Difference between revisions of "Simulation Methods in Physics II SS 2014"
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−  +  == Overview ==  
+  
+  ;Type  
+  :Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)  
+  :  
+  ;Lecturer  
+  :JP. Dr. [[Maria Fyta]], (Lecture), Prof. Dr. [[Christian Holm]]; Dr. [[Jens Smiatek]]; Mr. [[Bibek Adhikari]]; Mr. [[Narayanan Krishnamoorthy Anand]] (Tutorials)  
+  ;Course language  
+  :English  
+  
+  ;Lectures  
+  :Time: Thursdays, 11:30  13:00, ICP, Allmandring 3, Seminarroom 1  
+  ;Tutorials  
+  :Time: Wednesdays, 8:009:30, 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 each worksheet  
+  
+  The final grade will be determined from the final oral examination.  
+  
+  === Oral Examination ===  
+  
+  '''Please email to [[Christian Holm]] in order to arrange a date in September or october for the oral examination.'''  
+  
+  
+  
+  === Recommended literature ===  
+  <bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry>  
+  
+  === Useful online resources ===  
+  
+  * Roethlisberger, Tavernarelli, EPFL, Lausanne, 2011: [http://lcbcpc21.epfl.ch/Group_members/ivano/bachelor.pdf Introduction to electronic structure methods.]  
+  
+  * 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.]  
+  
+  * Linux cheat sheet {{DownloadSim_Meth_I_T0_cheat_sheet_10_11.pdfhere}}.  
+  
+  * 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://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]  
+  
+  * [http://www.filibeto.org/sun/lib/development/shell/intr_to_bash_scr.html Short introduction to shell scripting (bash)]  
+  
+  * [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.  
+  
+  == 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.>  
+  
+  <!  
+  <font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Downloadsimmeth2_vorlesungsmitschrieb.pdfScript}}.'''</font>  
+  >  
+  { class="wikitable"  
+  valign="top"  
+  !Date !! Subject  Resources  
+  
+    
+   10.04.2014  Introduction, electronic stucture  {{DownloadsimmethodsII_ss14_lecture1.pdfLecture Notes}}  
+  
+    
+   15.04.2014  Elements of quantum mechanics, Hartree and HartreeFock approximations  {{DownloadsimmethodsII_ss14_lecture2.pdfLecture Notes}}  
+  
+    
+   22.04.2014  Density functional theory (DFT), functionals, pseudopotentials, elements on solid state physics  {{DownloadsimmethodsII_ss14_lecture3.pdf Lecture Notes}} {{DownloadsimmethodsII_ss14_lecture3_solidstate.pdf Solid State Phys.}}  
+  
+    
+   24.04.2014  Timedependent density functional theory, postHartreeFock methods ab initio MD  {{DownloadsimmethodsII_ss14_lecture4.pdf Lecture Notes}}  
+  
+    
+   01.05.2014  '' Holiday (Labor Day) ''   
+  
+    
+   08.05.2014  Water models (explicit, implicit), Born model of solvation  {{DownloadLecture5_SMII_SS2014.pdf Lecture Notes}}  
+  
+    
+   15.05.2014  Coarsegrained models, simulations of macromolecules and soft matter  {{DownloadLecture_Notes.pdf Lecture Notes}}  
+  
+    
+   22.05.2014  Continuation: CG models  {{DownloadL7_addendum_macromolecules.pdf Lecture Notes}}  
+  
+    
+   29.05.2014  '' Holiday (Christi Himmelfahrt) ''  
+  
+    
+   05.06.2014  Long range interactions in periodic boundary conditions  {{Download20140605SM2.pdfLecture Notes}}  
+  
+    
+   12.06.2014  '' Holiday (Pfingsten) ''   
+  
+    
+   19.06.2014  '' Holiday (Fronleichnam) ''   
+  
+    
+   26.06.2014  PoissonBoltzmann theory, charged polymers  {{DownloadLecture9_PB_aufschrieb.pdfLecture Notes}}  
+  
+    
+   03.07.2014  Free energy methods  {{DownloadLecture_Free_NRG_Methods.pdfLecture Notes}}  
+  
+    
+   10.07.2014  Advanced MC/MD methods {{Download10.7.2014_advanced2.pdfLecture Notes}}  
+  
+    
+   17.07.2014  Hydrodynamic methods: DPD, LatticeBoltzmann {{Download17.7.2014_Hydrodynamics.pdfLecture Notes}}  
+  
+  }  
+  
+  == Tutorials ==  
+  
+  *The tutorials will take place in the ICP CIPPool every Wednesday at 8:009:30.  
+  
+  *New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 10.04. 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 the responsible tutor ([[Bibek Adhikari]] or [[Narayanan Krishnamoorthy Anand]]) 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.  
+  
+  *The worksheets should be handed in every second Tuesday until 10 am (see dates below).  
+  
+  * Assessment of the tutorials  
+  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.  
+  
+  * Dates:  
+  
+  { class="wikitable"  
+  valign="top"  
+  !Worksheet !! Handed out To be handed in  
+  
+    
+   Worksheet 1  10.04.2014 22.04.2014  
+  
+    
+   Worksheet 2  24.04.2014 06.05.2014  
+  
+    
+   Worksheet 3  08.05.2014 20.05.2014  
+  
+    
+   Worksheet 4  22.05.2014 03.06.2014  
+  
+    
+   Worksheet 5  12.06.2014 01.07.2014  
+  
+    
+   Worksheet 6  03.07.2014 15.07.2014  
+  
+  }  
+  
+  == Worksheets ==  
+  
+  *'''[[Media:Sim_MethodsII_2014_ws1.zipWorksheet 1 (zipFile with SIESTA input files and attachments)]]''' ''Quantum mechanical approaches  Hückel approximation and DFT methods''  
+  ** [[Media:Sim_MethodsII_2014_worksheet1.pdfWorksheet 1 (the work sheet as a single PDF file)]]  
+  ** [http://icmab.cat/leem/siesta/CodeAccess/Code/downloads.html SIESTA Download]  
+  ** [http://www.pa.msu.edu/people/tomanek/SIESTAinstallation.html SIESTA Installation Guide]  
+  ** [http://icmab.cat/leem/siesta/Documentation/Tutorials/Lyon2007/index.html Handsontutorial for SIESTA, Lyon 2007]  
+  
+  *'''[[Media:Sim_MethodsII_worksheet2.zipWorksheet 2 (zipFile with si.fdf)]]''' ''Properties of fermions and Density functional theory''  
+  ** [[Media:Sim_MethodsII_2014_worksheet2.pdfWorksheet 2 (the work sheet as a single PDF file)]]  
+  
+  *'''[[Media:ws3_SMII_2014.zipWorksheet 3 (zipFile with water topology and input files for GROMACS)]]''' ''Diffusion processes and properties of atomistic water models''  
+  ** [[Media:tut3_SMII_2014.pdfWorksheet 3 (the work sheet as a single PDF file)]]  
+  ** [http://www.gromacs.org GROMACS Download]  
+  ** [http://www.csc.fi/english/csc/courses/archive/material/gmxgpumaterials/vmdgromacsexercises.pdf How to visualize GROMACS trajectories with VMD]  
+  
+  *'''[[Media:tutorial.pdfWorksheet 4 (pdffile of the tutorial sheet)]]''' ''Coarsegrained polymers and their properties''  
+  ** [[Media:poly.tclESPResSo scriptfile of the tutorial sheet]]'''  
+  ** [[Media:Hint.tar.gzHint for theoretical task]]'''  
+  ** [http://espressomd.org/ ESPResSoHomepage]  
+  ** [http://www.espressomd.org/wordpress/download Espresso Download]  
+  ** [http://espressomd.org/jenkins/job/masterdoc/lastSuccessfulBuild/artifact/doc/ug/ug.pdf Espresso Manual]  
+  
+  *'''[[Media:ws5_SMII_2014.tar.gzWorksheet 5 (Tar.gzfile of the tutorial sheet with source code)]]''' ''Long range interactions: Direct sum and Ewald summation''  
+  ** [[Media:tut5_SMII_2014.pdfWorksheet 5 (the work sheet as a single PDF file)]]  
+  ** [[Media:Literature_Sim_MethodsII.zipUseful literature]]'''  
+  
+  *'''[[Media:Ws6_SMII_2014_version1.tar.gzRevised Worksheet 6 (Tar.gzfile with the tutorial sheet, source code and literature)]]''' ''Charge distribution around a charged rod''  
+  ** [[Media:tut6_ver1.pdfRevised Worksheet 6 (the work sheet as a single PDF file)]]  
+  ** [[Media:tutorial6.tcltutorial6.tcl (TclScript for ESPResSo)]]'''  
+  
+  == Examination ==  
+  
+  There is an oral examination at the end of the semester. All students having obtained 50% of the points from each tutorial are eligible to take the exam. The duration of the exam depends on the module this lecture is part of. Briefly,  
+  
+  ; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)  
+  ; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918005): 30 min exam (content only from SMII will be examined).  
+  ; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).  
+  
+  For additional information/modules, please contact us ([[Maria Fyta]], [[Jens Smiatek]]).  
+  <!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)  
+  > 
Latest revision as of 15:22, 3 September 2014
Contents
Overview
 Type
 Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
 Lecturer
 JP. Dr. Maria Fyta, (Lecture), Prof. Dr. Christian Holm; Dr. Jens Smiatek; Mr. Bibek Adhikari; Mr. Narayanan Krishnamoorthy Anand (Tutorials)
 Course language
 English
 Lectures
 Time: Thursdays, 11:30  13:00, ICP, Allmandring 3, Seminarroom 1
 Tutorials
 Time: Wednesdays, 8:009:30, 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 each worksheet
The final grade will be determined from the final oral examination.
Oral Examination
Please email to Christian Holm 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, 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
Date  Subject  Resources 

10.04.2014  Introduction, electronic stucture  Lecture Notes (3.23 MB) 
15.04.2014  Elements of quantum mechanics, Hartree and HartreeFock approximations  Lecture Notes (7.83 MB) 
22.04.2014  Density functional theory (DFT), functionals, pseudopotentials, elements on solid state physics  Lecture Notes (7.34 MB) Solid State Phys. (7.75 MB) 
24.04.2014  Timedependent density functional theory, postHartreeFock methods ab initio MD  Lecture Notes (7.9 MB) 
01.05.2014  Holiday (Labor Day)  
08.05.2014  Water models (explicit, implicit), Born model of solvation  Lecture Notes (3.81 MB) 
15.05.2014  Coarsegrained models, simulations of macromolecules and soft matter  Lecture Notes (4.27 MB) 
22.05.2014  Continuation: CG models  Lecture Notes (3.78 MB) 
29.05.2014  Holiday (Christi Himmelfahrt)  
05.06.2014  Long range interactions in periodic boundary conditions  Lecture Notes (2.32 MB) 
12.06.2014  Holiday (Pfingsten)  
19.06.2014  Holiday (Fronleichnam)  
26.06.2014  PoissonBoltzmann theory, charged polymers  Lecture Notes (8.55 MB) 
03.07.2014  Free energy methods  Lecture Notes (3.44 MB) 
10.07.2014  Advanced MC/MD methods  Lecture Notes (3.61 MB) 
17.07.2014  Hydrodynamic methods: DPD, LatticeBoltzmann  Lecture Notes (3.84 MB) 
Tutorials
 The tutorials will take place in the ICP CIPPool every Wednesday at 8:009:30.
 New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 10.04. 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 the responsible tutor (Bibek Adhikari or Narayanan Krishnamoorthy Anand) 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.
 The worksheets should be handed in every second Tuesday until 10 am (see dates below).
 Assessment of the tutorials
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.
 Dates:
Worksheet  Handed out  To be handed in 

Worksheet 1  10.04.2014  22.04.2014 
Worksheet 2  24.04.2014  06.05.2014 
Worksheet 3  08.05.2014  20.05.2014 
Worksheet 4  22.05.2014  03.06.2014 
Worksheet 5  12.06.2014  01.07.2014 
Worksheet 6  03.07.2014  15.07.2014 
Worksheets
 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 properties of atomistic water models
 Worksheet 4 (pdffile of the tutorial sheet) Coarsegrained polymers and their properties
 Worksheet 5 (Tar.gzfile of the tutorial sheet with source code) Long range interactions: Direct sum and Ewald summation
 Revised Worksheet 6 (Tar.gzfile with the tutorial sheet, source code and literature) Charge distribution around a charged rod
Examination
There is an oral examination at the end of the semester. All students having obtained 50% of the points from each tutorial are eligible to take the exam. The duration of the exam depends on the module this lecture is part of. Briefly,
 BSc/MSc Physik, Modul "Simulationsmethoden in der Physik"
 60 min exam (contents from both parts SMI + SMII will be examined)
 International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918005)
 30 min exam (content only from SMII will be examined).
 BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II"
 40 min (content from SMII will be examined).
For additional information/modules, please contact us (Maria Fyta, Jens Smiatek).