Simulation Methods in Physics II SS 2017

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, 15:45 – 17:15 (Tutors: Dr. Frank Uhlig, David Sean; 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. Obtaining 50% of the possible marks in the hand-in exercises.

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
13.04.2017	Classical force fields, Atomistic simulations, Biomolecules
20.04.2017	Water models	Lecture Notes}}
27.04.2017	Coarse-grained models, simulations of macromolecules and soft matter	Lecture Notes}}
04.05.2017	Poisson-Boltzmann theory	Lecture Notes}}
11.05.2017	Hydrodynamic methods	Lecture Notes}}
18.05.2017	Free energy methods	Lecture Notes}}
25.05.2017	Holiday (Christi Himmelfahrt)
01.06.2017	Advanced MC/MD methods
08.06.2017	Holiday (Pfingsten)	Lecture Notes}}
15.06.2017	Holiday (Fronleichnam)	Lecture Notes}}
22.06.2017	Ab initio methods, Hartree-Fock	Lecture Notes}}
29.06.2017	post Hartree Fock	Lecture Notes}}
06.07.2017	Density functional theory and functionals	Lecture Notes}}
13.07.2017	ab initio MD, Car-Parrinello MD	Lecture Notes}}
20.07.2017	Long range interactions in periodic boundary conditions	Lecture Notes}}

Tutorials

Location and Time

• The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu, 15:45 – 17:15 (Tutors: Frank Uhlig / David Sean )

Worksheets

Worksheet 1: Properties and Fitting of Atomistic Water models

• Deadline: May 1, 2017
• Worksheet (274 KB)
• templates.tar.gz (110 KB)
• latex-template.tex (7 KB) - LaTeX template for the report