Difference between revisions of "Simulation Methods in Physics II SS 2018"
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−  +  {{Infobox Possible exam dates:  
−  For you preferred date and time, send an email to  +  
−  +  Tuesday 24.07.2018 between 10am2pm, <br>  
+  Wednesday 25.07.2018 between 10am2pm, <br>  
+  Thursday 26.07.2018 between 10am2pm, <br>  
+  Tuesday 31.07.2018 between 11am2pm, <br>  
+  Wednesday 01.08.2018 between 10am2pm, <br>  
+  <!Thursday 02.08.2018 between 11am2pm, <br>  
+  Tuesday 11.09.2018 between 12pm2pm, <br>  
+  Wednesday 12.09.2018 between 11am2pm, <br>  
+  <!Monday 01.10.2018 between 1pm2pm, <br>  
+  Tuesday 02.10.2018 between 12pm2pm, <br>  
+  <! Thursday 04.10.2018 between 12pm2pm, <br>  
+  Monday 22.10.2018 between 12pm14pm. <br>  
+  
+  For you preferred date and time, send an email to [[Maria Fyta]]. }}  
+  
== Overview ==  == Overview ==  
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=== Useful online resources ===  === Useful online resources ===  
−  * Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://  +  * Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0] 
−  * EBook: Kieron Burke et al.,University of California, 2007: [http://  +  * EBook: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf EBook: The ABC of DFT.] 
* Linux cheat sheet {{DownloadSim_Meth_I_T0_cheat_sheet_10_11.pdfhere}}.  * Linux cheat sheet {{DownloadSim_Meth_I_T0_cheat_sheet_10_11.pdfhere}}.  
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!Date !! Subject  Resources  !Date !! Subject  Resources  
    
−   12.04.2018  Introduction/organisation, electronic structure  +   12.04.2018  Introduction/organisation, electronic structure  {{DownloadsimmethodsII_ss18_lecture1.pdfSlides}}, {{DownloadsimmethodsII_ss18_lecture1notes.pdfLecture Notes}} 
    
−   19.04.2018  Hartree and HartreeFock (HF) approximations, post HF   +   19.04.2018  Hartree and HartreeFock (HF) approximations, post HF  {{DownloadsimmethodsII_ss18_lecture2.pdfLecture Notes}} 
    
−   26.04.2018   +   26.04.2018  Density Functional Theory (DFT)  {{DownloadsimmethodsII_ss18_lecture3.pdfLecture Notes (1)}}, {{DownloadsimmethodsII_ss18_lecture3b.pdfLecture Notes (2)}} 
    
 03.05.2018  <i>ab initio</i> MD, QM/MM {{DownloadsimmethodsII_ss18_lecture4.pdfLecture Notes}}   03.05.2018  <i>ab initio</i> MD, QM/MM {{DownloadsimmethodsII_ss18_lecture4.pdfLecture Notes}}  
    
−   10.05.2018  Holiday (Christi Himmelfahrt)   +   10.05.2018  Holiday (Christi Himmelfahrt)   
    
−   17.05.2018   +   17.05.2018  Classical force fields and water models  {{DownloadsimmethodsII_ss18_lecture5slides.pdfSlides}}, {{DownloadsimmethodsII_ss18_lecture5.pdfLecture Notes}} 
    
−   24.05.2018  '' Holiday (Pfingsten) ''   +   24.05.2018  '' Holiday (Pfingsten) ''   
    
−   31.05.2018  Holiday (Fronleichnam) ''   +   31.05.2018  Holiday (Fronleichnam) ''   
    
−   07.06.2018  Simulations of macromolecules and soft matter   +   07.06.2018  Simulations of macromolecules and soft matter  {{DownloadsimmethodsII_ss18_lecture6.pdfLecture Notes}} 
    
−   14.06.2018  PoissonBoltzmann theory, charged polymers   +   14.06.2018  PoissonBoltzmann theory, charged polymers  {{DownloadPoissonBoltzmannDavidNotes.pdf PoissonBoltzmann}} {{DownloadFloryDavidNotes.pdfPolymer scaling}} 
    
−   21.06.2018  Hydrodynamic methods I (  +   21.06.2018  Hydrodynamic methods I (Brownian and Langevin Dynamics)  {{DownloadsimmethodsII_ss18_lecture8.pdfLecture Notes}} 
    
−   28.06.2018  Hydrodynamic methods  +   28.06.2018  Hydrodynamic methods II (DPD, LatticeBoltzmann) (contd.)  {{DownloadsimmethodsII_ss18_lecture9.pdfLecture Notes}} 
    
−   05.07.2018   +   05.07.2018  LatticeBoltzmann (contd.) {{DownloadsimmethodsII_ss18_lecture9b.pdfLecture Notes (LBM)}} 
    
−   12.07.2018  Free energy methods   +   12.07.2018  Free energy methods <!Energy minimization, Interatomic potentials (pairpotentials, EAM) (solidstate systems)> {{DownloadsimmethodsII_ss18_lecture10.pdfLecture Notes}}, ><!{{DownloadsimmethodsII_ss18_lecture12.pdfLecture Notes (TB, DFTB)}} > 
    
 19.07.2018 Coarsegraining, multiscale simulations    19.07.2018 Coarsegraining, multiscale simulations   
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<b>The first worksheet will be uploaded on Wed. April 18th. The deadline will be Wed. May 2nd. </b>  <b>The first worksheet will be uploaded on Wed. April 18th. The deadline will be Wed. May 2nd. </b>  
−  +  <!  
==== Worksheet 1: Quantum chemistry and simple models ====  ==== Worksheet 1: Quantum chemistry and simple models ====  
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.  * Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.  
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==== Worksheet 2: Density Functional Theory ====  ==== Worksheet 2: Density Functional Theory ====  
+  * additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout  
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.  * Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.  
* {{DownloadSimmethodsII_SS18_worksheet2.pdfWorksheet 2}}  * {{DownloadSimmethodsII_SS18_worksheet2.pdfWorksheet 2}}  
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* {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  * {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  
−  +  ==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====  
−  +  * Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.  
−  ==== Worksheet  +  * {{DownloadSimmethodsII_SS18_worksheet3.pdfWorksheet 3}} 
−  +  * {{Downloadtemplates_SMII_SS2018_WS3.ziptemplate}}  input files  
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−  * Deadline: '''May  
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−  * {{Download  
−  * {{Download  
* {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  * {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  
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−  +  ==== Worksheet 4: Properties of Coarsegrained Polymers ====  
−  ==== Worksheet  +  * Deadline: '''June 20, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line. 
−  * Deadline: '''  +  * {{DownloadSimmethodsII_ss18_worksheet4.pdfWorksheet}} 
−  * {{Download  +  * {{DownloadSimmethodsII_ss18_template.pytemplate}} 
−  * {{Download  
* {{DownloadSimmethodsII_ss17_espresso_install.shESPResSo install}}  * {{DownloadSimmethodsII_ss17_espresso_install.shESPResSo install}}  
* {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  * {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  
−  ==== Worksheet  +  ==== Worksheet 5: Charge distribution around a charged rod ==== 
−  * Deadline: '''  +  * Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line. 
−  * {{Download  +  * {{DownloadSimmethodsII_ss18_worksheet5.pdf the Worksheet}} 
−  * {{Download  +  * {{DownloadSimmethodsII_ss18_worksheet5NEW.pdf NEW Worksheet}} 
+  * {{DownloadSimmethodsII_ss18_template5.pytemplate}}  ESPResSo sample script  
* {{Downloadespresso_install_script_rod.shESPResSo install}}  * {{Downloadespresso_install_script_rod.shESPResSo install}}  
−  +  ==== Worksheet 6: Flow Between Plates and Free Energy ====  
−  ==== Worksheet  +  * Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line. 
−  * Deadline: '''  +  * {{DownloadSimmethodsII_ss18_worksheet6.pdfWorksheet}} 
−  * {{Download  +  * {{DownloadSimmethodsII_ss18_template6.pytemplate}}  ESPResSo sample script 
−  * {{Download  
* {{Downloadespresso_install_script_LB.shESPResSo install}}  * {{Downloadespresso_install_script_LB.shESPResSo install}}  
* {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  * {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  
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==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====  ==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====  
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* {{DownloadSimmethodsII_ss17_template6.tar.gztemplate}}  CP2K input files  * {{DownloadSimmethodsII_ss17_template6.tar.gztemplate}}  CP2K input files  
* {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  * {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  
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>  >  
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* For the tutorials, you will get a [[ICP Unix Accounts for Studentspersonal account for the ICP machines]].  * For the tutorials, you will get a [[ICP Unix Accounts for Studentspersonal account for the ICP machines]].  
−  * All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/  +  * All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>. 
* For the reports, we have a nice {{Downloadlatextemplate.texLaTeX templatetxt}}.  * For the reports, we have a nice {{Downloadlatextemplate.texLaTeX templatetxt}}.  
* You can do the exercises in the CIPPool when it is not [[CIP Pool Occupancyoccupied by another course]]. The pool is accessible on all days, except weekends and late evenings.  * You can do the exercises in the CIPPool when it is not [[CIP Pool Occupancyoccupied by another course]]. The pool is accessible on all days, except weekends and late evenings. 
Latest revision as of 14:17, 17 June 2019
Possible exam dates:
Tuesday 24.07.2018 between 10am2pm, 
Contents
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, 14:0015:30 (Tutors: Dr. Miriam Kohagen, Dr. 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.

D. C. Rapaport.
"The Art of Molecular Dynamics Simulation".
Cambridge University Press, 2004.

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 

12.04.2018  Introduction/organisation, electronic structure  Slides (2.62 MB), Lecture Notes (2.65 MB) 
19.04.2018  Hartree and HartreeFock (HF) approximations, post HF  Lecture Notes (2.78 MB) 
26.04.2018  Density Functional Theory (DFT)  Lecture Notes (1) (5.64 MB), Lecture Notes (2) (3.76 MB) 
03.05.2018  ab initio MD, QM/MM  Lecture Notes (3.76 MB) 
10.05.2018  Holiday (Christi Himmelfahrt)   
17.05.2018  Classical force fields and water models  Slides (3.1 MB), Lecture Notes (3.93 MB) 
24.05.2018  Holiday (Pfingsten)   
31.05.2018  Holiday (Fronleichnam)   
07.06.2018  Simulations of macromolecules and soft matter  Lecture Notes (2.81 MB) 
14.06.2018  PoissonBoltzmann theory, charged polymers  PoissonBoltzmann (2.19 MB) Polymer scaling (975 KB) 
21.06.2018  Hydrodynamic methods I (Brownian and Langevin Dynamics)  Lecture Notes (4.1 MB) 
28.06.2018  Hydrodynamic methods II (DPD, LatticeBoltzmann) (contd.)  Lecture Notes (5.69 MB) 
05.07.2018  LatticeBoltzmann (contd.)  Lecture Notes (LBM) (2.29 MB) 
12.07.2018  Free energy methods  Lecture Notes (5.55 MB), > 
19.07.2018  Coarsegraining, multiscale simulations 
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: Miriam Kohagen / David Sean )
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 18th. The deadline will be Wed. May 2nd.
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 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 (Miriam Kohagen 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.