Difference between revisions of "Simulation Methods in Physics II SS 2012"

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* [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/KremerGrest86.pdf Article of Kremer and Grest, 1986]
  
 
=== Tutorial 4 - {{es}}: Simulation of a charged rod with counterions ===
 
=== Tutorial 4 - {{es}}: Simulation of a charged rod with counterions ===

Revision as of 12:38, 1 June 2012

Overview

Type
Lecture (2 SWS) and Tutorials (2 SWS)
Lecturer
Prof. Dr. Christian Holm, (Lecture); Olaf Lenz, Peter Košovan, Florian Dommert, Georg Rempfer, Tobias Richter (Tutorials)
Course language
English
Lectures
Time: Thursdays, 11:30 - 13:00, Room V 57.06
Tutorials
Time: Wednesday, 14:00-15.30, 2 hours, Room U 104

The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 104. 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 (preferably C or C++). 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 the hand-in exercises

There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II) determined at the end of lecture Simulation Methods II.

The final grade will be determined in the following way: There will be an oral examination performed at (or after) the end of the course Simulation Methods II (SS 2011).

Recommended literature


Useful online resources

  • Linux cheat sheet application_pdf.pnghere (53 KB)Info circle.png.
  • 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
12.04.2012 Ab initio methods, Quantum mechanics,Hartree-Fock, Density functional theory, Carr-Parinello MD
19.04.2012 Classical force fields, Atomistic simulations, Biomolecules
26.04.2012 Water models, Born model of solvation
03.05.2012 Coarse-grained models, simulations of macromolecules and soft matter
10.05.2012 Long range interactions in periodic boundary conditions
17.05.2012 Holiday (Christi Himmelfahrt)
24.05.2012 Long range interactions in periodic boundary conditions, Poisson-Boltzmann theory
31.05.2012 Holiday (Pfingsten)
07.06.2012 Holiday (Fronleichnam)
14.06.2012 Hydrodynamic methods: Lattice-Boltzmann, Brownian Dynamics, DPD, SRD
21.06.2012 Hydrodynamic methods II
28.06.2012 t.b.a.
05.07.2012 Advanced MC/MD methods
12.07.2012 Free energy methods I
19.07.2012 Free energy methods II

Tutorials

Scheduling of tutorials
New worksheets are handed out every two weeks (see the list below). 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.

Tutorial 1 - Error analysis and correlations

Tutorial 2 - GROMACS

Tutorial 3 - ESPResSo: Simulation of a coarse-grained polymer

Tutorial 4 - ESPResSo: Simulation of a charged rod with counterions

Tutorial 5 - ESPResSo: Lattice-Boltzmann fluid

Tutorial 6 - Advanced MC/MD

Tutorial 7 - Closing ceremony


Tutorials in 2012 are mostly based on the ones from previous year. Updated worksheets will be made available online on the day when they should be handed out. If you want to take a look ahead and see what is coming, have a look at the worksheets from the previous year.

Obtaining extra points
The first person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. The same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints, but these are not awarded extra points.
Guidelines for submitting tutorial reports
Same as as in the previous semester.