Simulation Methods in Physics II SS 2022

Please register for this course on CAMPUS, so that every student can get access to ILIAS. The course will be administered through ILIAS.

Overview

Type

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

Lecturers

Prof. Dr. Christian Holm

Tutorials

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".

Tutors

Dr. Azade Yazdanyar, Samuel Tovey and David Beyer

Location and Time

Lecture: Lectures are held in the ICP seminar room.

Tutorials: Thu. 14:00 - 15:30, and Fri. 11:30 - 13:00 (Only one session should be attended)

Course language

English

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. Obtaining 50% of the possible marks in each of the hand-in exercises.

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

Oral Examination

Please email Christian Holm in order to arrange a date for the oral examination.

There is an oral examination at the end of the semester. All students having obtained 50% of the points from each tutorial are eligible to take the exam. The duration of the exam depends on the module this lecture is part of. Briefly,

BSc/MSc Physik, Modul "Simulationsmethoden in der Physik"

60 min exam (contents from both parts SMI + SMII will be examined)

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

30 min exam (content only from SMII will be examined).

BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II"

40 min (content from SMII will be examined).

For additional information/modules, please contact Christian Holm.

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.
  
• Timm Krüger, Halim Kusumaatmaja, Alexandr Kuzmin, Orest Shardt, Goncalo Silva, Erlend Magnus Viggen.
  The Lattice Boltzmann Method: Principles and Practice.
  Springer International Publishing, Cham, 2017. ISBN: 9783319446479.
  [PDF] (14 MB) [DOI]
• 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.
  
• Attila Szabo, Neil S. Ostlund.
  Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory.
  Edition 1.
  Dover Publications, 2014. ISBN: 978-0-486-69186-2.
  

Useful Online Resources

• Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [1]

• 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

• 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)

• Density-functional-theory tight-binding (DFTB): Phil. Trans. R. Soc. A, 372(2011), 20120483. [2], Computational Materials Science 47 (2009) 237–253 [3]

• "Ab Initio Molecular Dynamics: Theory and Implementation" in Modern Methods and Algorithms, NIC Series Vol 1. (2000) [4]

• University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [5]

• 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.

Lectures Timetable

The lecture notes will be uploaded in due time after each lecture on the ILIAS course.

Date	Subject	Resources
14.04.2022	Quantum-mechanical Methods I - Hartree/Hartree-Fock/post Hartree-Fock
21.04.2022	Quantum-mechanical Methods II - Density Functional Theory/ab-initio MD
28.04.2022	Classical Force Fields, Water Models
05.05.2022	Machine learning and Force Fields
12.05.2022	Implicit Water, Coarse-grained Simulations and Soft Matter, part 1
19.05.2022	Coarse-grained Simulations and Soft Matter, ML continued
26.05.2022	Holiday (Christi Himmelfahrt)
02.06.2022	Polyelectrolytes and Poisson-Boltzmann Theory I
09.06.2022	Holiday week Pfingstferien
16.06.2022	Holiday (Fronleichnam)
23.06.2022	Polyelectrolytes and Poisson-Boltzmann Theory II
30.06.2022	Hydrodynamic Interactions I (Brownian and Langevin Dynamics)
07.07.2022	Hydrodynamic Interactions II (DPD, Lattice-Boltzmann)
14.07.2022	Advanced MC/MD Methods, Free Energy Methods
21.07.2022	Electrostatics and Ewald Summation

Resources can be found in the respective Ilias folder

Tutorials

Tutorials 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.

Location and Time

• The time and place of the tutorials will be announced.

General Remarks

• For the tutorials, you will get a personal account for the ICP machines.
• For the reports, we have a nice LaTeX template (7 KB).

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 (Azade Yazdanyar, Samuel Tovey or David Beyer).
• 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.
• 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.