Difference between revisions of "Simulation Methods in Physics II SS 2017"
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−  +  {{Infobox Possible exam dates:  
+  *Fri 28.07.2017 between 11am1pm,  
+  <!*Fri 04.08.2017 between 11am2pm,>  
+  <!*Wed 04.10.2017 1pm2pm>  
+  <! *Thu 05.10.2017 between 10am2pm,  
+  *Fri 06.10.2017 at 10am or between 12pm2pm,>  
+  *Thu 14.09.2017 between 1pm3pm,  
+  *from MonTue 09.1010.10.2017 between 1pm3pm,  
+  <!*Wed 11.10.2017 at 2pm.>  
+  
+  For you preferred date and time, send an email to [[Christian Holm]] and [[Maria Fyta]]. }}  
+  
+  
== Overview ==  == Overview ==  
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=== Useful online resources ===  === Useful online resources ===  
−  * Roethlisberger,  +  * Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_20151.pdf] 
* EBook: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf EBook: The ABC of DFT.]  * EBook: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf EBook: The ABC of DFT.]  
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* A good and freely available book about using Linux: [http://writers.fultus.com/garrels/ebooks/Machtelt_Garrels_Introduction_to_Linux_3nd_Ed.pdf Introduction to Linux by M. Garrels]  * A good and freely available book about using Linux: [http://writers.fultus.com/garrels/ebooks/Machtelt_Garrels_Introduction_to_Linux_3nd_Ed.pdf Introduction to Linux by M. Garrels]  
−  * [http://t16web.lanl.gov/Kawano/gnuplot/indexe.html Not so frequently asked questions about GNUPLOT]  +  <!* [http://t16web.lanl.gov/Kawano/gnuplot/indexe.html Not so frequently asked questions about GNUPLOT]> 
−  
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]  * [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]  
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* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]  * [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]  
+  
+  * Densityfunctionaltheory tightbinding (DFTB): Phil. Trans. R. Soc. A, 372(2011), 20120483. [http://rsta.royalsocietypublishing.org/content/372/2011/20120483], Computational Materials Science 47 (2009) 237–253 [http://www.sciencedirect.com/science/article/pii/S0927025609003036]  
+  
+  * "Ab Initio Molecular Dynamics: Theory and Implementation" in Modern Methods and Algorithms, NIC Series Vol 1. (2000) [https://juser.fzjuelich.de/record/44687/files/NICBand1.pdf]  
+  
+  * University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/9783658094102]  
* 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.  * 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.  
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 13.04.2017  Classical force fields, Atomistic simulations, Biomolecules  <!{{ DownloadsimmethodsII_ss16_lecture1.pdfLecture Notes}} {{ DownloadsimmethodsII_ss16_lecture1notes.pdfLecture Notes}}>   13.04.2017  Classical force fields, Atomistic simulations, Biomolecules  <!{{ DownloadsimmethodsII_ss16_lecture1.pdfLecture Notes}} {{ DownloadsimmethodsII_ss16_lecture1notes.pdfLecture Notes}}>  
    
−   20.04.2017  Water models  {{ Lecture Notes}}  +   20.04.2017  Water models  <!{{ Lecture Notes}} > 
    
 27.04.2017  Coarsegrained models, simulations of macromolecules and soft matter {{DownloadExt/teaching/2015sssim_methods/lecture05_notes.pdfLecture Notes}}   27.04.2017  Coarsegrained models, simulations of macromolecules and soft matter {{DownloadExt/teaching/2015sssim_methods/lecture05_notes.pdfLecture Notes}}  
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 04.05.2017  Charged macromolecules  {{DownloadExt/teaching/2015sssim_methods/lecture07_notes.pdfSlides}}   04.05.2017  Charged macromolecules  {{DownloadExt/teaching/2015sssim_methods/lecture07_notes.pdfSlides}}  
    
−   11.05.2017  PoissonBoltzmann theory  {{Lecture Notes}}  +   11.05.2017  PoissonBoltzmann theory  <!{{Lecture Notes}} > 
    
 18.05.2017  Hydrodynamic methods  [[:File:Lecture Notes Hydrodynamics.pdfLecture Notes Hydrodynamics]] {{DownloadExt/teaching/2015sssim_methods/lecture10_notes.pdfLecture Notes LB}} [[:File:Latticeboltzmann intro.pdfIntro to LB]]   18.05.2017  Hydrodynamic methods  [[:File:Lecture Notes Hydrodynamics.pdfLecture Notes Hydrodynamics]] {{DownloadExt/teaching/2015sssim_methods/lecture10_notes.pdfLecture Notes LB}} [[:File:Latticeboltzmann intro.pdfIntro to LB]]  
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 25.05.2017  '' Holiday (Christi Himmelfahrt) ''     25.05.2017  '' Holiday (Christi Himmelfahrt) ''    
    
−   01.06.2017  Free energy methods   +   01.06.2017  Free energy methods  [[:File:SKMBT_C454e17072118140.pdfFree energy calculations]] 
    
−   08.06.2017  '' Holiday (Pfingsten) ''   +   08.06.2017  '' Holiday (Pfingsten) ''  
    
−   15.06.2017  '' Holiday (Fronleichnam) ''   +   15.06.2017  '' Holiday (Fronleichnam) ''  
    
−   22.06.2017   +   22.06.2017  Quantummechanical methods, introduction  {{DownloadsimmethodsII_ss17_lecture1.pdfSlides}} {{ DownloadsimmethodsII_ss17_lecture1notes.pdfLecture Notes}} 
    
−   29.06.2017  post Hartree Fock  {{Lecture Notes}}  +   29.06.2017 HartreeFock, post Hartree Fock  {{DownloadsimmethodsII_ss17_lecture2.pdfLecture Notes}} 
    
−   06.07.2017  Density functional theory and functionals  {{Lecture Notes}}  +   06.07.2017  Density functional theory and functionals  {{DownloadsimmethodsII_ss17_lecture3.pdfLecture Notes}} 
    
−   13.07.2017  <i>ab initio</i>  +   13.07.2017  Timedependent DFT, <i>ab initio</i> MD {{DownloadsimmethodsII_ss17_lecture4.pdfLecture Notes}} 
    
−   20.07.2017   +   20.07.2017  stateofthe art, review  <!{{DownloadsimmethodsII_ss17_QM_summary.pdf QM summary}} {{DownloadsimmethodsII_ss17_multiscale.pdfMultiscale examples}} {{Lecture Notes}}> 
}  }  
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* {{DownloadSS_2015_SM2_worksheet2_templates.tar.gztemplates.tar.gztgz}}  Archive containing GROMACS input files  * {{DownloadSS_2015_SM2_worksheet2_templates.tar.gztemplates.tar.gztgz}}  Archive containing GROMACS input files  
* {{DownloadSS_2016_SM2_WS2_solution.pdfSolutionpdf}}  Sample solution  * {{DownloadSS_2016_SM2_WS2_solution.pdfSolutionpdf}}  Sample solution  
−  +  
==== Worksheet 1: Properties and Fitting of Atomistic Water models ====  ==== Worksheet 1: Properties and Fitting of Atomistic Water models ====  
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* {{DownloadSS_2015_SM2_WS1_solution.tar.gzsolution.tar.gztgz}}  Archive containing the sample solution  * {{DownloadSS_2015_SM2_WS1_solution.tar.gzsolution.tar.gztgz}}  Archive containing the sample solution  
>  >  
−  +  <!  
==== Worksheet 2: Properties of Coarsegrained Polymers ====  ==== Worksheet 2: Properties of Coarsegrained Polymers ====  
* Deadline: '''May 15, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_02''' as subject line.  * Deadline: '''May 15, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_02''' as subject line.  
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* {{DownloadSimmethodsII_ss17_template3.pytemplate}}  ESPResSo sample script  * {{DownloadSimmethodsII_ss17_template3.pytemplate}}  ESPResSo sample script  
* {{Downloadespresso_install_script_rod.shESPResSo install}}  * {{Downloadespresso_install_script_rod.shESPResSo install}}  
+  
==== Worksheet 4: Flow Between Plates and Free Energy ====  ==== Worksheet 4: Flow Between Plates and Free Energy ====  
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* {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  * {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  
+  ==== Worksheet 5: Quantum chemistry and simple models ====  
+  * Deadline: '''July 3, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_05''' as subject line.  
+  * {{DownloadSimmethodsII_ss17_worksheet5.pdfWorksheet 5}}  
+  * {{DownloadSimmethodsII_ss17_template5.tar.gztemplate}}  CP2K input files  
+  * {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  
+  
+  ==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====  
+  * Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.  
+  * {{DownloadSimmethodsII_ss17_worksheet6.pdfWorksheet 6}}  
+  * {{DownloadSimmethodsII_ss17_template6.tar.gztemplate}}  CP2K input files  
+  * {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  
+  >  
=== General Remarks ===  === General Remarks ===  
Latest revision as of 16:59, 2 June 2019
Possible exam dates:

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, 15:45 – 17:15 (Tutors: Dr. Frank Uhlig, David Sean; ICP, Allmandring 3, CIPPool (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 handsontutorials will take place in the CIPPool 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 handin 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 in September or October for the oral examination.
Recommended literature

Daan Frenkel and Berend Smit.
"Understanding Molecular Simulation".
Academic Press, San Diego, 2002.
[DOI] 
Mike P. Allen and Dominik J. Tildesley.
"Computer Simulation of Liquids".
Oxford Science Publications, Clarendon Press, Oxford, 1987.

Rapaport, D. C..
"The Art of Molecular Dynamics Simulation".
Cambridge University Press, 2004.
[DOI] 
D. P. Landau and K. Binder.
"A guide to Monte Carlo Simulations in Statistical Physics".
Cambridge, 2005.

Michael Rubinstein and Ralph H. Colby.
"Polymer Physics".
Oxford University Press, Oxford, UK, 2003.

M. E. J. Newman and G. T. Barkema.
"Monte Carlo Methods in Statistical Physics".
Oxford University Press, 1999.

S. Succi.
"The lattice Boltzmann equation for fluid dynamics and beyond".
Oxford University Press, New York, USA, 2001.
[PDF] (13 MB) 
M. E. Tuckermann.
"Statistical Mechanics: Theory and Molecular Simulation".
Oxfor University Press Oxford Graduate Texts, Oxford, 2010.

F. Martin and 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.
Useful online resources
 Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [1]
 EBook: Kieron Burke et al.,University of California, 2007: EBook: 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
 Densityfunctionaltheory tightbinding (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
Date  Subject  Resources  

13.04.2017  Classical force fields, Atomistic simulations, Biomolecules  
20.04.2017  Water models  
27.04.2017  Coarsegrained models, simulations of macromolecules and soft matter  Lecture Notes (4.25 MB)  
04.05.2017  Charged macromolecules  Slides (6.94 MB)  
11.05.2017  PoissonBoltzmann theory  
18.05.2017  Hydrodynamic methods  Lecture Notes Hydrodynamics Lecture Notes LB (2.63 MB) Intro to LB  
25.05.2017  Holiday (Christi Himmelfahrt)  
01.06.2017  Free energy methods  Free energy calculations  
08.06.2017  Holiday (Pfingsten)  
15.06.2017  Holiday (Fronleichnam)  
22.06.2017  Quantummechanical methods, introduction  Slides (2.7 MB) Lecture Notes (2.94 MB)  
29.06.2017  HartreeFock, post Hartree Fock  Lecture Notes (4.21 MB)  
06.07.2017  Density functional theory and functionals  Lecture Notes (6.48 MB)  
13.07.2017  Timedependent DFT, ab initio MD  Lecture Notes (9.12 MB)  
20.07.2017  stateofthe art, review 
Tutorials
Location and Time
 The tutorials take place in the CIPPool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu, 15:45 – 17:15 (Tutors: Frank Uhlig / David Sean )
Worksheets
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/2017
.  For the reports, we have a nice LaTeX template (7 KB).
 You can do the exercises in the CIPPool 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 CIPPool, all required software and tools are available.
Handinexercises
 The worksheets are to be solved in groups of two or three people. We will not accept handinexercises 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 David Sean).
 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.