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

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;Lecturer
 
;Lecturer
:Prof. Dr. [[Christian Holm]], (Lecture); [[Olaf Lenz]], [[Peter Košovan]], [[Florian Dommert]], [[Georg Rempfer]], [[Tobias Richter]] (Tutorials)
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:Prof. Dr. [[Christian Holm]], (Lecture); [[Peter Košovan]], [[Florian Dommert]], [[Georg Rempfer]], [[Tobias Richter]] (Tutorials)
 
;Course language
 
;Course language
 
:English
 
:English
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== Lecture  ==
 
== Lecture  ==
{| class="prettytable"
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To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.
 +
 
 +
{| class="wikitable"
 
|-valign="top"
 
|-valign="top"
!Date !! Subject
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!Date !! Subject || Ressources
 +
 
 +
|-
 +
| 12.04.2012 || Ab initio methods, Quantum mechanics,Hartree-Fock, Density functional theory || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L1_QM.pdf Lecture Notes]
 +
 
 
|-
 
|-
| 12.04.2012 || Ab initio methods, Quantum mechanics,Hartree-Fock, Density functional theory, Carr-Parinello MD
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| 19.04.2012 || Classical force fields, Atomistic simulations, Biomolecules ||
 +
[http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L2_classical_forcefields.pdf Lecture Notes] [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L2_PastedGraphic-1.pdf Graphic]
 
|-
 
|-
| 19.04.2012 || Classical force fields, Atomistic simulations, Biomolecules
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| 26.04.2012 || Water models, Born model of solvation || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L3_Water.pdf Lecture Notes]
  
 
|-
 
|-
| 26.04.2012 || Water models, Born model of solvation
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| 03.05.2012 || Coarse-grained models, simulations of macromolecules and soft matter || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L4_Macrocmolecules_and_Soft_matter.pdf Lecture Notes]
 +
 
 
|-
 
|-
| 03.05.2012 || Coarse-grained models, simulations of macromolecules and soft matter
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| 10.05.2012 || Long range interactions in periodic boundary conditions ||[http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L5_Ewald.pdf Lecture Notes]
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|-
 
|-
| 10.05.2012 || Long range interactions in periodic boundary conditions
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| 17.05.2012 || Holiday (Christi Himmelfahrt) ||
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|-
 
|-
| 17.05.2012 || Holiday (Christi Himmelfahrt)
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| 24.05.2012 ||Long range interactions in periodic boundary conditions,
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||[http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L5_supplement_Ewald.pdf Further reading]
 +
 
 
|-
 
|-
| 24.05.2012 ||Long range interactions in periodic boundary conditions, Poisson-Boltzmann theory
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| 31.05.2012 || '' Holiday (Pfingsten) '' ||
 +
 
 
|-
 
|-
| 31.05.2012 || '' Holiday (Pfingsten) ''
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| 07.06.2012 || '' Holiday (Fronleichnam) '' ||
 +
 
 
|-
 
|-
| 07.06.2012 || '' Holiday (Fronleichnam) ''
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| 14.06.2012 || Poisson-Boltzmann theory, charged polymers
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||[http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L7_PB.pdf Lecture Notes] [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L7_PB_slides.pdf Presentation slides]
 +
 
 
|-
 
|-
| 14.06.2012 || Hydrodynamic methods: Lattice-Boltzmann, Brownian Dynamics, DPD, SRD
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| 21.06.2012 || Hydrodynamic methods: Lattice-Boltzmann, Brownian Dynamics, DPD, SRD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L8_Hydrodynamics.pdf Lecture Notes]
 +
 
 
|-
 
|-
| 21.06.2012 || Hydrodynamic methods II
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| 28.06.2012 || Hydrodynamic methods II ||
 +
 
 
|-
 
|-
| 28.06.2012 || t.b.a.
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| 05.07.2012 || Advanced MC/MD methods || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L9_Free_energy_I.pdf Lecture Notes]
 +
 
 
|-
 
|-
| 05.07.2012 || Advanced MC/MD methods  
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| 12.07.2012 || Free energy methods I || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L10_Free_energy_II.pdf Lecture Notes]
|-
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| 12.07.2012 || Free energy methods I
 
 
|-
 
|-
| 19.07.2012 || Free energy methods II
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| 19.07.2012 || Free energy methods II || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2012-ss-sim_methods/L11_Advanced_MC_MD.pdf Lecture Notes]
 
|}
 
|}
  
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;Scheduling of 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.
 
: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.
 +
 +
;Please send the report to the responsible person indicated with the given tutorial.
 +
:In general, it should be the same person who handed out the tutorial. The name and e-mail in the worksheet are those of the worksheet author, not the responsible tutor!
  
 
=== Tutorial 1 - Error analysis and correlations ===
 
=== Tutorial 1 - Error analysis and correlations ===
* '''Handed out on 18.04.2012, continuead on 25.04.2012''' ([[Peter Košovan]])
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* '''Handed out on 18.04.2012, continuead on 25.04.2012'''
 +
* Send reports to [[Peter Košovan]]
 
* {{Download|Sim_Meth_II_T1_SS_11_12.pdf|Worksheet}}
 
* {{Download|Sim_Meth_II_T1_SS_11_12.pdf|Worksheet}}
 
* {{Download|Sim_Meth_II_T1_SS_11_12.tar.gz|Sourde Code|tar}}
 
* {{Download|Sim_Meth_II_T1_SS_11_12.tar.gz|Sourde Code|tar}}
  
 
=== Tutorial 2 - GROMACS ===
 
=== Tutorial 2 - GROMACS ===
* '''Handed out on 2.5.2012, continued on 9.5.2012''' ([[Florian Dommert]])
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* '''Handed out on 2.5.2012, continued on 9.5.2012'''  
 +
* Send reports to [[Florian Dommert]]
 
* {{Download|Sim_Meth_II_T1_SS_12.pdf|Worksheet}}
 
* {{Download|Sim_Meth_II_T1_SS_12.pdf|Worksheet}}
 
<!--
 
<!--
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=== Tutorial 3 - {{es}}: Simulation of a coarse-grained polymer ===
 
=== Tutorial 3 - {{es}}: Simulation of a coarse-grained polymer ===
* '''Handed out on 16.5.2012, continued on 23.5.2012''' ([[Olaf Lenz]], [[Peter Košovan]])
+
* '''Handed out on 16.5.2012, continued on 23.5.2012'''  
 +
* Send reports to [[Peter Košovan]]
 
* {{Download|Sim_Meth_II_T3_SS_11_12.pdf|Worksheet}}
 
* {{Download|Sim_Meth_II_T3_SS_11_12.pdf|Worksheet}}
 
* {{Download|Sim_Meth_II_SS_10_11_tutorial3.tcl.txt|tutorial3.tcl|text_x_tcl}}
 
* {{Download|Sim_Meth_II_SS_10_11_tutorial3.tcl.txt|tutorial3.tcl|text_x_tcl}}
* {{Download|Sim_Meth_II_SS_10_11_KremerGrest86.pdf|Article of Kremer and Grest, 1986}}
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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 ===
* '''Handed out on 6.6.2012, continued on 13.6.2012''' ([[Peter Košovan]], [[Florian Dommert]])
+
* '''Handed out on 6.6.2012, continued on 13.6.2012'''
<!--
+
* Send reports to [[Florian Dommert]]
* {{Download|Sim_Meth_II_T4_SS_10_11.pdf|Worksheet for tutorial 4}}
+
* {{Download|SimMeth_SoSe2012_Tutorial4.pdf|Worksheet for tutorial 4}}
* {{Download|Sim_Meth_II_SS_10_11_tutorial4.tcl.txt|tutorial4.tcl|text_x_tcl}}
+
* {{Download|SimMeth_SoSe2012_Tutorial4.tcl.txt|tutorial4.tcl|text_x_tcl}}
* {{Download|Deserno00a.pdf|Article of Deserno, 2000}}
 
-->
 
  
 
=== Tutorial 5 - {{es}}: Lattice-Boltzmann fluid ===
 
=== Tutorial 5 - {{es}}: Lattice-Boltzmann fluid ===
* '''Handed out on 20.6.2012, continued on 27.6.2012''' ([[Georg Rempfer]])
+
* '''Handed out on 20.6.2012, continued on 27.6.2012'''
<!--
+
* Send reports to [[Georg Rempfer]]
* {{Download|Sim_Meth_II_T5_SS_10_11.pdf|Worksheet for tutorial 5}}
+
* {{Download|Sim_Meth_II_T5_SS_12.pdf|Worksheet for tutorial 5}} (Updated: Section about ssh tunnels)
* {{Download|Sim_Meth_II_SS_10_11_tutorial5-1.tcl.txt|tutorial5-1.tcl|text_x_tcl}}
+
* {{Download|Sim_Meth_II_T5_SS_12_additional.zip|Additional material}}
* {{Download|Sim_Meth_II_SS_10_11_tutorial5-2.tcl.txt|tutorial5-2.tcl|text_x_tcl}}
+
* [http://www.youtube.com/watch?v=QthmfNoxGbA Demonstration Video]
* {{Download|Sim_Meth_II_SS_10_11_msd.pl.txt|msd.pl|application_x_perl}}
 
-->
 
  
 
=== Tutorial 6 - Advanced MC/MD ===
 
=== Tutorial 6 - Advanced MC/MD ===
* '''Handed out on 4.7.2012, continued on 11.7.2012''' ([[Tobias Richter]])
+
* '''Handed out on 4.7.2012, continued on 11.7.2012'''
<!--
+
* Send reports to [[Tobias Richter]]
* {{Download|Sim_Meth_II_T6_SS_10_11.pdf|Worksheet for tutorial 6}}
+
 
* {{Download|Sim_Meth_II_SS_10_11_tutorial6_src.tgz|tutorial6.tgz|tgz}}
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* {{Download|Sim_Meth_II_T6_SS_12.pdf|Worksheet for tutorial 6}}
-->
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* {{Download|Sim_Meth_II_SS_12_tutorial6_src.zip|Source files tutorial 6}}
  
 
=== Tutorial 7 - Closing ceremony ===
 
=== Tutorial 7 - Closing ceremony ===
* '''18.7.2011''' ([[Peter Košovan]], [[Olaf Lenz]], [[Florian Dommert]], [[Georg Rempfer]], [[Tobias Richter]])
+
* '''18.7.2011'''  
<!--
+
* Discussion of the last tutorial
 
* Evaluation and discussion of the whole course
 
* Evaluation and discussion of the whole course
 
* In case of interest, we may go out together after the end of the tutorial
 
* In case of interest, we may go out together after the end of the tutorial
-->
 
  
 
<br>
 
<br>

Latest revision as of 17:41, 24 October 2012

Overview

Type
Lecture (2 SWS) and Tutorials (2 SWS)
Lecturer
Prof. Dr. Christian Holm, (Lecture); 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

To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.

Date Subject Ressources
12.04.2012 Ab initio methods, Quantum mechanics,Hartree-Fock, Density functional theory Lecture Notes
19.04.2012 Classical force fields, Atomistic simulations, Biomolecules

Lecture Notes Graphic

26.04.2012 Water models, Born model of solvation Lecture Notes
03.05.2012 Coarse-grained models, simulations of macromolecules and soft matter Lecture Notes
10.05.2012 Long range interactions in periodic boundary conditions Lecture Notes
17.05.2012 Holiday (Christi Himmelfahrt)
24.05.2012 Long range interactions in periodic boundary conditions, Further reading
31.05.2012 Holiday (Pfingsten)
07.06.2012 Holiday (Fronleichnam)
14.06.2012 Poisson-Boltzmann theory, charged polymers Lecture Notes Presentation slides
21.06.2012 Hydrodynamic methods: Lattice-Boltzmann, Brownian Dynamics, DPD, SRD Lecture Notes
28.06.2012 Hydrodynamic methods II
05.07.2012 Advanced MC/MD methods Lecture Notes
12.07.2012 Free energy methods I Lecture Notes
19.07.2012 Free energy methods II Lecture Notes

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.
Please send the report to the responsible person indicated with the given tutorial.
In general, it should be the same person who handed out the tutorial. The name and e-mail in the worksheet are those of the worksheet author, not the responsible tutor!

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

  • Handed out on 4.7.2012, continued on 11.7.2012
  • Send reports to Tobias Richter

Tutorial 7 - Closing ceremony

  • 18.7.2011
  • Discussion of the last tutorial
  • Evaluation and discussion of the whole course
  • In case of interest, we may go out together after the end of the tutorial


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.