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

Tutorials

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.

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, 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

• 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

• Not so frequently asked questions about GNUPLOT

• Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)

• Short introduction to shell scripting (bash)

• A more detailed introduction to bash scripting

• MIT Opencourseware "Reactive potentials and applications"

• University of Virginia, Introduction to atomistic simulations

• Principles of Multiscale Modeling, Weinan E (2011)

• 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 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)
12.06.2014	Holiday (Pfingsten)
19.06.2014	Holiday (Fronleichnam)
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)

Tutorials

• 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.

• 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	12.06.2014	01.07.2014
Worksheet 6	03.07.2014	15.07.2014

Worksheets

• Worksheet 1 (zip-File with SIESTA input files and attachments) Quantum mechanical approaches - Hückel approximation and DFT methods
  • Worksheet 1 (the work sheet as a single PDF file)
  • SIESTA Download
  • SIESTA Installation Guide
  • Hands-on-tutorial for SIESTA, Lyon 2007

• Worksheet 2 (zip-File with si.fdf) Properties of fermions and Density functional theory
  • Worksheet 2 (the work sheet as a single PDF file)

• Worksheet 3 (zip-File with water topology and input files for GROMACS) Diffusion processes and properties of atomistic water models
  • Worksheet 3 (the work sheet as a single PDF file)
  • GROMACS Download
  • How to visualize GROMACS trajectories with VMD

• Worksheet 4 (pdf-file of the tutorial sheet) Coarse-grained polymers and their properties
  • ESPResSo script-file of the tutorial sheet
  • Hint for theoretical task
  • ESPResSo-Homepage
  • Espresso Download
  • Espresso Manual

• Worksheet 5 (Tar.gz-file of the tutorial sheet with source code) Long range interactions: Direct sum and Ewald summation
  • Worksheet 5 (the work sheet as a single PDF file)
  • Useful literature

• Revised Worksheet 6 (Tar.gz-file with the tutorial sheet, source code and literature) Charge distribution around a charged rod
  • Revised Worksheet 6 (the work sheet as a single PDF file)
  • tutorial6.tcl (Tcl-Script for ESPResSo)

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" (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).