Difference between revisions of "Simulation Methods in Physics I WS 2013"
(→Course Material) 

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=== Scope ===  === Scope ===  
−  The first part of the course intends to give an overview about modern simulation methods used in physics today. The  +  The first part of the course intends to give an overview about modern simulation methods used in physics today. The lecture should introduce different approaches to simulate a physical systems. In this respect, rather a broad range of methods will be outlined than an exhaustive presentation of specific computational methods. Roughly, the lecture will consist of: 
+  
+  ; General overview  
+  : The first 23 weeks will be dedicated on the general common aspects of computer simulations, elements of statistical ensemble theory and elements of elasticity theory, which are essential in understanding and performing simulations.  
+  
+  ; Quantum Mechanics  
+  : An extensive presentation of quantum mechanical simulations will be given in the second part of this course. Here, a general overview of the ideas behind these kinds of simulations will be given.  
; Molecular Dynamics  ; Molecular Dynamics  
−  :The first problem that comes to mind when thinking about simulating physics is solving Newtons  +  : A more extensive investigation of classical Molecular Dynamics (MD) simulations is planned. This includes the algorithm, the integrators, the thermostats, to name a few necessary to perform MD simulations. 
−  :  +  <!The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for some particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.> 
+  :In terms of the respective tutorials, the goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.  
+  
+  ; Monte Carlo Simulations  
+  : A part of the lecture will be dedicated on Monte Carlo (MC) methods and their algorithms. Specific examples, such as the Ising model will be studied.  
+  <! sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models like the Isingmodel.>  
; Error Analysis  ; Error Analysis  
−  :Autocorrelation, Jackknifing, Bootstrapping  +  :The way errors come into the simulations and how to estimate these will be outlined.<!!Autocorrelation, Jackknifing, Bootstrapping> 
+  
+  ; Potentials  
+  : An important component of molecular simulations are the potentials or force fields chosen to model the interactions within the simulated system. The efficiency of the simulations is stongly dependent on this choice. To this purpose, various methods can be applied for obtaining efficient potentials for different methods. Here, representative examples will be outlined.  
+  <!; Short interlude on Quantum Mechanical Systems  
+  :It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).>  
+  
+  ; Simulation of liquids  
+  : Methods such as the lattice Boltzmann method and specific details on simulating liquids will be briefly given.  
+  
+  ; Advanced simulation techniques  
+  : In the end of the course, a short overview of other more advanced methods than the ones studied here will be presented. Examples include MC beyond the Metropolis algorithm, metadynamics or rare events sampling.  
+  
+  === Prerequisites ===  
+  We expect the participants to have basic knowledge in quantum, classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations, as well as knowledge of a programming language.  
+  
+  === 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 ===  
+  <bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry>  
+  === Useful online resources ===  
+  * Roethlisberger, Tavernarelli, EPFL, Lausanne, 2011: [http://lcbcpc21.epfl.ch/Group_members/ivano/bachelor.pdf Introduction to electronic structure methods.]  
+  
+  * 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://people.virginia.edu/~lz2n/mse627/notes/Intro.pdf University of Virginia, Introduction to atomistic simulations]  
−  :  
+  * 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.  
=== Course Material ===  === Course Material ===  
Line 65:  Line 112:  
    
−  12.12.2013  Monte Carlo (MC)  +  12.12.2013  Introduction to Monte Carlo (MC)  
    
Line 83:  Line 130:  
    
−  06.02.2014  Advanced simulation techniques <!Elements on thermodynamic integration, freeenergy calculations, metadynamics>  +  06.02.2014  Advanced simulation techniques <!Elements on thermodynamic integration, freeenergy calculations, metadynamics>  
+  }  
+  
+  == 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) 
Revision as of 09:06, 19 September 2013
Contents
Overview
 Type
 Lecture (2 SWS) and Tutorials (2 SWS)
 Lecturer
 JP Dr. Maria Fyta (Lecture); Dr. Olaf Lenz, Bibek Adhikari, Elena Minina (Tutorials)
 Course language
 English
 Location and Time
 Lecture: Thu, 11:30  13:00 (Seminar room ICP, Allmandring 3); Tutorials: tba (CIPPool ICP, Allmandring 3)
 Prerequisites
 We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python or C).
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 upon each other, therefore continuous attendance is expected.
Lecture
Scope
The first part of the course intends to give an overview about modern simulation methods used in physics today. The lecture should introduce different approaches to simulate a physical systems. In this respect, rather a broad range of methods will be outlined than an exhaustive presentation of specific computational methods. Roughly, the lecture will consist of:
 General overview
 The first 23 weeks will be dedicated on the general common aspects of computer simulations, elements of statistical ensemble theory and elements of elasticity theory, which are essential in understanding and performing simulations.
 Quantum Mechanics
 An extensive presentation of quantum mechanical simulations will be given in the second part of this course. Here, a general overview of the ideas behind these kinds of simulations will be given.
 Molecular Dynamics
 A more extensive investigation of classical Molecular Dynamics (MD) simulations is planned. This includes the algorithm, the integrators, the thermostats, to name a few necessary to perform MD simulations.
 In terms of the respective tutorials, the goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.
 Monte Carlo Simulations
 A part of the lecture will be dedicated on Monte Carlo (MC) methods and their algorithms. Specific examples, such as the Ising model will be studied.
 Error Analysis
 The way errors come into the simulations and how to estimate these will be outlined.<!!Autocorrelation, Jackknifing, Bootstrapping>
 Potentials
 An important component of molecular simulations are the potentials or force fields chosen to model the interactions within the simulated system. The efficiency of the simulations is stongly dependent on this choice. To this purpose, various methods can be applied for obtaining efficient potentials for different methods. Here, representative examples will be outlined.
 Simulation of liquids
 Methods such as the lattice Boltzmann method and specific details on simulating liquids will be briefly given.
 Advanced simulation techniques
 In the end of the course, a short overview of other more advanced methods than the ones studied here will be presented. Examples include MC beyond the Metropolis algorithm, metadynamics or rare events sampling.
Prerequisites
We expect the participants to have basic knowledge in quantum, classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations, as well as knowledge of a programming language.
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 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.

M. E. J. Newman and G. T. Barkema.
"Monte Carlo Methods in Statistical Physics".
Oxford University Press, 1999.
Useful online resources
 Roethlisberger, Tavernarelli, EPFL, Lausanne, 2011: Introduction to electronic structure methods.
 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.
Course Material
Date  Subject  Resources 

17.10.2013  Course Content, Introduction  
24.10.2013  Introduction to quantummechanical methods  
31.10.2013  Common features in computer simulations (boundary conditions, longrange interactions, finite size effects, etc.)  
07.11.2013  Basics of Stat Mech, ensembles, observables  
14.11.2013  Elements of elasticity theory  
21.11.2013  Introduction to Molecular Dynamics (MD)  
28.11.2013  MD (integrators, Liouville formulation, Lyapunov instability)  
05.12.2013  MD (thermostats/barostats)  
12.12.2013  Introduction to Monte Carlo (MC)  
19.12.2013  MC (examples  Ising model, beyond Metropolis)  
09.01.2014  Building potentials  
16.01.2014  Langevin dynamics, Brownian dynamics  
23.01.2014  Error analysis  
30.01.2014  Simulating liquids  
06.02.2014  Advanced simulation techniques 
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)