Simulation Methods in Physics II SS 2016
Contents
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: tba , Seminar Room (room 01.079)
 Tutorials: tba (Tutors: Dr. Frank Uhlig, Johannes Zeman; ICP, Allmandring 3, CIPPool (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 handsontutorials will take place in the CIPPool 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 and Berend Smit.
"Understanding Molecular Simulation".
Academic Press, San Diego, 2002.
[DOI] 
Mike P. Allen and Dominik J. Tildesley.
"Computer Simulation of Liquids".
Oxford Science Publications, Clarendon Press, Oxford, 1987.

D. C. Rapaport.
"The Art of Molecular Dynamics Simulation".
Cambridge University Press, 2004.

D. P. Landau and K. Binder.
"A guide to Monte Carlo Simulations in Statistical Physics".
Cambridge, 2005.

Michael Rubinstein and Ralph H. Colby.
"Polymer Physics".
Oxford University Press, Oxford, UK, 2003.

M. E. J. Newman and G. T. Barkema.
"Monte Carlo Methods in Statistical Physics".
Oxford University Press, 1999.

S. Succi.
"The lattice Boltzmann equation for fluid dynamics and beyond".
Oxford University Press, New York, USA, 2001.
[PDF] (13 MB) 
M. E. Tuckermann.
"Statistical Mechanics: Theory and Molecular Simulation".
Oxfor University Press Oxford Graduate Texts, Oxford, 2010.

F. Martin and 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.
Useful online resources
 Roethlisberger, Tavernarelli, EPFL, Lausanne, 2011: Introduction to electronic structure methods.
 EBook: Kieron Burke et al.,University of California, 2007: EBook: 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
 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 

7.04.2015  Introduction, Ab initio methods, Quantum mechanics, HartreeFock  Lecture Notes}} 
14.04.2015  Density functional theory, CarParrinello MD  Lecture Notes}} 
21.04.2015  Classical force fields, Atomistic simulations, Biomolecules  Lecture Notes}} 
28.05.2015  Water models, Born model of solvation  Lecture Notes}} 
05.05.2015  Holiday (Christi Himmelfahrt)  
12.05.2015  Coarsegrained models, simulations of macromolecules and soft matter  Lecture Notes}} 
19.05.2015  Holiday (Pfingsten)  
26.05.2015  Holiday (Fronleichnam)  
02.06.2015  Long range interactions in periodic boundary conditions  Lecture Notes}} 
09.06.2015  PoissonBoltzmann theory, charged polymers I  Slides}} 
16.06.2015  PoissonBoltzmann theory, charged polymers II  Lecture Notes}} 
23.06.2015  Hydrodynamic methods I Stokesian and Brownian Dynamics  Slides}} 
30.06.2015  Hydrodynamic methods II LatticeBoltzmann, DPD, MPCD  Lecture Notes}} 
07.07.2015  Advanced MC/MD methods  Lecture Notes}} 
14.07.2015  Free energy methods  Lecture Notes}} 
Tutorials
Location and Time
 The tutorials take place in the CIPPool on the first floor of the ICP (Room 01.033, Allmandring 3), time tba