Difference between revisions of "Simulation Methods in Physics II SS 2013"
Dschwoerer (talk  contribs) 

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+  == Exams ==  
+  The following dates and times have been scheduled for the oral exams.Please send an email ([[Maria Fyta]], [[Jens Smiatek]]) noting your preference. We will send an email back confirming (or not) the date.  
+  
+  Thu. Sep 19: 10:00, 11:00, 13:00, and 14:00  
+  
== Overview ==  == Overview ==  
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;Course language  ;Course language  
:English  :English  
+  
+  :{{Infobox<b> NO lecture on 11.07.The lecture on 18.07 will start earlier at 11am</b>.}}  
;Lectures  ;Lectures  
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=== Recommended literature ===  === Recommended literature ===  
−  <bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a,thijssen07,  +  <bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a,thijssen07,succi01a,tuckerman10a,steinhauser08a,martin04a,kaxiras03a,leach01a</bibentry> 
=== Useful online resources ===  === Useful online resources ===  
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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://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]  * [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]  
+  
+  * [http://ocw.mit.edu/courses/materialsscienceandengineering/3021jintroductiontomodelingandsimulationspring2011/lecturenotesandreadings/MIT3_021JS11_P1_L8.pdf MIT Opencourseware "Reactive potentials and applications"]  
+  
+  * [http://people.virginia.edu/~lz2n/mse627/notes/Intro.pdf University of Virginia, Introduction to atomistic simulations]  
+  
+  * [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]  
* 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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== Lecture ==  == Lecture ==  
To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.  To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.  
+  
+  <font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Downloadsimmeth2_vorlesungsmitschrieb.pdfScript}}.'''</font>  
{ class="wikitable"  { class="wikitable"  
valign="top"  valign="top"  
−  !Date !! Subject   +  !Date !! Subject  Resources 
    
−   11.04.  +   11.04.2013  Introduction, electronic stucture  [{{DownloadsimmethodsII_ss13_lecture1.pdfLecture Notes}}] 
    
−   18.04.  +   18.04.2013  Elements of quantum mechanics, Hartree and HartreeFock approximations  [{{DownloadsimmethodsII_ss13_lecture2.pdfLecture Notes}}] 
    
−   25.04.  +   25.04.2013  Density functional theory (DFT), functionals, pseudopotentials, elements of solid state physics  [{{DownloadsimmethodsII_ss13_lecture3.pdfLecture Notes}}] 
    
−   30.04.  +   30.04.2013  Timedependent density functional theory, postHartreeFock methods [{{DownloadsimmethodsII_ss13_lecture4.pdfLecture Notes}}] 
    
−   09.05.  +   09.05.2013  ''Holiday (Christi Himmelfahrt)''  
    
−   16.05.  +   16.05.2013 QM forces, energy minimization, CPMD, quantum Monte Carlo, QM/MM, tightbinding<!simulations of macromolecules and soft matter>  [{{DownloadsimmethodsII_ss13_lecture5.pdfLecture Notes}}] 
    
−   23.05.  +   23.05.2013  '' Holiday (Pfingsten) ''  
    
−   30.05.  +   30.05.2013  '' Holiday (Fronleichnam) ''  
    
−   06.06.  +   06.06.2013 Classical force fields, explicit water models<!Long range interactions in periodic boundary conditions>  [{{DownloadsimmethodsII_ss13_lecture6_watermodels.pdfLecture Notes 1}}, {{DownloadsimmethodsII_ss13_lecture6_MD.pdfLecture Notes 2}}] 
    
−   13.06.  +   13.06.2013  Implicit solvent models  {{DownloadsimmethodsII_ss13_lecture7.pdfLecture Notes}} 
−    
    
−   20.06.  +   20.06.2013  MD simulations of biomolecules, force fields  [{{DownloadsimmethodsII_ss13_lecture8.pdfLecture Notes}}] 
    
−   27.06.  +   27.06.2013  Hydrodynamic methods: Brownian Dynamics, DPD, LatticeBoltzmann  [{{DownloadsimmethodsII_ss13_lecture9.pdfLecture Notes}}] 
    
−   04.07.  +   04.07.2013  Interatomic potentials <!Advanced MC/MD methods>  [{{DownloadsimmethodsII_ss13_lecture10.pdfLecture Notes}}] 
    
−   11.07.  +   11.07.2013  Cancelled <!Free energy methods > [] 
    
−   18.07.  +   18.07.2013  EAM, coarsegraining and nuggets on multiscale simulations  [{{DownloadsimmethodsII_ss13_lecture12.pdfLecture Notes 1}}, {{DownloadsimmethodsII_ss13_lecture12_multiscale.pdfLecture Notes 2}}] 
}  }  
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*The tutorials will take place on Tuesdays between 810 am in the ICP CIPPool.  *The tutorials will take place on Tuesdays between 810 am in the ICP CIPPool.  
−  *New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 18.04. The following week is dedicated to working on problems related to the last worksheet. Homework in the form of a report should be sent to [[Jens Smiatek]]  +  *New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 18.04. The following week is dedicated to working on problems related to the last worksheet. Homework in the form of a report should be sent to [[Jens Smiatek]] before the next worksheet will be handed out. The twoweek cycle ends with the discussion of results of the previous worksheet and handing out a new one. 
== Work sheets ==  == Work sheets ==  
−  *'''[[Media:worksheet1.zipWorksheet 1 (zipFile with SIESTA input files and attachments)]]''' ''Quantum mechanical approaches  Hückel approximation and DFT methods''  +  *'''[[Media:worksheet1.zipWorksheet 1 (zipFile with SIESTA input files and attachments)]]''' ''Quantum mechanical approaches  Hückel approximation and DFT methods'' 
** [[Media:tutorial1.pdfWorksheet 1 (the work sheet as a single PDF file)]]  ** [[Media:tutorial1.pdfWorksheet 1 (the work sheet as a single PDF file)]]  
** [http://icmab.cat/leem/siesta/CodeAccess/Code/downloads.html SIESTA Download]  ** [http://icmab.cat/leem/siesta/CodeAccess/Code/downloads.html SIESTA Download]  
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** [http://icmab.cat/leem/siesta/Documentation/Tutorials/Lyon2007/index.html Handsontutorial for SIESTA, Lyon 2007]  ** [http://icmab.cat/leem/siesta/Documentation/Tutorials/Lyon2007/index.html Handsontutorial for SIESTA, Lyon 2007]  
+  *'''[[Media:worksheet2.zipWorksheet 2 (zipFile with si.fdf)]]''' ''Properties of fermions and Density functional theory''  
+  
+  *'''[[Media:ws3.zipWorksheet 3 (zipFile with water topology and input files for GROMACS)]]''' ''Diffusion processes and atomistic water model properties''  
+  ** [[Media:tut3.pdfWorksheet 3 (the work sheet as a single PDF file)]]  
+  ** [http://www.gromacs.org GROMACS Download]  
+  
+  *'''[[Media:alanine_dipeptide.zipWorksheet 4 (zipFile with input files)]]''' ''Allatom Molecular Dynamics simulations of the alanine dipeptide''  
+  ** [[Media:alanine_dipeptide.pdfWorksheet 4 (the work sheet as a single PDF file)]]  
+  ** [http://www.gromacs.org GROMACS Download]  
+  ** [http://www.gromacs.org/Documentation/Manual GROMACS Manual]  
+  ** [http://manual.gromacs.org/online/speptide.html Example: How to set up a GROMACS simulation]  
+  ** [http://www.csc.fi/english/csc/courses/archive/material/gmxgpumaterials/vmdgromacsexercises.pdf How to visualize GROMACS trajectories with VMD]  
+  
+  *'''[[Media:ws5.zipWorksheet 5 (zipFile with script files for ESPResSo)]]''' ''Coarsegrained simulations with ESPResSo''  
+  ** [[Media:tut5.pdfWorksheet 5 (the work sheet as a single PDF file)]]  
+  ** [http://espressomd.org/ ESPResSoHomepage]  
+  ** [http://espressomd.org/wordpress/download/ ESPResSoDownload]  
+  ** [http://espressomd.org/jenkins/job/ESPResSo/lastSuccessfulBuild/artifact/doc/ug/ug.pdf ESPResSoManual]  
== Examination ==  == Examination ==  
Latest revision as of 00:04, 28 November 2013
Exams
The following dates and times have been scheduled for the oral exams.Please send an email (Maria Fyta, Jens Smiatek) noting your preference. We will send an email back confirming (or not) the date.
Thu. Sep 19: 10:00, 11:00, 13:00, and 14:00
Overview
 Type
 Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
 Lecturer
 JP. Dr. Maria Fyta, (Lecture); Dr. Jens Smiatek(Tutorials)
 Course language
 English
NO lecture on 11.07.The lecture on 18.07 will start earlier at 11am.  Lectures
 Time: Thursdays, 11:30  13:00, ICP, Allmandring 3, Seminarroom 1
Exception: the lecture of 02.05 will NOT take place that day, but on 30.04 at 08:3010:00.  Tutorials
 Time: Tuesdays, 08:0010:00, ICP, Allmandring 3, CIPPool
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 that contains the lecture "Simulation Methods in Physics II".
The lecture is accompanied by handsontutorials which 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. Attendance of the exercise classes
 2. Obtaining 50% of the possible marks in the handin exercises
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II) determined at the end of lecture Simulation Methods II.
The final grade will be determined in the following way: There will be an oral examination performed at (or after) the end of the course Simulation Methods II (SS 2012).
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: 9780122673511.
[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.

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.

Martin O. Steinhauser, Kai Grass, Elmar Strassburger, Alexander Blumen.
Impact failure of granular materials – Nonequilibrium multiscale simulations and highspeed experiments.
International Journal of Plasticity XXX:XXX, 2008.
[PDF] (5.2 MB) 
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: 9780582382107.
Useful online resources
 Roethlisberger, Tavernarelli, EPFL, Lausanne, 2011: Introduction to electronic structure methods.
 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
 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
To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.
A script on the course material is now available, thanks to Larissa Dill Script (670 KB).
Date Subject Resources 11.04.2013 Introduction, electronic stucture Lecture Notes (3.19 MB) 18.04.2013 Elements of quantum mechanics, Hartree and HartreeFock approximations Lecture Notes (3.22 MB) 25.04.2013 Density functional theory (DFT), functionals, pseudopotentials, elements of solid state physics Lecture Notes (5.51 MB) 30.04.2013 Timedependent density functional theory, postHartreeFock methods Lecture Notes (5.12 MB) 09.05.2013 Holiday (Christi Himmelfahrt) 16.05.2013 QM forces, energy minimization, CPMD, quantum Monte Carlo, QM/MM, tightbinding Lecture Notes (7.41 MB) 23.05.2013 Holiday (Pfingsten) 30.05.2013 Holiday (Fronleichnam) 06.06.2013 Classical force fields, explicit water models Lecture Notes 1 (3.1 MB), Lecture Notes 2 (2.11 MB) 13.06.2013 Implicit solvent models Lecture Notes (4.71 MB) 20.06.2013 MD simulations of biomolecules, force fields Lecture Notes (5.91 MB) 27.06.2013 Hydrodynamic methods: Brownian Dynamics, DPD, LatticeBoltzmann Lecture Notes (4.66 MB) 04.07.2013 Interatomic potentials Lecture Notes (4 MB) 11.07.2013 Cancelled [] 18.07.2013 EAM, coarsegraining and nuggets on multiscale simulations Lecture Notes 1 (2.04 MB), Lecture Notes 2 (5.96 MB) Tutorials
 The tutorials will take place on Tuesdays between 810 am in the ICP CIPPool.
 New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 18.04. The following week is dedicated to working on problems related to the last worksheet. Homework in the form of a report should be sent to Jens Smiatek before the next worksheet will be handed out. The twoweek cycle ends with the discussion of results of the previous worksheet and handing out a new one.
Work sheets
 Worksheet 1 (zipFile with SIESTA input files and attachments) Quantum mechanical approaches  Hückel approximation and DFT methods
 Worksheet 2 (zipFile with si.fdf) Properties of fermions and Density functional theory
 Worksheet 3 (zipFile with water topology and input files for GROMACS) Diffusion processes and atomistic water model properties
 Worksheet 4 (zipFile with input files) Allatom Molecular Dynamics simulations of the alanine dipeptide
 Worksheet 5 (zipFile with script files for ESPResSo) Coarsegrained simulations with ESPResSo
Examination
Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:
 BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSIONEP

 Obtain 50% of the possible points in the handsin excercises of this lecture as well as for the first part of the lecture as a prerequisite for the examination (USLV)
 60 min of oral examination (PL)
 After the lecture (i.e. Summer 2013)
 Contents: both lectures and the excercises of "Simulation Methods in Physics I"
 International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918005)

 Obtain 50% of the possible points in the handsin excercises of this lecture as a prerequisite for the examination
 30 min of oral examination (PL) about the lecture and the excercises
 BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????)

 Obtain 50% of the possible points in the handsin excercises of this lecture as a prerequisite for the examination (USLV)
 40 min of oral examination (PL) about the lecture and the excercises
 MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????)

 The marks for the module are the marks obtained in the excercises (BSL)