Difference between revisions of "Simulation Methods in Physics II SS 2015"
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==== Worksheet 2: Diffusion processes and properties of atomistic water models ====  ==== Worksheet 2: Diffusion processes and properties of atomistic water models ====  
* Deadline: '''May 25, 2015, 12:00 p.m. (noon)'''  * Deadline: '''May 25, 2015, 12:00 p.m. (noon)''' 
Revision as of 18:58, 9 July 2015
Overview
 Type
 Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
 Lecturer
 Prof. Dr. Christian Holm
 Course language
 English
 Location and Time
 Lecture: Thu, 11:30  13:00; ICP, Allmandring 3, Seminar Room (room 01.079)
 Tutorials: Thu, 14:00  15:30 (Tutors: Bibek Adhikari, Johannes Zeman, and Florian Weik); 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 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.

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 

16.04.2015  Introduction, Ab initio methods, Quantum mechanics, HartreeFock  Lecture Notes (4.78 MB) 
23.04.2015  Density functional theory, CarrParinello MD  Lecture Notes (1.84 MB) 
30.04.2015  Classical force fields, Atomistic simulations, Biomolecules  Lecture Notes (1.37 MB) 
07.05.2015  Water models, Born model of solvation  Lecture Notes (3.81 MB) 
14.05.2015  Holiday (Christi Himmelfahrt) 

21.05.2015  Coarsegrained models, simulations of macromolecules and soft matter  Lecture Notes (4.25 MB) 
28.05.2015  Holiday (Pfingsten)  
04.06.2015  Holiday (Fronleichnam)  
11.06.2015  Long range interactions in periodic boundary conditions  Lecture Notes (4.01 MB) 
18.06.2015  PoissonBoltzmann theory, charged polymers I  Slides (6.94 MB) 
25.06.2015  PoissonBoltzmann theory, charged polymers II  Lecture Notes (171 kB)

02.07.2015  Hydrodynamic methods I Stokesian and Brownian Dynamics  Lecture Notes (3.84 MB), Slides (2 MB) 
09.07.2015  Hydrodynamic methods II LatticeBoltzmann, DPD, MPCD  
16.07.2015  Advanced MC/MD methods  
23.07.2015  Free energy methods I 

Tutorials
Location and Time
 The tutorials take place in the CIPPool on the first floor of the ICP (Room 01.033, Allmandring 3) on
 Thu 14:0015:30 (Tutor: Bibek Adhikari / Johannes Zeman / Florian Weik)
Worksheets
Worksheet 5: Hydrodynamics and the LatticeBoltzmann Method
 Deadline: July 13, 2015, 12:00 p.m. (noon)
 Worksheet 5 (503 KB)
 templates.tar.gz (1.26 MB)  Archive containing template scripts
 Sample Movie (33.2 MB)
Worksheet 4: Charge Distribution Around a Charged Rod
 Deadline: June 29, 2015, 12:00 p.m. (noon)
 Worksheet 4 (286 KB)
 template.tcl (7 KB)  ESPResSo sample script
 solution.pdf (409 KB)  Sample solution
Worksheet 3: Coarsegrained polymers and their properties
 Deadline: June 15, 2015, 12:00 p.m. (noon)
 Worksheet 3 (241 KB)
 template.tcl (7 KB)  ESPResSo sample script
 solution.pdf (265 KB)  Sample solution
Worksheet 2: Diffusion processes and properties of atomistic water models
 Deadline: May 25, 2015, 12:00 p.m. (noon)
 Worksheet 2 (265 KB)
 templates.tar.gz (12 KB)  Archive containing GROMACS input files
 solution.pdf (445 KB)  Sample solution
Worksheet 1: Quantum mechanical approaches: Hückel approximation and abinitio methods
 Deadline: May 5, 2015, 12:00 p.m. (noon)
 Worksheet 1 (149 KB)
 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/2015
.  For the reports, we have a nice latextemplate.tex (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 (Bibek Adhikari or Johannes Zeman).
 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.
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 (Christian Holm, Jens Smiatek).