Difference between revisions of "Simulation Methods in Physics II SS 2019"
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−  +  {{Infobox Possible exam dates:  
−  +  Monday 22.07.2019 between 10am2pm, <br>  
−  +  Tuesday 23.07.2019 between 10am2pm, <br>  
−  +  Tuesday 30.07.2019 between 11am2pm, <br>  
−  +  Wednesday 31.07.2019 between 10am11am, <br>  
−  Wednesday  +  <!Tuesday 17.09.2019 between 1pm2pm, <br> 
+  <!Wednesday 18.09.2019 between 1pm2pm, <br>  
+  <!Wednesday 09.10.2019 between 12pm2pm, <br>  
+  <!Thursday 10.10.2019 between 10am2pm, <br>  
+  Tuesday 15.10.2019 between 1pm2pm, <br>  
For you preferred date and time, send an email to [[Maria Fyta]]. }}  For you preferred date and time, send an email to [[Maria Fyta]]. }}  
−  +  
== Overview ==  == Overview ==  
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!Date !! Subject  Resources  !Date !! Subject  Resources  
    
−   11.04.2019  Introduction/  +   11.04.2019  Introduction/organization, electronic structure  {{DownloadsimmethodsII_ss19_lecture1.pdf Lecture Notes}} 
    
−   16.04.2019  QM methods ingredients, Hartree approximations  {{DownloadsimmethodsII_ss19_QMingred.pdf QM ingredients}}, {{DownloadsimmethodsII_ss19_lecture1notes.pdf Lecture Notes}}  +   16.04.2019  QM methods ingredients, Hartree approximations  {{DownloadsimmethodsII_ss19_QMingred.pdf QM ingredients}}, {{DownloadsimmethodsII_ss19_lecture1notes.pdf Lecture Notes}}<! , {{DownloadsimmethodsII_ss19_lecture2a.pdf Hartree}} > 
    
−   18.04.2019  HartreeFock (HF) and post HF methods   +   18.04.2019  HartreeFock (HF) and post HF methods  {{DownloadsimmethodsII_ss19_lecture3.pdf Lecture Notes}} 
    
−    +   02.05.2019  MollerPlesset theory, Density Functional Theory (DFT)  {{DownloadsimmethodsII_ss19_lecture4.pdf Perturbation TheoryMPn}}, {{DownloadsimmethodsII_ss19_lecture4b.pdf DFT}} 
    
−    +   09.05.2019  DFT (continued)  {{DownloadsimmethodsII_ss19_lecture5.pdf Lecture Notes}} 
    
−    +   16.05.2019  TDDFT, <i>ab initio</i> MD {{DownloadsimmethodsII_ss19_lecture6a.pdf TDDFT}}, {{DownloadsimmethodsII_ss19_lecture6b.pdf ab initio MD}} 
−  
−    
    
−   23.05.2019   +   23.05.2019  QM/MM, Classical water models  {{DownloadsimmethodsII_ss19_lecture7a.pdf QMMM}}, {{DownloadsimmethodsII_ss19_lecture7slides.pdf explicit models}}, {{DownloadsimmethodsII_ss19_lecture7b.pdf implicit models}} 
    
 30.05.2019  '' Holiday (Christi Himmelfahrt)''     30.05.2019  '' Holiday (Christi Himmelfahrt)''    
    
−   06.06.2019   +   06.06.2019  <!Simulations of macromolecules and soft matter,Classical force fields PoissonBoltzmann theory, charged polymers> Polymer Models  {{DownloadsimmethodsII_ss19_lecture8.pdf Lecture Notes}} 
    
 13.06.2019  '' Holiday (Pfingsten) ''     13.06.2019  '' Holiday (Pfingsten) ''    
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 20.06.2018  '' Holiday (Fronleichnam) ''     20.06.2018  '' Holiday (Fronleichnam) ''    
    
−   27.06.2019   +   27.06.2019  Polymer dynamics, Flory theory, PoissonBoltzmann theory  {{DownloadsimmethodsII_ss19_lecture9.pdf Lecture Notes}} 
    
−   04.07.2019  LatticeBoltzmann  +   04.07.2019  Hydrodynamic methods <!(Brownian, Langevin, DPD) LatticeBoltzmann>  {{DownloadsimmethodsII_ss19_lecture10.pdf  Lecture Notes}} 
    
−   11.07.2019  Free energy methods   +   11.07.2019  Free energy methods  {{DownloadsimmethodsII_ss19_lecture11.pdf  Lecture Notes}} 
    
−   18.07.2019 Coarsegraining, multiscale simulations   +   18.07.2019  Particle interactions <! Coarsegraining, multiscale simulations > {{DownloadsimmethodsII_ss19_lecture12.pdf Lecture Notes}}, {{DownloadsimmethodsII_ss19_lecture12_slides.pdf slides}} 
}  }  
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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.  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.  
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b>  <b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b>  
−  
==== Worksheet 1: Quantum chemistry and simple models ====  ==== Worksheet 1: Quantum chemistry and simple models ====  
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* {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  * {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  
−  +  
==== Worksheet 2: Density Functional Theory ====  ==== Worksheet 2: Density Functional Theory ====  
−  +  * Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.  
−  * Deadline: '''May  +  * {{DownloadSMII_2019_w2.pdfWorksheet 2}} 
−  * {{Download  +  * {{Downloadtemplate_sm2_2019_w2.ziptemplate}}  input files 
−  * {{Download  
* {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  * {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  
−  ==== Worksheet 3:  +  
−  * Deadline: '''May  +  ==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ==== 
−  * {{Download  +  * Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line. 
−  * {{Download  +  * {{DownloadSMII_2019_w3.pdfWorksheet 3}} 
+  * {{Downloadtemplate_SMII_SS2019_W3.ziptemplate}}  input files  
* {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  * {{Downloadlatextemplate.texlatextemplate.textxt}}  LaTeX template for the report  
+  
==== Worksheet 4: Properties of Coarsegrained Polymers ====  ==== Worksheet 4: Properties of Coarsegrained Polymers ====  
−  * Deadline: '''June  +  * Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line. 
−  * {{Download  +  * {{DownloadSimmethodsII_ss19_worksheet4.pdfWorksheet}} 
−  * {{Download  +  * {{DownloadSimmethodsII_ss19_template.pytemplate}} 
−  * {{Download  +  * {{DownloadSimmethodsII_ss19_espresso_install.shESPResSo install}} 
−  
−  ==== Worksheet 5: Charge distribution  +  ==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ==== 
−  * Deadline: '''July  +  * Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line. 
−  * {{Download  +  * {{DownloadSimmethodsII_ss19_worksheet5.pdfWorksheet 5}} 
−  * {{Download  +  * {{DownloadSimmethodsII_ss19_template5.pytemplate}}  ESPResSo sample script 
−  
* {{Downloadespresso_install_script_rod.shESPResSo install}}  * {{Downloadespresso_install_script_rod.shESPResSo install}}  
+  * {{Downloaddeserno_cell_PBE_2001.pdf M. Deserno and C. Holm, 2001 }}  Paper for the cell model and the charged rod.  
−  ==== Worksheet 6:  +  ==== Worksheet 6: Computational Fluid Dynamics and Free Energy ==== 
−  * Deadline: '''July  +  * Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line. 
−  * {{Download  +  * {{DownloadSimmethodsII_ss19_worksheet6.pdfWorksheet}} 
−  * {{Download  +  * {{DownloadSimmethodsII_ss19_template6.pytemplate}}  ESPResSo sample script 
* {{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  
+  
>  > 
Latest revision as of 09:27, 3 August 2019
Possible exam dates:
Monday 22.07.2019 between 10am2pm, 
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 09:4511:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. Maofeng Dou, Dr. Kartik Jain; 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 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
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  HartreeFock (HF) and post HF methods  Lecture Notes (2.93 MB) 
02.05.2019  MollerPlesset theory, Density Functional Theory (DFT)  Perturbation TheoryMPn (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, PoissonBoltzmann 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 CIPPool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00  15:30; Thu 09:4511:15 (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
 latextemplate.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
 latextemplate.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
 latextemplate.tex (7 KB)  LaTeX template for the report
Worksheet 4: Properties of Coarsegrained 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)
 latextemplate.tex (7 KB)  LaTeX template for the report
>
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 (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.