Difference between revisions of "Simulation Methods in Physics II SS 2017"

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*Fri 06.10.2017 at 10am or between 12pm-2pm,
 
*Fri 06.10.2017 at 10am or between 12pm-2pm,
 
*from Mon-Tue 09.10-10.10.2017 between 1pm-3pm,
 
*from Mon-Tue 09.10-10.10.2017 between 1pm-3pm,
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*Wed 11.10.2017 at 2pm.
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<!--*Wed 11.10.2017 at 2pm.-->
  
 
For you preferred date and time, send an e-mail to [[Christian Holm]] and [[Maria Fyta]]. }}
 
For you preferred date and time, send an e-mail to [[Christian Holm]] and [[Maria Fyta]]. }}

Revision as of 19:36, 10 July 2017

Information icon-40x40.png Possible exam dates:
  • Fri 28.07.2017 between 11am-1pm,
  • Wed 04.10.2017 1pm-2pm
  • Thu 05.10.2017 between 10am-2pm,
  • Fri 06.10.2017 at 10am or between 12pm-2pm,
  • from Mon-Tue 09.10-10.10.2017 between 1pm-3pm,
For you preferred date and time, send an e-mail to Christian Holm and Maria Fyta.

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, CIP-Pool (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 hands-on-tutorials 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.

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 hand-in 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, 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.
    [DOI]
  • 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.
    Edition 2.
    Cambridge University Press, 2004. ISBN: 9780511816581.
    [DOI]
  • D. P. Landau, K. Binder.
    A guide to Monte Carlo Simulations in Statistical Physics.
    Edition second edition.
    Cambridge, 2005.
  • Michael Rubinstein, Ralph H. Colby.
    Polymer Physics.
    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.
  • Sauro Succi.
    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.
  • E. Kaxiras.
    Atomic and electronic structure of solids.
    apud Cambridge, Cambridge, 2003.
  • Andrew Leach.
    Molecular Modelling: Principles and Applications.
    apud Pearson Education Ltd., 2001. ISBN: 978-0582382107.


Useful online resources

  • Linux cheat sheet application_pdf.pnghere (53 KB)Info circle.png.
  • Density-functional-theory tight-binding (DFTB): Phil. Trans. R. Soc. A, 372(2011), 20120483. [1], Computational Materials Science 47 (2009) 237–253 [2]
  • 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 Coarse-grained models, simulations of macromolecules and soft matter Lecture Notes (4.25 MB)
04.05.2017 Charged macromolecules Slides (6.94 MB)
11.05.2017 Poisson-Boltzmann 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
08.06.2017 Holiday (Pfingsten)
15.06.2017 Holiday (Fronleichnam)
22.06.2017 Quantum-mechanical methods, introduction application_pdf.pngSlides (2.7 MB)Info circle.png application_pdf.pngLecture Notes (2.94 MB)Info circle.png
29.06.2017 Hartree-Fock, post Hartree Fock application_pdf.pngLecture Notes (4.21 MB)Info circle.png
06.07.2017 Density functional theory and functionals application_pdf.pngLecture Notes (6.48 MB)Info circle.png
13.07.2017 Time-dependent DFT, ab initio MD
20.07.2017 state-of-the art, review

Tutorials

Location and Time

  • The tutorials take place in the CIP-Pool 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


Worksheet 2: Properties of Coarse-grained Polymers


Worksheet 3: Charge distribution around a charged rod


Worksheet 4: Flow Between Plates and Free Energy

Worksheet 5: Quantum chemistry and simple models

Worksheet 6: Density functional theory and ab initio molecular dynamics

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 txt.pngLaTeX template (7 KB)Info circle.png.
  • You can do the exercises in the CIP-Pool 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 CIP-Pool, all required software and tools are available.

Hand-in-exercises

  • The worksheets are to be solved in groups of two or three people. We will not accept hand-in-exercises 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.
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