Difference between revisions of "Simulation Methods in Physics II SS 2016"

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{{Infobox| Exam dates: Mo 19.9.2016 between 10am-14pm and Wed 12.10.2016 between 10am-12pm and 14-15pm. Please, send an e-mail to [[Christian Holm]] with your preferred date and time. }}
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== Overview ==
 
== Overview ==
  
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;Location and Time
 
;Location and Time
:'''Lecture''': tba <!-- Thu, 11:30 - 13:00; ICP, Allmandring 3-->, Seminar Room (room 01.079)
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:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3-->, Seminar Room (room 01.079)
:'''Tutorials''': tba <!-- Thu, 14:00 - 15:30--> (Tutors: Dr. [[Frank Uhlig]], [[Johannes Zeman]]; ICP, Allmandring 3, CIP-Pool (room 01.033)
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:'''Tutorials''': Thu, 14:00 - 15:30 (Tutors: Dr. [[Frank Uhlig]], [[Johannes Zeman]]; 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".
 
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".
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!Date !! Subject || Resources
 
!Date !! Subject || Resources
 
|-
 
|-
| 07.04.2016 || Introduction, Ab initio methods, Quantum mechanics, Hartree-Fock || {{  Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}} {{  Download|simmethodsII_ss16_lecture1notes.pdf|Lecture Notes}} {{Download|SimmethodsII_ss16_worksheet1.pdf|Worksheet}}
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| 07.04.2016 || Introduction, Ab initio methods, Quantum mechanics, Hartree-Fock || {{  Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}} {{  Download|simmethodsII_ss16_lecture1notes.pdf|Lecture Notes}}
 
|-
 
|-
| 14.04.2016 || Density functional theory, Car-Parrinello MD  || <!--{{|Lecture Notes}}-->
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| 14.04.2016 || Density functional theory, Car-Parrinello MD  || {{ Download|simmethodsII_ss16_lecture2.compressed.pdf|Lecture Notes}}  
 
|-
 
|-
| 21.04.2016 || Classical force fields, Atomistic simulations, Biomolecules || <!--{{|Lecture Notes}}-->
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| 21.04.2016 || ab initio MD, post Hartree-Fock methods ||{{ Download|simmethodsII_ss16_lecture3.pdf |Lecture Notes}}  
 
|-
 
|-
| 28.04.2016 || Water models, Born model of solvation || <!--{{|Lecture Notes}}-->
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| 28.04.2016 || Classical force fields, Atomistic simulations, Biomolecules, Water models || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture03_notes.pdf|Lecture Notes}} {{DownloadExt|/teaching/2015-ss-sim_methods/lecture04_notes.pdf|Lecture Notes}}
 
|-
 
|-
 
| 05.05.2016 || '' Holiday (Christi Himmelfahrt) ''  ||
 
| 05.05.2016 || '' Holiday (Christi Himmelfahrt) ''  ||
 
|-
 
|-
| 12.05.2016 || Coarse-grained models, simulations of macromolecules and soft matter || <!--{{|Lecture Notes}}-->
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| 12.05.2016 || Coarse-grained models, simulations of macromolecules and soft matter || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}
 
|-
 
|-
 
| 19.05.2016 || '' Holiday (Pfingsten) ''  ||  
 
| 19.05.2016 || '' Holiday (Pfingsten) ''  ||  
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| 26.05.2016 ||  '' Holiday (Fronleichnam) '' ||  
 
| 26.05.2016 ||  '' Holiday (Fronleichnam) '' ||  
 
|-
 
|-
| 02.06.2016 || Long range interactions in periodic boundary conditions || <!--{{|Lecture Notes}}-->
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| 02.06.2016 || Poisson-Boltzmann theory, charged polymers || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture07_notes.pdf|Slides}}
 
|-
 
|-
| 09.06.2016 || Poisson-Boltzmann theory, charged polymers || <!--{{|Slides}}-->
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| 09.06.2016 || Poisson-Boltzmann theory, charged polymers cont. || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture08_notes.pdf|Lecture Notes}}
 
|-
 
|-
| 16.06.2016 || Poisson-Boltzmann theory, charged polymers II  || <!--{{|Lecture Notes}}-->
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| 16.06.2016 || Long range interactions in periodic boundary conditions || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture06_notes.pdf|Lecture Notes}}
 
|-
 
|-
| 23.06.2016 || Hydrodynamic methods I Stokesian and Brownian Dynamics || <!--{{|Slides}}-->
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| 23.06.2016 || Hydrodynamic methods I Stokesian and Brownian Dynamics || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture09_slides.pdf|Lecture Notes}} {{DownloadExt|/teaching/2015-ss-sim_methods/lecture09_notes.pdf|Lecture Notes}}
 
|-
 
|-
| 30.06.2016 || Hydrodynamic methods II Lattice-Boltzmann, DPD, MPCD || <!--{{|Lecture Notes}}-->
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| 30.06.2016 || Hydrodynamic methods II Lattice-Boltzmann, DPD, MPCD || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture10_notes.pdf|Lecture Notes}}
 
|-
 
|-
| 07.07.2016 || Advanced MC/MD methods || <!--{{|Lecture Notes}}-->
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| 07.07.2016 || Free energy methods || {{DownloadExt|/teaching/2016-ss-sim_methods/lecture11_notes.pdf|Lecture Notes}}
 
|-
 
|-
| 14.07.2016 || Free energy methods || <!--{{|Lecture Notes}}-->
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| 14.07.2016 || Advanced MC/MD methods || {{DownloadExt|/teaching/2016-ss-sim_methods/lecture12_notes.pdf|Lecture Notes}}
 
|}
 
|}
  
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=== Location and Time ===
 
=== Location and Time ===
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), time TBA
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* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), time Thu 14:00-15:30 (Tutors: [[Frank Uhlig]] / [[Johannes Zeman]] )
<!-- ** Thu 14:00-15:30 (Tutors: [[Frank Uhlig]] / [[Johannes Zeman]] )-->
 
  
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<!--
 
=== Worksheets ===
 
=== Worksheets ===
  
<!--
 
 
==== Worksheet 6: Advanced MD/MC: The Widom insertion method ====
 
==== Worksheet 6: Advanced MD/MC: The Widom insertion method ====
* Deadline: '''July 21, 2015, 12:00 p.m. (noon)'''
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* Available online: June 27, 2016
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* Deadline: '''July 11, 2016'''
 
* {{Download|SS_2016_SM2_worksheet6.pdf|Worksheet 6}}
 
* {{Download|SS_2016_SM2_worksheet6.pdf|Worksheet 6}}
 
* {{Download|SS_2016_SM2_worksheet6_template.tcl|template.tcl|txt}} - ESPResSo sample script
 
* {{Download|SS_2016_SM2_worksheet6_template.tcl|template.tcl|txt}} - ESPResSo sample script
-->
 
 
<!--
 
<!--
 
* {{Download|SS_2016_SM2_WS6_solution.pdf|Solution|pdf}} - Sample solution
 
* {{Download|SS_2016_SM2_WS6_solution.pdf|Solution|pdf}} - Sample solution
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<!--
 
<!--
 
==== Worksheet 5: Hydrodynamics and the Lattice-Boltzmann method ====
 
==== Worksheet 5: Hydrodynamics and the Lattice-Boltzmann method ====
* Deadline: '''July 13, 2015, 12:00 p.m. (noon)'''
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* Deadline: '''June 27, 2016'''
 
* {{Download|SS_2016_SM2_worksheet5.pdf|Worksheet 5}}
 
* {{Download|SS_2016_SM2_worksheet5.pdf|Worksheet 5}}
* {{Download|SS_2016_SM2_worksheet5_templates.tar.gz|templates.tar.gz|tgz}} - Archive containing template scripts
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* {{Download|SS_2016_SM2_worksheet5_template.tcl|template.tcl|txt}} - ESPResSo sample script
-->
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<!--
 
 
* {{Download|SS_2016_SM2_WS5_solution.pdf|Solution|pdf}} - Sample solution
 
* {{Download|SS_2016_SM2_WS5_solution.pdf|Solution|pdf}} - Sample solution
 
-->
 
-->
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* Sample videos:
 
* Sample videos:
 
{{#widget:YouTube|id=A2zCOfrjH-Q|width=400|height=225}} {{#widget:YouTube|id=GYRRGuYoNF4|width=400|height=225}}
 
{{#widget:YouTube|id=A2zCOfrjH-Q|width=400|height=225}} {{#widget:YouTube|id=GYRRGuYoNF4|width=400|height=225}}
-->
 
<!--
 
 
==== Worksheet 4: Charge distribution around a charged rod ====
 
==== Worksheet 4: Charge distribution around a charged rod ====
* Deadline: '''June 29, 2015, 12:00 p.m. (noon)'''
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* Available online: May 30, 2016
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* Deadline: '''June 13, 2016'''
 
* {{Download|SS_2016_SM2_worksheet4.pdf|Worksheet 4}}
 
* {{Download|SS_2016_SM2_worksheet4.pdf|Worksheet 4}}
 
* {{Download|SS_2016_SM2_worksheet4_template.tcl|template.tcl|txt}} - ESPResSo sample script
 
* {{Download|SS_2016_SM2_worksheet4_template.tcl|template.tcl|txt}} - ESPResSo sample script
-->
+
 
<!--
 
 
* {{Download|SS_2016_SM2_WS4_solution.pdf|Solution|pdf}} - Sample solution
 
* {{Download|SS_2016_SM2_WS4_solution.pdf|Solution|pdf}} - Sample solution
 
-->
 
-->
 
<!--
 
<!--
 
==== 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)'''
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* Deadline: '''May 30, 2016'''
 
* {{Download|SS_2016_SM2_worksheet3.pdf|Worksheet 3}}
 
* {{Download|SS_2016_SM2_worksheet3.pdf|Worksheet 3}}
 
* {{Download|SS_2016_SM2_worksheet3_template.tcl|template.tcl|txt}} - ESPResSo sample script
 
* {{Download|SS_2016_SM2_worksheet3_template.tcl|template.tcl|txt}} - ESPResSo sample script
-->
 
 
<!--
 
<!--
 
* {{Download|SS_2016_SM2_WS3_solution.pdf|Solution|pdf}} - Sample solution
 
* {{Download|SS_2016_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)'''
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* Deadline: '''May 9, 2016'''
* {{Download|SS_2016_SM2_worksheet2.pdf|Worksheet 2}}
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* {{Download|SimmethodsII ss16 worksheet2.pdf|Worksheet 2}}
* {{Download|SS_2016_SM2_worksheet2_templates.tar.gz|templates.tar.gz|tgz}} - Archive containing GROMACS input files
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* {{Download|SS_2015_SM2_worksheet2_templates.tar.gz|templates.tar.gz|tgz}} - Archive containing GROMACS input files
 
-->
 
-->
 +
 
<!--
 
<!--
 
* {{Download|SS_2016_SM2_WS2_solution.pdf|Solution|pdf}} - Sample solution
 
* {{Download|SS_2016_SM2_WS2_solution.pdf|Solution|pdf}} - Sample solution
 
-->
 
-->
 
<!--
 
<!--
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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: '''April 18, 2016'''
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* Deadline: '''April 25, 2016'''
* {{Download|SS_2016_SM2_worksheet1.pdf|Worksheet 1|pdf}}
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* {{Download|SimmethodsII_ss16_worksheet1.pdf|Worksheet}}
 
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report
 
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report
 
-->
 
-->
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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
 
-->
 
-->
 
 
=== General Remarks ===
 
=== General Remarks ===
  

Latest revision as of 17:01, 2 June 2019

Overview

Type
Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
Lecturer
Prof. Dr. Christian Holm, JP Dr. Maria Fyta
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: Dr. Frank Uhlig, Johannes Zeman; 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 or Maria Fyta 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
07.04.2016 Introduction, Ab initio methods, Quantum mechanics, Hartree-Fock application_pdf.pngLecture Notes (2.7 MB)Info circle.png application_pdf.pngLecture Notes (3.11 MB)Info circle.png
14.04.2016 Density functional theory, Car-Parrinello MD application_pdf.pngLecture Notes (2.99 MB)Info circle.png
21.04.2016 ab initio MD, post Hartree-Fock methods application_pdf.pngLecture Notes (5.59 MB)Info circle.png
28.04.2016 Classical force fields, Atomistic simulations, Biomolecules, Water models Lecture Notes (1.37 MB) Lecture Notes (3.81 MB)
05.05.2016 Holiday (Christi Himmelfahrt)
12.05.2016 Coarse-grained models, simulations of macromolecules and soft matter Lecture Notes (4.25 MB)
19.05.2016 Holiday (Pfingsten)
26.05.2016 Holiday (Fronleichnam)
02.06.2016 Poisson-Boltzmann theory, charged polymers Slides (6.94 MB)
09.06.2016 Poisson-Boltzmann theory, charged polymers cont. Lecture Notes (171 kB)
16.06.2016 Long range interactions in periodic boundary conditions Lecture Notes (4.01 MB)
23.06.2016 Hydrodynamic methods I Stokesian and Brownian Dynamics Lecture Notes (2 MB) Lecture Notes (3.84 MB)
30.06.2016 Hydrodynamic methods II Lattice-Boltzmann, DPD, MPCD Lecture Notes (2.63 MB)
07.07.2016 Free energy methods Lecture Notes (6.13 MB)
14.07.2016 Advanced MC/MD methods Lecture Notes (3.17 MB)

Tutorials

Location and Time

  • The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), time Thu 14:00-15:30 (Tutors: Frank Uhlig / Johannes Zeman )


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/2016.
  • For the reports, we have a nice txt.pngLaTeX template (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 (Frank Uhlig 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.