Difference between revisions of "Simulation Techniques for Soft Matter Sciences (SS 2007)"
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− | = | + | == Overview == |
− | + | ;Type | |
− | + | :Lecture (2 SWS) and Tutorials (2 SWS) | |
− | PD Dr. Christian Holm | + | ;Lecturer |
− | Lecture | + | :PD Dr. [[Christian Holm]] (Lecture) and working group (Tutorials) |
− | Course language: | + | ;Course language |
− | Time and Room: Thu 12:00 - | + | :English |
+ | ;Time and Room | ||
+ | :Lecture: Thu 12:15 - 13:45, Phys 1.114<br/>Tutorials: Thu 14:00-16:00, Phys 1.120 | ||
− | + | Soft matter science is the science of "soft" materials, like polymers, liquid crystals, colloidal suspensions, ionic solutions, hydrogels and most biological matter. The phenomena that define the properties of these materials occur on mesoscopic length and time scales, where thermal fluctuations play a major role. These scales are hard to tackle both experimentally and theoretically. Instead, computer simulations and other computational techniques play a major role. | |
− | |||
− | + | The course will give an introduction to the computational tools that are used in soft matter science, like Monte-Carlo (MC) and Molecular dynamics (MD) simulations (on- and off-lattice) and Poisson-Boltzmann theory (and extensions). | |
− | == | + | == Prerequisites == |
− | + | The course is intended for participants in the Master Program "Computational Science", but should also be useful for FIGSS students and for other interested science students. | |
− | + | 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++). | |
− | === Recommended literature | + | == Lecture and tutorials == |
− | < | + | |
+ | The lecture is accompanied by hands-on-tutorials which will be held in the computer room (Physics, 1.120). They consist of practical excercises at the computer, like small programming tasks, simulations, visualisation and data analysis. | ||
+ | |||
+ | The tutorials build on each other, therefore continous attendance is expected. | ||
+ | |||
+ | '''The dates of the tutorials will be scheduled in the first lecture.''' | ||
+ | |||
+ | === Lecture === | ||
+ | {| | ||
+ | |-valign="top" | ||
+ | !Date !! Subject | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 19.4. | ||
+ | | Monte-Carlo integration/simulation (Simple vs. Importance sampling) | ||
+ | |||
+ | Look at Zuse's Z3 computer from 1941: [http://upload.wikimedia.org/wikipedia/de/4/4c/Z3_Deutsches_Museum.JPG Z3] and | ||
+ | read something about the first big US computer at Los Alamos [http://www.lanl.gov/history/atomicbomb/computers.shtml Evolving from Calculators to Computers] | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 26.4. | ||
+ | | 2D Random walks (RW) and Self-avoiding random walks (SAW)--Ising model I (Phase transitions, Critical phenomena, Finite size scaling) | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 3.5. | ||
+ | | 2D Ising model II (Reweighting, Cluster Algorithm) | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 10.5. | ||
+ | | Error Analysis (Binning, Jackknife, ...) | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 17.5. | ||
+ | | '''Holiday''' | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 24.5. | ||
+ | | Molecular Dynamics I (Velocity Verlet algorithm, Reduced units, Langevin thermostat, Potentials, Forces, Atomistic force fields) | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 31.5. | ||
+ | | Molecular Dynamics II | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 7.6. | ||
+ | | '''Holiday''' | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 14.6. | ||
+ | | Long range interactions (Direct sum, Ewald summation, P3M, Fast Multipole method) | ||
+ | This pdf file {{Download|long_range_lecture.pdf|long_range_lecture.pdf}} contains surely too many details, but I will walk you through in class. In case you like to have some more background material, here is a review article by A. Arnold and me about this topic ({{Download|arnold05a.pdf|arnold05a.pdf}}) | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 21.6. | ||
+ | | Continuation of long range lecture, beginning of ''How to simulate Polymers and Polyelectrolytes''. | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 28.6. | ||
+ | | 12:15 Tutorial--14:30 Talk by Prof. Binder in Seminar room 2.116, | ||
+ | |||
+ | Afterwards we meet in the Computer room: Continuation on ''How to simulate Polymers and Polyelectrolytes'' and background of Poisson-Boltzmann Theory. | ||
+ | |-valign="top" | ||
+ | ! 5.7. | ||
+ | | Introduction to the Project work: charged infinite rods in ionic solution-comparison to PB theory. {{Download|CompMethods.pdf|CompMethods.pdf}} | ||
+ | |||
+ | A good background reading is the thesis of M. Deserno {{Download|deserno00b.pdf|thesis_deserno.pdf}} | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 12.7. | ||
+ | | Extended tutorial I: project work | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 19.7. | ||
+ | | Extended tutorial II: project work | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 23.7. | ||
+ | | <span style="color:black;border: solid red"> On this Monday from 10:00 on we will have the oral examination in my office 01.218! </span>. | ||
+ | |||
+ | |} | ||
+ | |||
+ | === Tutorials === | ||
+ | Materials on the tutorials can be found behind the links! | ||
+ | |||
+ | {| | ||
+ | |||
+ | |-valign="top" | ||
+ | !Date !! Subject !! Tutors | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 19.4. | ||
+ | | [[/Introduction|Introductory tutorial]] | ||
+ | | [[Kai Grass]] | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 26.4. | ||
+ | | [[/Random walks|Random walks]] | ||
+ | | [[Kai Grass]] | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 3.5. | ||
+ | | [[/Ising 1|Monte Carlo: The Ising model I]] | ||
+ | | [[Marcello Sega]] | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 10.5. | ||
+ | | [[/Ising 2|Monte Carlo: The Ising model II]] | ||
+ | | [[Marcello Sega]] | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 17.5. | ||
+ | | '''Holiday''' | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 24.5. | ||
+ | | [[/Error analysis|Error analysis]] | ||
+ | | [[Joan Josep Cerdà]] | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 31.5. | ||
+ | | [[/Molecular Dynamics|Molecular Dynamics: Lennard-Jones liquid]] | ||
+ | | [[Qiao Baofu]] | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 7.6. | ||
+ | | '''Holiday''' | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 14.6. | ||
+ | | [[/ESPResSo|Introduction to MD simulations with ESPResSo]] | ||
+ | | [[Mehmet Süzen]] | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 21.6. | ||
+ | | [[/Ewald summation|Long range interactions: Direct sum and Ewald summation]] | ||
+ | | [[Joan Josep Cerdà]] | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 28.6. | ||
+ | | [[/VMD|Visualisation of MD simulations with VMD]] | ||
+ | | [[Olaf Lenz]] | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 5.7. | ||
+ | | [[/Simulating polymers|Simulation of polymers and polyeletrolytes]] | ||
+ | | [[Qiao Baofu]] | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 12.7. | ||
+ | | [[/Project|Extended tutorial I: project work]] | ||
+ | | [[Olaf Lenz]] and [[Mehmet Süzen]] | ||
+ | |||
+ | |-valign="top" | ||
+ | ! 19.7. | ||
+ | | [[/Project|Extended tutorial II: project work]] | ||
+ | | [[Olaf Lenz]] and [[Mehmet Süzen]] | ||
+ | |||
+ | |} | ||
+ | |||
+ | == Recommended literature == | ||
+ | <bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a</bibentry> |
Latest revision as of 12:47, 16 July 2007
Overview
- Type
- Lecture (2 SWS) and Tutorials (2 SWS)
- Lecturer
- PD Dr. Christian Holm (Lecture) and working group (Tutorials)
- Course language
- English
- Time and Room
- Lecture: Thu 12:15 - 13:45, Phys 1.114
Tutorials: Thu 14:00-16:00, Phys 1.120
Soft matter science is the science of "soft" materials, like polymers, liquid crystals, colloidal suspensions, ionic solutions, hydrogels and most biological matter. The phenomena that define the properties of these materials occur on mesoscopic length and time scales, where thermal fluctuations play a major role. These scales are hard to tackle both experimentally and theoretically. Instead, computer simulations and other computational techniques play a major role.
The course will give an introduction to the computational tools that are used in soft matter science, like Monte-Carlo (MC) and Molecular dynamics (MD) simulations (on- and off-lattice) and Poisson-Boltzmann theory (and extensions).
Prerequisites
The course is intended for participants in the Master Program "Computational Science", but should also be useful for FIGSS students and for other interested science students.
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++).
Lecture and tutorials
The lecture is accompanied by hands-on-tutorials which will be held in the computer room (Physics, 1.120). They consist of practical excercises at the computer, like small programming tasks, simulations, visualisation and data analysis.
The tutorials build on each other, therefore continous attendance is expected.
The dates of the tutorials will be scheduled in the first lecture.
Lecture
Date | Subject |
---|---|
19.4. | Monte-Carlo integration/simulation (Simple vs. Importance sampling)
Look at Zuse's Z3 computer from 1941: Z3 and read something about the first big US computer at Los Alamos Evolving from Calculators to Computers |
26.4. | 2D Random walks (RW) and Self-avoiding random walks (SAW)--Ising model I (Phase transitions, Critical phenomena, Finite size scaling) |
3.5. | 2D Ising model II (Reweighting, Cluster Algorithm) |
10.5. | Error Analysis (Binning, Jackknife, ...) |
17.5. | Holiday |
24.5. | Molecular Dynamics I (Velocity Verlet algorithm, Reduced units, Langevin thermostat, Potentials, Forces, Atomistic force fields) |
31.5. | Molecular Dynamics II |
7.6. | Holiday |
14.6. | Long range interactions (Direct sum, Ewald summation, P3M, Fast Multipole method)
This pdf file |
21.6. | Continuation of long range lecture, beginning of How to simulate Polymers and Polyelectrolytes. |
28.6. | 12:15 Tutorial--14:30 Talk by Prof. Binder in Seminar room 2.116,
Afterwards we meet in the Computer room: Continuation on How to simulate Polymers and Polyelectrolytes and background of Poisson-Boltzmann Theory. |
5.7. | Introduction to the Project work: charged infinite rods in ionic solution-comparison to PB theory. ![]() ![]() A good background reading is the thesis of M. Deserno |
12.7. | Extended tutorial I: project work |
19.7. | Extended tutorial II: project work |
23.7. | On this Monday from 10:00 on we will have the oral examination in my office 01.218! . |
Tutorials
Materials on the tutorials can be found behind the links!
Date | Subject | Tutors |
---|---|---|
19.4. | Introductory tutorial | Kai Grass |
26.4. | Random walks | Kai Grass |
3.5. | Monte Carlo: The Ising model I | Marcello Sega |
10.5. | Monte Carlo: The Ising model II | Marcello Sega |
17.5. | Holiday | |
24.5. | Error analysis | Joan Josep Cerdà |
31.5. | Molecular Dynamics: Lennard-Jones liquid | Qiao Baofu |
7.6. | Holiday | |
14.6. | Introduction to MD simulations with ESPResSo | Mehmet Süzen |
21.6. | Long range interactions: Direct sum and Ewald summation | Joan Josep Cerdà |
28.6. | Visualisation of MD simulations with VMD | Olaf Lenz |
5.7. | Simulation of polymers and polyeletrolytes | Qiao Baofu |
12.7. | Extended tutorial I: project work | Olaf Lenz and Mehmet Süzen |
19.7. | Extended tutorial II: project work | Olaf Lenz and Mehmet Süzen |
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.
-
M. E. J. Newman, G. T. Barkema.
Monte Carlo Methods in Statistical Physics.
Edition 2002 edition.
Oxford University Press, 1999.