Difference between revisions of "Simulation Methods in Physics II SS 2015"

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!Date !! Subject || Resources
 
!Date !! Subject || Resources
 
 
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| 16.04.2015 || Introduction, Ab initio methods, Quantum mechanics, Hartree-Fock || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture01_notes.pdf|Lecture Notes}}
 
| 16.04.2015 || Introduction, Ab initio methods, Quantum mechanics, Hartree-Fock || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture01_notes.pdf|Lecture Notes}}
 
|-
 
|-
| 23.04.2015 || Density functional theory, Carr-Parinello MD  || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture02_notes.pdf|Lecture Notes}}
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| 23.04.2015 || Density functional theory, Car-Parrinello MD  || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture02_notes.pdf|Lecture Notes}}
 
 
 
|-
 
|-
 
| 30.04.2015 || Classical force fields, Atomistic simulations, Biomolecules || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture03_notes.pdf|Lecture Notes}}
 
| 30.04.2015 || Classical force fields, Atomistic simulations, Biomolecules || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture03_notes.pdf|Lecture Notes}}
 
 
|-
 
|-
 
| 07.05.2015 || Water models, Born model of solvation || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture04_notes.pdf|Lecture Notes}}
 
| 07.05.2015 || Water models, Born model of solvation || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture04_notes.pdf|Lecture Notes}}
 
 
|-
 
|-
 
| 14.05.2015 || '' Holiday (Christi Himmelfahrt) ''  ||
 
| 14.05.2015 || '' Holiday (Christi Himmelfahrt) ''  ||
 
 
 
|-
 
|-
 
| 21.05.2015 || Coarse-grained models, simulations of macromolecules and soft matter || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}
 
| 21.05.2015 || Coarse-grained models, simulations of macromolecules and soft matter || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}
 
 
|-
 
|-
 
| 28.05.2015 || '' Holiday (Pfingsten) ''  ||  
 
| 28.05.2015 || '' Holiday (Pfingsten) ''  ||  
 
 
|-
 
|-
 
| 04.06.2015 ||  '' Holiday (Fronleichnam) '' ||  
 
| 04.06.2015 ||  '' Holiday (Fronleichnam) '' ||  
 
 
|-
 
|-
 
| 11.06.2015 ||  Long range interactions in periodic boundary conditions || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture06_notes.pdf|Lecture Notes}}
 
| 11.06.2015 ||  Long range interactions in periodic boundary conditions || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture06_notes.pdf|Lecture Notes}}
 
|-
 
|-
| 18.06.2015 || Poisson-Boltzmann theory, charged polymers I  || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture07_notes.pdf|Lecture Notes}}
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| 18.06.2015 || Poisson-Boltzmann theory, charged polymers I  || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture07_notes.pdf|Slides}}
 
 
 
|-
 
|-
| 25.06.2015 || Poisson-Boltzmann theory, charged polymers I || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture08_notes.pdf|Lecture Notes}}
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| 25.06.2015 || Poisson-Boltzmann theory, charged polymers II || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture08_notes.pdf|Lecture Notes}}
 
 
 
 
 
|-
 
|-
| 02.07.2015 || Hydrodynamic methods I Stokesian and Brownian Dynamics || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture09_notes.pdf|Lecture Notes}} {{DownloadExt|/teaching/2015-ss-sim_methods/lecture09_slides.pdf|Slides}}
+
| 02.07.2015 || Hydrodynamic methods I Stokesian and Brownian Dynamics || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture09_notes.pdf|Lecture Notes}}, {{DownloadExt|/teaching/2015-ss-sim_methods/lecture09_slides.pdf|Slides}}
 
|-
 
|-
| 09.07.2015 || Hydrodynamic methods II Lattice-Boltzmann, DPD, MPCD ||
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| 09.07.2015 || Hydrodynamic methods II Lattice-Boltzmann, DPD, MPCD || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture10_notes.pdf|Lecture Notes}}
 
 
 
|-
 
|-
| 16.07.2015 || Advanced MC/MD methods ||
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| 16.07.2015 || Advanced MC/MD methods || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture11_notes.pdf|Lecture Notes}}
 
 
 
|-
 
|-
| 23.07.2015 || Free energy methods I ||
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| 23.07.2015 || Free energy methods || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture12_notes.pdf|Lecture Notes}}
 
 
 
 
 
|}
 
|}
  
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* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) on
 
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) on
 
** Thu 14:00-15:30 (Tutor: [[Bibek Adhikari]] / [[Johannes Zeman]] / [[Florian Weik]])
 
** Thu 14:00-15:30 (Tutor: [[Bibek Adhikari]] / [[Johannes Zeman]] / [[Florian Weik]])
 +
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=== Worksheets ===
  
=== Worksheets ===
+
==== Worksheet 6: Advanced MD/MC: The Widom insertion method ====
 +
* Deadline: '''July 21, 2015, 12:00 p.m. (noon)'''
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* {{Download|SS_2015_SM2_worksheet6.pdf|Worksheet 6}}
 +
* {{Download|SS_2015_SM2_worksheet6_template.tcl|template.tcl|txt}} - ESPResSo sample script
 
<!--
 
<!--
==== Worksheet 6: Free energy methods ====
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* {{Download|SS_2015_SM2_WS6_solution.pdf|Solution|pdf}} - Sample solution
* Deadline: '''February 09, 2015, 10:00 a.m.'''
 
* {{Download|SS_2015_SM2_worksheet6.pdf|Worksheet 6}}
 
* {{Download|SS_2015_SM2_WS6_solution.tar.gz|solution.tar.gz|tgz}} - Archive containing the sample solution
 
 
-->
 
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+
<!--
==== Worksheet 5: Hydrodynamics and the Lattice-Boltzmann Method ====
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==== Worksheet 5: Hydrodynamics and the Lattice-Boltzmann method ====
 
* Deadline: '''July 13, 2015, 12:00 p.m. (noon)'''
 
* Deadline: '''July 13, 2015, 12:00 p.m. (noon)'''
 
* {{Download|SS_2015_SM2_worksheet5.pdf|Worksheet 5}}
 
* {{Download|SS_2015_SM2_worksheet5.pdf|Worksheet 5}}
 
* {{Download|SS_2015_SM2_worksheet5_templates.tar.gz|templates.tar.gz|tgz}} - Archive containing template scripts
 
* {{Download|SS_2015_SM2_worksheet5_templates.tar.gz|templates.tar.gz|tgz}} - Archive containing template scripts
* {{DownloadExt|/videos/turbulent_video_web.avi|Sample Movie}}
 
 
<!--
 
<!--
* {{Download|SS_2015_SM2_WS5_solution.tar.gz|solution.tar.gz|tgz}} - Archive containing the sample solution
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* {{Download|SS_2015_SM2_WS5_solution.pdf|Solution|pdf}} - Sample solution
 
-->
 
-->
==== Worksheet 4: Charge Distribution Around a Charged Rod ====
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* Sample videos:
 +
{{#widget:YouTube|id=A2zCOfrjH-Q|width=400|height=225}} {{#widget:YouTube|id=GYRRGuYoNF4|width=400|height=225}}
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-->
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 +
<!--
 +
==== Worksheet 4: Charge distribution around a charged rod ====
 
* Deadline: '''June 29, 2015, 12:00 p.m. (noon)'''
 
* Deadline: '''June 29, 2015, 12:00 p.m. (noon)'''
 
* {{Download|SS_2015_SM2_worksheet4.pdf|Worksheet 4}}
 
* {{Download|SS_2015_SM2_worksheet4.pdf|Worksheet 4}}
 
* {{Download|SS_2015_SM2_worksheet4_template.tcl|template.tcl|txt}} - ESPResSo sample script
 
* {{Download|SS_2015_SM2_worksheet4_template.tcl|template.tcl|txt}} - ESPResSo sample script
 
<!--
 
<!--
* {{Download|SS_2015_SM2_WS4_solution.tar.gz|solution.tar.gz|tgz}} - Archive containing the sample solution
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* {{Download|SS_2015_SM2_WS4_solution.pdf|Solution|pdf}} - Sample solution
 
-->
 
-->
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-->
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 +
<!--
 
==== Worksheet 3: Coarse-grained polymers and their properties ====
 
==== Worksheet 3: Coarse-grained polymers and their properties ====
 
* Deadline: '''June 15, 2015, 12:00 p.m. (noon)'''
 
* Deadline: '''June 15, 2015, 12:00 p.m. (noon)'''
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* {{Download|SS_2015_SM2_worksheet3_template.tcl|template.tcl|txt}} - ESPResSo sample script
 
* {{Download|SS_2015_SM2_worksheet3_template.tcl|template.tcl|txt}} - ESPResSo sample script
 
<!--
 
<!--
* {{Download|SS_2015_SM2_WS3_solution.tar.gz|solution.tar.gz|tgz}} - Archive containing the sample solution
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* {{Download|SS_2015_SM2_WS3_solution.pdf|Solution|pdf}} - Sample solution
 
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==== Worksheet 2: Diffusion processes and properties of atomistic water models ====
 
==== Worksheet 2: Diffusion processes and properties of atomistic water models ====
 
* Deadline: '''May 25, 2015, 12:00 p.m. (noon)'''
 
* Deadline: '''May 25, 2015, 12:00 p.m. (noon)'''
 
* {{Download|SS_2015_SM2_worksheet2.pdf|Worksheet 2}}
 
* {{Download|SS_2015_SM2_worksheet2.pdf|Worksheet 2}}
 
* {{Download|SS_2015_SM2_worksheet2_templates.tar.gz|templates.tar.gz|tgz}} - Archive containing GROMACS input files
 
* {{Download|SS_2015_SM2_worksheet2_templates.tar.gz|templates.tar.gz|tgz}} - Archive containing GROMACS input files
* {{Download|SS_2015_SM2_WS2_solution.pdf|solution.pdf|pdf}} - Sample solution
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<!--
 +
* {{Download|SS_2015_SM2_WS2_solution.pdf|Solution|pdf}} - Sample solution
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-->
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 +
<!--
 
==== Worksheet 1: Quantum mechanical approaches: Hückel approximation and ab-initio methods ====
 
==== Worksheet 1: Quantum mechanical approaches: Hückel approximation and ab-initio methods ====
 
* Deadline: '''May 5, 2015, 12:00 p.m. (noon)'''
 
* Deadline: '''May 5, 2015, 12:00 p.m. (noon)'''
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* {{Download|SS_2015_SM2_WS1_solution.tar.gz|solution.tar.gz|tgz}} - Archive containing the sample solution
 
* {{Download|SS_2015_SM2_WS1_solution.tar.gz|solution.tar.gz|tgz}} - Archive containing the sample solution
 
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=== General Remarks ===
 
=== General Remarks ===

Latest revision as of 17:03, 2 June 2019

Overview

Type
Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
Lecturer
Prof. Dr. Christian Holm
Course language
English
Location and Time
Lecture: Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)
Tutorials: Thu, 14:00 - 15:30 (Tutors: Bibek Adhikari, Johannes Zeman, and Florian Weik); 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. 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


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 Resources
16.04.2015 Introduction, Ab initio methods, Quantum mechanics, Hartree-Fock Lecture Notes (4.78 MB)
23.04.2015 Density functional theory, Car-Parrinello MD Lecture Notes (1.84 MB)
30.04.2015 Classical force fields, Atomistic simulations, Biomolecules Lecture Notes (1.37 MB)
07.05.2015 Water models, Born model of solvation Lecture Notes (3.81 MB)
14.05.2015 Holiday (Christi Himmelfahrt)
21.05.2015 Coarse-grained models, simulations of macromolecules and soft matter Lecture Notes (4.25 MB)
28.05.2015 Holiday (Pfingsten)
04.06.2015 Holiday (Fronleichnam)
11.06.2015 Long range interactions in periodic boundary conditions Lecture Notes (4.01 MB)
18.06.2015 Poisson-Boltzmann theory, charged polymers I Slides (6.94 MB)
25.06.2015 Poisson-Boltzmann theory, charged polymers II Lecture Notes (171 kB)
02.07.2015 Hydrodynamic methods I Stokesian and Brownian Dynamics Lecture Notes (3.84 MB), Slides (2 MB)
09.07.2015 Hydrodynamic methods II Lattice-Boltzmann, DPD, MPCD Lecture Notes (2.63 MB)
16.07.2015 Advanced MC/MD methods Lecture Notes (1.59 MB)
23.07.2015 Free energy methods Lecture Notes (4.2 MB)

Tutorials

Location and Time

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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/2015.
  • For the reports, we have a nice txt.pnglatex-template.tex (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 (Bibek Adhikari or Johannes Zeman).
  • 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.

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 (Christian Holm, Jens Smiatek).