Simulation Methods in Physics II SS 2014
- Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
- JP. Dr. Maria Fyta, (Lecture), Prof. Dr. Christian Holm; Dr. Jens Smiatek; Mr. Bibek Adhikari; Mr. Narayanan Krishnamoorthy Anand (Tutorials)
- Course language
- Time: Thursdays, 11:30 - 13:00, ICP, Allmandring 3, Seminarroom 1
- Time: Wednesdays, 8:00-9:30, ICP, Allmandring 3, CIP-Pool
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 hands-on-tutorials which 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.
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.
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.
- 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.
Please email to Christian Holm in order to arrange a date in September or october for the oral examination.
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.
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.
Cambridge University Press, 2004. ISBN: 9780511816581.
D. P. Landau, K. Binder.
A guide to Monte Carlo Simulations in Statistical Physics.
Edition second edition.
Michael Rubinstein, Ralph H. Colby.
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.
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.
Atomic and electronic structure of solids.
apud Cambridge, Cambridge, 2003.
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
- 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.
|10.04.2014||Introduction, electronic stucture||Lecture Notes (3.23 MB)|
|15.04.2014||Elements of quantum mechanics, Hartree and Hartree-Fock 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||Time-dependent density functional theory, post-Hartree-Fock 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||Coarse-grained models, simulations of macromolecules and soft matter||Lecture Notes (4.27 MB)|
|22.05.2014||Continuation: CG models||Lecture Notes (3.78 MB)|
|29.05.2014||Holiday (Christi Himmelfahrt)|
|05.06.2014||Long range interactions in periodic boundary conditions||Lecture Notes (2.32 MB)|
|26.06.2014||Poisson-Boltzmann theory, charged polymers||Lecture Notes (8.55 MB)|
|03.07.2014||Free energy methods||Lecture Notes (3.44 MB)|
|10.07.2014||Advanced MC/MD methods||Lecture Notes (3.61 MB)|
|17.07.2014||Hydrodynamic methods: DPD, Lattice-Boltzmann||Lecture Notes (3.84 MB)|
- The tutorials will take place in the ICP CIP-Pool every Wednesday at 8:00-9:30.
- 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 two-week 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.
|Worksheet||Handed out||To be handed in|
- Worksheet 1 (zip-File with SIESTA input files and attachments) Quantum mechanical approaches - Hückel approximation and DFT methods
- Worksheet 2 (zip-File with si.fdf) Properties of fermions and Density functional theory
- Worksheet 3 (zip-File with water topology and input files for GROMACS) Diffusion processes and properties of atomistic water models
- Worksheet 4 (pdf-file of the tutorial sheet) Coarse-grained polymers and their properties
- Worksheet 5 (Tar.gz-file of the tutorial sheet with source code) Long range interactions: Direct sum and Ewald summation
- Revised Worksheet 6 (Tar.gz-file with the tutorial sheet, source code and literature) Charge distribution around a charged rod
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" (240918-005)
- 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).