Simulation Methods in Physics II SS 2014
Overview
 Type
 Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
 Lecturer
 JP. Dr. Maria Fyta, (Lecture), Prof. Dr. Christian Holm; Dr. Jens Smiatek; Mr. Bibek Adhikari; Mr. Narayanan Krishnamoorthy Anand (Tutorials)
 Course language
 English
 Lectures
 Time: Thursdays, 11:30  13:00, ICP, Allmandring 3, Seminarroom 1
Exception: the lecture on 17.04 will be moved to Tue 15.04 at 9:0010:30. There will be two lectures in the week 2125.04 (Tue 22:04 at 910:30 and Thu 24.04 at 11:3013:00) and NO lecture on the 05.06.  Tutorials
 Time: Wednesdays, 8:009:30, ICP, Allmandring 3, CIPPool
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 that contains the lecture "Simulation Methods in Physics II".
The lecture is accompanied by handsontutorials which 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.
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.

Rapaport, D. C..
"The Art of Molecular Dynamics Simulation".
Cambridge University Press, 2004.
[DOI] 
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 10.04.2014 Introduction, electronic stucture Lecture Notes (3.23 MB) 15.04.2014 Elements of quantum mechanics, Hartree and HartreeFock approximations Lecture Notes (7.83 MB) 22.04.2014 Density functional theory (DFT), functionals, pseudopotentials, elements on solid state physics Lecture Notes (7.34 MB) Solid State Phys. (7.75 MB) 24.04.2014 Timedependent density functional theory, postHartreeFock methods ab initio MD Lecture Notes (7.9 MB) 01.05.2014 Holiday (Labor Day) 08.05.2014 Water models (explicit, implicit), Born model of solvation Lecture Notes (3.81 MB) 15.05.2014 Coarsegrained models, simulations of macromolecules and soft matter Lecture Notes (4.27 MB) 22.05.2014 Long range interactions in periodic boundary conditions 29.05.2014 Holiday (Christi Himmelfahrt) 12.06.2014 Holiday (Pfingsten) Implicit solvent models 19.06.2014 Holiday (Fronleichnam) 26.06.2014 PoissonBoltzmann theory, charged polymers 03.07.2014 Hydrodynamic methods: DPD, LatticeBoltzmann 10.07.2014 Advanced MC/MD methods 17.07.2014 Free energy methods Tutorials
 The tutorials will take place in the ICP CIPPool every Wednesday at 8:009:30.
 New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 10.04. The following week is dedicated to working on problems related to the last worksheet. Homework in the form of a report should be sent to the responsible tutor (Bibek Adhikari or Narayanan Krishnamoorthy Anand) before the next worksheet will be handed out. The twoweek cycle ends with the discussion of results of the previous worksheet and handing out a new one.
 The worksheets should be handed in every second Tuesday until 10 am (see dates below).
 Assessment of the tutorials
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.
 Dates:
Worksheet Handed out To be handed in Worksheet 1 10.04.2014 22.04.2014 Worksheet 2 24.04.2014 06.05.2014 Worksheet 3 08.05.2014 20.05.2014 Worksheet 4 22.05.2014 03.06.2014 Worksheet 5 05.06.2014 24.06.2014 Worksheet 6 03.07.2014 15.07.2014 Worksheets
 Worksheet 1 (zipFile with SIESTA input files and attachments) Quantum mechanical approaches  Hückel approximation and DFT methods
 Worksheet 2 (zipFile with si.fdf) Properties of fermions and Density functional theory
 Worksheet 3 (zipFile with water topology and input files for GROMACS) Diffusion processes and properties of atomistic water models
 Worksheet 4 (zipFile with script files for ESPResSo) Coarsegrained simulations with ESPResSo
 Worksheet 4 (pdffile of the tutorial sheet) Coarsegrained polymers and their properties
 ESPResSoHomepage
 Espresso Download
 Espresso Manual
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" (240918005)
 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 us (Maria Fyta, Jens Smiatek).