Simulation Methods in Physics II SS 2019

Possible exam dates: Monday 22.07.2019 between 10am-2pm, Tuesday 23.07.2019 between 10am-2pm, Tuesday 30.07.2019 between 11am-2pm, Wednesday 31.07.2019 between 10am-11am, Tuesday 15.10.2019 between 1pm-2pm, For you preferred date and time, send an e-mail to Maria Fyta.

Overview

Type

Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)

Lecturer

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; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. Maofeng Dou, Dr. Kartik Jain; 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. Obtaining 50% of the possible marks in the hand-in exercises.

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 for the oral examination.

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.
  
• Michael Rubinstein, Ralph H. Colby.
  Polymer Physics.
  Oxford University Press, Oxford, UK, 2003.
  
• M. E. J. Newman, G. T. Barkema.
  Monte Carlo Methods in Statistical Physics.
  Edition 2002 edition.
  Oxford University Press, 1999.
  
• Sauro Succi.
  The lattice Boltzmann equation for fluid dynamics and beyond.
  Oxford University Press, New York, USA, 2001. ISBN: 9780198503989.
  [PDF] (13 MB)
• M. E. Tuckermann.
  Statistical Mechanics: Theory and Molecular Simulation.
  Oxfor University Press Oxford Graduate Texts, Oxford, 2010.
  
• F. Martin, H. Zipse.
  Charge Distribution in the Water Molecule - A Comparison of Methods.
  Journal of Computational Chemistry 26(1):97–105, 2004.
  
• E. Kaxiras.
  Atomic and electronic structure of solids.
  apud Cambridge, Cambridge, 2003.
  
• Andrew Leach.
  Molecular Modelling: Principles and Applications.
  apud Pearson Education Ltd., 2001. ISBN: 978-0582382107.
  

Useful online resources

• Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [1]

• 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

• Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)

• A more detailed introduction to bash scripting

• Principles of Multiscale Modeling, Weinan E (2011)

• Density-functional-theory tight-binding (DFTB): Phil. Trans. R. Soc. A, 372(2011), 20120483. [2], Computational Materials Science 47 (2009) 237–253 [3]

• "Ab Initio Molecular Dynamics: Theory and Implementation" in Modern Methods and Algorithms, NIC Series Vol 1. (2000) [4]

• University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [5]

• 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

The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).

Date	Subject	Resources
11.04.2019	Introduction/organization, electronic structure	Lecture Notes (2.62 MB)
16.04.2019	QM methods ingredients, Hartree approximations	QM ingredients (1.43 MB), Lecture Notes (2.82 MB)
18.04.2019	Hartree-Fock (HF) and post HF methods	Lecture Notes (2.93 MB)
02.05.2019	Moller-Plesset theory, Density Functional Theory (DFT)	Perturbation Theory-MPn (3.4 MB), DFT (2.37 MB)
09.05.2019	DFT (continued)	Lecture Notes (4.77 MB)
16.05.2019	TDDFT, ab initio MD	TDDFT (2.31 MB), ab initio MD (5 MB)
23.05.2019	QM/MM, Classical water models	QMMM (713 KB), explicit models (998 KB), implicit models (4.33 MB)
30.05.2019	Holiday (Christi Himmelfahrt)	---
06.06.2019	Polymer Models	Lecture Notes (10.2 MB)
13.06.2019	Holiday (Pfingsten)	---
20.06.2018	Holiday (Fronleichnam)	---
27.06.2019	Polymer dynamics, Flory theory, Poisson-Boltzmann theory	Lecture Notes (10.26 MB)
04.07.2019	Hydrodynamic methods	Lecture Notes (14.24 MB)
11.07.2019	Free energy methods	Lecture Notes (10.75 MB)
18.07.2019	Particle interactions	Lecture Notes (9.69 MB), slides (1.01 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), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: Maofeng Dou / Kartik Jain )

Worksheets

There will be in total 6 worksheets, which will be handed out every two weeks on Wednesdays at 14:00. The deadline for the solutions will be two weeks after on Wednesdays before 13:00. The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st.

Worksheet 1: Quantum chemistry and simple models

• Deadline: May 1, 2019, 13:00 by email to Maofeng Dou use SM2_01 as subject line.
• Worksheet 1 (100 KB)
• template (2 KB) - input files
• latex-template.tex (7 KB) - LaTeX template for the report

Worksheet 2: Density Functional Theory

• Deadline: May 15, 2019, 13:00 noon by email to Maofeng Dou use SM2_02 as subject line.
• Worksheet 2 (141 KB)
• template (3.4 MB) - input files
• latex-template.tex (7 KB) - LaTeX template for the report

Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer

• Deadline: May 29, 2019, 13:00 noon by email to Maofeng Dou use SM2_03 as subject line.
• Worksheet 3 (142 KB)
• template (434 KB) - input files
• latex-template.tex (7 KB) - LaTeX template for the report

Worksheet 4: Properties of Coarse-grained Polymers

• Deadline: June 19, 2019, 12:00 noon by email to Kartik Jain use SM2_04 as subject line.
• Worksheet (318 KB)
• template (9 KB)
• ESPResSo install (419 bytes)

Worksheet 5: Charge distribution and Poisson Boltzmann theory

• Deadline: July 3, 2019, 12:00 noon by email to Kartik Jain use SM2_05 as subject line.
• Worksheet 5 (346 KB)
• template (7 KB) - ESPResSo sample script
• ESPResSo install (417 bytes)
• M. Deserno and C. Holm, 2001 (304 KB) - Paper for the cell model and the charged rod.

Worksheet 6: Computational Fluid Dynamics and Free Energy

• Deadline: July 17, 2019, 12:00 noon by email to Kartik Jain use SM2_06 as subject line.
• Worksheet (285 KB)
• template (2 KB) - ESPResSo sample script
• ESPResSo install (423 bytes)
• latex-template.tex (7 KB) - LaTeX template for the report

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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/2018.
• 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.

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 (Maofeng Dou or Kartik Jain).
• 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.