approaches: Hückel approximation and ab-initio methods

• Deadline: April 25, 2016
• Worksheet (244 KB)
• latex-template.tex (7 KB) - LaTeX template for the report

General Remarks

• 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/2016.
• For the reports, we have a nice LaTeX template (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.

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 (Frank Uhlig or Johannes Zeman).
• Each task within the tutorial is assigned a given number of points. Each student should have 50 % of the points from each tutorial as a prerequisite for the oral examination.

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.