Simulation Methods in Physics II SS 2017
Possible exam dates:

Contents
 1 Overview
 2 Lecture
 3 Tutorials
 3.1 Location and Time
 3.2 Worksheets
 3.2.1 Worksheet 1: Properties and Fitting of Atomistic Water models
 3.2.2 Worksheet 2: Properties of Coarsegrained Polymers
 3.2.3 Worksheet 3: Charge distribution around a charged rod
 3.2.4 Worksheet 4: Flow Between Plates and Free Energy
 3.2.5 Worksheet 5: Quantum chemistry and simple models
 3.2.6 Worksheet 6: Density functional theory and ab initio molecular dynamics
 3.3 General Remarks
 3.4 Handinexercises
 3.5 What happens in a tutorial
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, 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. Obtaining 50% of the possible marks in the handin 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 and Berend Smit.
"Understanding molecular simulation".
Academic Press, San Diego, 2002.

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, Tavernelli, EPFL, Lausanne, 2015: [1]
 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
 Densityfunctionaltheory tightbinding (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.
Lecture
Date  Subject  Resources  

13.04.2017  Classical force fields, Atomistic simulations, Biomolecules  
20.04.2017  Water models  
27.04.2017  Coarsegrained models, simulations of macromolecules and soft matter  Lecture Notes (4.25 MB)  
04.05.2017  Charged macromolecules  Slides (6.94 MB)  
11.05.2017  PoissonBoltzmann theory  
18.05.2017  Hydrodynamic methods  Lecture Notes Hydrodynamics Lecture Notes LB (2.63 MB) Intro to LB  
25.05.2017  Holiday (Christi Himmelfahrt)  
01.06.2017  Free energy methods  Free energy calculations  
08.06.2017  Holiday (Pfingsten)  
15.06.2017  Holiday (Fronleichnam)  
22.06.2017  Quantummechanical methods, introduction  Slides (2.7 MB) Lecture Notes (2.94 MB)  
29.06.2017  HartreeFock, post Hartree Fock  Lecture Notes (4.21 MB)  
06.07.2017  Density functional theory and functionals  Lecture Notes (6.48 MB)  
13.07.2017  Timedependent DFT, ab initio MD  Lecture Notes (9.12 MB)  
20.07.2017  stateofthe art, review 
Tutorials
Location and Time
 The tutorials take place in the CIPPool 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)
 latextemplate.tex (7 KB)  LaTeX template for the report
Worksheet 2: Properties of Coarsegrained Polymers
 Deadline: May 15, 2017, 12:00 noon by email to David Sean use SM2_02 as subject line.
 Worksheet (318 KB)
 template (9 KB)
 ESPResSo install (419 bytes)
 latextemplate.tex (7 KB)  LaTeX template for the report
Worksheet 3: Charge distribution around a charged rod
 Deadline: May 29, 2017, 12:00 noon by email to David Sean use SM2_03 as subject line.
 Worksheet 3 (339 KB)
 template (7 KB)  ESPResSo sample script
 ESPResSo install (417 bytes)
Worksheet 4: Flow Between Plates and Free Energy
 Deadline: June 19, 2017, 12:00 noon by email to David Sean use SM2_04 as subject line.
 Worksheet 4 (279 KB)
 template (2 KB)  ESPResSo sample script
 ESPResSo install (409 bytes)
 latextemplate.tex (7 KB)  LaTeX template for the report
Worksheet 5: Quantum chemistry and simple models
 Deadline: July 3, 2017, 12:00 noon by email to Frank Uhlig use SM2_05 as subject line.
 Worksheet 5 (300 KB)
 template (4 KB)  CP2K input files
 latextemplate.tex (7 KB)  LaTeX template for the report
Worksheet 6: Density functional theory and ab initio molecular dynamics
 Deadline: July 17, 2017, 12:00 noon by email to Frank Uhlig use SM2_06 as subject line.
 Worksheet 6 (272 KB)
 template (433 KB)  CP2K input files
 latextemplate.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/2017
.  For the reports, we have a nice LaTeX template (7 KB).
 You can do the exercises in the CIPPool 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 CIPPool, all required software and tools are available.
Handinexercises
 The worksheets are to be solved in groups of two or three people. We will not accept handinexercises 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 David Sean).
 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.