Simulation Methods in Physics II SS 2016
|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.|
- 1 Overview
- 1.1 Scope
- 1.2 Prerequisites
- 1.3 Certificate Requirements
- 1.4 Oral Examination
- 1.5 Recommended literature
- 1.6 Useful online resources
- 1.7 Lecture
- 1.8 Tutorials
- 1.8.1 Location and Time
- 1.8.2 Worksheets
- 184.108.40.206 Worksheet 6: Advanced MD/MC: The Widom insertion method
- 220.127.116.11 Worksheet 5: Hydrodynamics and the Lattice-Boltzmann method
- 18.104.22.168 Worksheet 4: Charge distribution around a charged rod
- 22.214.171.124 Worksheet 3: Coarse-grained polymers and their properties
- 126.96.36.199 Worksheet 2: Diffusion processes and properties of atomistic water models
- 188.8.131.52 Worksheet 1: Quantum mechanical approaches: Hückel approximation and ab-initio methods
- 1.8.3 General Remarks
- 1.8.4 Hand-in-exercises
- 1.8.5 What happens in a tutorial
- Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
- Prof. Dr. Christian Holm, JP Dr. Maria Fyta
- Course language
- 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.
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.
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.
- 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.
Useful online resources
- Roethlisberger, Tavernarelli, EPFL, Lausanne, 2011: Introduction to electronic structure methods.
- E-Book: Kieron Burke et al.,University of California, 2007: E-Book: The ABC of DFT.
- Linux cheat sheet here (53 KB).
- A good and freely available book about using Linux: Introduction to Linux by M. Garrels
- 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.
|07.04.2016||Introduction, Ab initio methods, Quantum mechanics, Hartree-Fock||Lecture Notes (2.7 MB) Lecture Notes (3.11 MB)|
|14.04.2016||Density functional theory, Car-Parrinello MD||Lecture Notes (2.99 MB)|
|21.04.2016||ab initio MD, post Hartree-Fock methods||Lecture Notes (5.59 MB)|
|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|
|02.06.2016||Poisson-Boltzmann theory, charged polymers|
|09.06.2016||Long range interactions in periodic boundary conditions|
|16.06.2016||Hydrodynamic methods I Stokesian and Brownian Dynamics|
|23.06.2016||Hydrodynamic methods II Lattice-Boltzmann, DPD, MPCD|
|30.06.2016||Advanced MC/MD methods|
|07.07.2016||Free energy methods||Lecture Notes (6.13 MB)|
|14.07.2016||Born model of solvation|
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 )
Worksheet 6: Advanced MD/MC: The Widom insertion method
- Available online: June 27, 2016
- Deadline: July 11, 2016
- Worksheet 6 (283 KB)
- template.tcl (14 KB) - ESPResSo sample script
Worksheet 5: Hydrodynamics and the Lattice-Boltzmann method
- Deadline: June 27, 2016
- Worksheet 5 (507 KB)
- template.tcl (1 KB) - ESPResSo sample script
- Sample videos:
Worksheet 4: Charge distribution around a charged rod
- Available online: May 30, 2016
- Deadline: June 13, 2016
- Worksheet 4 (287 KB)
- template.tcl (7 KB) - ESPResSo sample script
- Solution (410 KB) - Sample solution
Worksheet 3: Coarse-grained polymers and their properties
- Deadline: May 30, 2016
- Worksheet 3 (246 KB)
- template.tcl (8 KB) - ESPResSo sample script
- Solution (286 KB) - Sample solution
Worksheet 2: Diffusion processes and properties of atomistic water models
- Deadline: May 9, 2016
- Worksheet 2 (266 KB)
- templates.tar.gz (12 KB) - Archive containing GROMACS input files
- Solution (447 KB) - Sample solution
Worksheet 1: Quantum mechanical approaches: Hückel approximation and ab-initio methods
- Deadline: April 25, 2016
- Worksheet (244 KB)
- latex-template.tex (7 KB) - LaTeX template for the report
- 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
- For the reports, we have a nice LaTeX template (7 KB).
- 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.
- 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.