https://www2.icp.uni-stuttgart.de/~icp/mediawiki/api.php?action=feedcontributions&user=Michel&feedformat=atomICPWiki - User contributions [en]2020-08-12T21:07:58ZUser contributionsMediaWiki 1.31.8https://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=11502Simulation Methods in Physics I 11 122012-02-14T10:37:55Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.00, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids, LJ Units || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_031111(3).pdf Lecture Notes 03.11.2011]<br />
|-<br />
| 10.11.2011 || Stat Mech in a Nutshell, efficiency considerations, Simple MD Program || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_101111(4).pdf Lecture Notes 10.11.2011]<br />
|-<br />
| 17.11.2011 || Observables in MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_171111(5).pdf Lecture Notes 17.11.2011]<br />
|-<br />
| 24.11.2011 || Diffusion, Brownian motion, RDF || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111(6).pdf Lecture Notes 24.11.2011]<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_011211(7).pdf Lecture Notes 01.12.2011] [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111_(6)Simulating_Brownian_Motion.pdf Presentation 01.12.2011 ]<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_081211(8).pdf Lecture Notes 08.12.2011]<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_151211(9).pdf Lecture Notes 15.12.2011]<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_221211(10).pdf Lecture Notes 22.12.2011]<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_120112(11).pdf Lecture Notes 12.01.2012]<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_190112(12).pdf Lecture Notes 19.01.2012]<br />
|-<br />
| 26.01.2012 || Finite Size Scaling || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_260112(13).pdf Lecture Notes 26.01.2012]<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_090212(15).pdf Lecture Notes 09.02.2012] [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_090212_Euclidian_Lattice_Theory.pdf Euclidian Lattice Theory ]<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2011 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2011 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* {{Download|Sim_Meth_I_T1_ 11_12.pdf| Worksheet for T1 }} (Update2)<br />
* {{Download|Sim_Meth_I_T1_11_12_Code.tar.gz|Source code for download|tar}} (Update1: bugfix)<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2011 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2011 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* {{Download|Sim_Meth_I_T2_ 11_12.pdf| Worksheet for T2 }} <br />
* {{Download|Sim_Meth_I_T2_11_12_Code.tar.gz|Source code for download|tar}}<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2011 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2011 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* {{Download|Sim_Meth_I_T3_11_12.pdf|Worksheet for T3 }}<br />
* {{Download|Sim_Meth_I_T3_11_12_Code.tar.gz|Source code for download|tar}}<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2011 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2011 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* {{Download|Sim_Meth_I_T4_11_12.pdf|Worksheet for T4 }}<br />
* {{Download|Sim_Meth_I_T4_11_12_Code.tar.gz|Source code for download|tar}}<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2011 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2012 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* {{Download|Sim_Meth_I_T5_11_12.pdf|Worksheet for T5 }}<br />
* {{Download|Sim_Meth_I_T5_11_12_Code.tar|Source code for download|tar}}<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2012 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2012 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* {{Download|Sim_Meth_I_T6_11_12.pdf|Worksheet for T6 }}<br />
* {{Download|Sim_Meth_I_T6_11_12_Code.tar|Source code for download|tar}}<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2012 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2012 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=11192Simulation Methods in Physics I 11 122012-01-23T11:21:16Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.00, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids, LJ Units || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_031111(3).pdf Lecture Notes 03.11.2011]<br />
|-<br />
| 10.11.2011 || Stat Mech in a Nutshell, efficiency considerations, Simple MD Program || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_101111(4).pdf Lecture Notes 10.11.2011]<br />
|-<br />
| 17.11.2011 || Observables in MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_171111(5).pdf Lecture Notes 17.11.2011]<br />
|-<br />
| 24.11.2011 || Diffusion, Brownian motion, RDF || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111(6).pdf Lecture Notes 24.11.2011]<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_011211(7).pdf Lecture Notes 01.12.2011] [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111_(6)Simulating_Brownian_Motion.pdf Presentation 01.12.2011 ]<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_081211(8).pdf Lecture Notes 08.12.2011]<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_151211(9).pdf Lecture Notes 15.12.2011]<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_221211(10).pdf Lecture Notes 22.12.2011]<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_120112(11).pdf Lecture Notes 12.01.2012]<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_190112(12).pdf Lecture Notes 19.01.2012]<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2011 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2011 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* {{Download|Sim_Meth_I_T1_ 11_12.pdf| Worksheet for T1 }} (Update2)<br />
* {{Download|Sim_Meth_I_T1_11_12_Code.tar.gz|Source code for download|tar}} (Update1: bugfix)<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2011 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2011 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* {{Download|Sim_Meth_I_T2_ 11_12.pdf| Worksheet for T2 }} <br />
* {{Download|Sim_Meth_I_T2_11_12_Code.tar.gz|Source code for download|tar}}<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2011 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2011 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* {{Download|Sim_Meth_I_T3_11_12.pdf|Worksheet for T3 }}<br />
* {{Download|Sim_Meth_I_T3_11_12_Code.tar.gz|Source code for download|tar}}<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2011 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2011 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* {{Download|Sim_Meth_I_T4_11_12.pdf|Worksheet for T4 }}<br />
* {{Download|Sim_Meth_I_T4_11_12_Code.tar.gz|Source code for download|tar}}<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2011 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2012 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* {{Download|Sim_Meth_I_T5_11_12.pdf|Worksheet for T5 }}<br />
* {{Download|Sim_Meth_I_T5_11_12_Code.tar|Source code for download|tar}}<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2012 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2012 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2012 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2012 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=11191Simulation Methods in Physics I 11 122012-01-23T11:20:46Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.00, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids, LJ Units || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_031111(3).pdf Lecture Notes 03.11.2011]<br />
|-<br />
| 10.11.2011 || Stat Mech in a Nutshell, efficiency considerations, Simple MD Program || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_101111(4).pdf Lecture Notes 10.11.2011]<br />
|-<br />
| 17.11.2011 || Observables in MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_171111(5).pdf Lecture Notes 17.11.2011]<br />
|-<br />
| 24.11.2011 || Diffusion, Brownian motion, RDF || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111(6).pdf Lecture Notes 24.11.2011]<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_011211(7).pdf Lecture Notes 01.12.2011] [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111_(6)Simulating_Brownian_Motion.pdf Presentation 01.12.2011 ]<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_081211(8).pdf Lecture Notes 08.12.2011]<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_151211(9).pdf Lecture Notes 15.12.2011]<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP ||<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_120112(11).pdf Lecture Notes 12.01.2012]<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_190112(12).pdf Lecture Notes 19.01.2012]<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2011 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2011 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* {{Download|Sim_Meth_I_T1_ 11_12.pdf| Worksheet for T1 }} (Update2)<br />
* {{Download|Sim_Meth_I_T1_11_12_Code.tar.gz|Source code for download|tar}} (Update1: bugfix)<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2011 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2011 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* {{Download|Sim_Meth_I_T2_ 11_12.pdf| Worksheet for T2 }} <br />
* {{Download|Sim_Meth_I_T2_11_12_Code.tar.gz|Source code for download|tar}}<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2011 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2011 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* {{Download|Sim_Meth_I_T3_11_12.pdf|Worksheet for T3 }}<br />
* {{Download|Sim_Meth_I_T3_11_12_Code.tar.gz|Source code for download|tar}}<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2011 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2011 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* {{Download|Sim_Meth_I_T4_11_12.pdf|Worksheet for T4 }}<br />
* {{Download|Sim_Meth_I_T4_11_12_Code.tar.gz|Source code for download|tar}}<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2011 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2012 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* {{Download|Sim_Meth_I_T5_11_12.pdf|Worksheet for T5 }}<br />
* {{Download|Sim_Meth_I_T5_11_12_Code.tar|Source code for download|tar}}<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2012 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2012 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2012 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2012 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10788Simulation Methods in Physics I 11 122011-12-15T12:01:45Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.00, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids, LJ Units || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_031111(3).pdf Lecture Notes 03.11.2011]<br />
|-<br />
| 10.11.2011 || Stat Mech in a Nutshell, efficiency considerations, Simple MD Program || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_101111(4).pdf Lecture Notes 10.11.2011]<br />
|-<br />
| 17.11.2011 || Observables in MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_171111(5).pdf Lecture Notes 17.11.2011]<br />
|-<br />
| 24.11.2011 || Diffusion, Brownian motion, RDF || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111(6).pdf Lecture Notes 24.11.2011]<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_011211(7).pdf Lecture Notes 01.12.2011] [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111_(6)Simulating_Brownian_Motion.pdf Presentation 01.12.2011 ]<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_081211(8).pdf Lecture Notes 08.12.2011]<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_151211(9).pdf Lecture Notes 15.12.2011]<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP ||<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. ||<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena ||<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2011 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2011 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* {{Download|Sim_Meth_I_T1_ 11_12.pdf| Worksheet for T1 }} (Update2)<br />
* {{Download|Sim_Meth_I_T1_11_12_Code.tar.gz|Source code for download|tar}} (Update1: bugfix)<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2011 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2011 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* {{Download|Sim_Meth_I_T2_ 11_12.pdf| Worksheet for T2 }} <br />
* {{Download|Sim_Meth_I_T2_11_12_Code.tar.gz|Source code for download|tar}}<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2011 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2011 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* {{Download|Sim_Meth_I_T3_11_12.pdf|Worksheet for T3 }}<br />
* {{Download|Sim_Meth_I_T3_11_12_Code.tar.gz|Source code for download|tar}}<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2011 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2011 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* {{Download|Sim_Meth_I_T4_11_12.pdf|Worksheet for T4 }}<br />
* {{Download|Sim_Meth_I_T4_11_12_Code.tar.gz|Source code for download|tar}}<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2011 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2012 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2012 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2012 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2012 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2012 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10702Simulation Methods in Physics I 11 122011-12-09T09:14:44Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.00, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids, LJ Units || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_031111(3).pdf Lecture Notes 03.11.2011]<br />
|-<br />
| 10.11.2011 || Stat Mech in a Nutshell, efficiency considerations, Simple MD Program || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_101111(4).pdf Lecture Notes 10.11.2011]<br />
|-<br />
| 17.11.2011 || Observables in MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_171111(5).pdf Lecture Notes 17.11.2011]<br />
|-<br />
| 24.11.2011 || Diffusion, Brownian motion, RDF || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111(6).pdf Lecture Notes 24.11.2011]<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_011211(7).pdf Lecture Notes 01.12.2011] [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111_(6)Simulating_Brownian_Motion.pdf Presentation 01.12.2011 ]<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_081211(8).pdf Lecture Notes 08.12.2011]<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs ||<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP ||<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. ||<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena ||<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2011 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2011 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* {{Download|Sim_Meth_I_T1_ 11_12.pdf| Worksheet for T1 }} (Update2)<br />
* {{Download|Sim_Meth_I_T1_11_12_Code.tar.gz|Source code for download|tar}} (Update1: bugfix)<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2011 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2011 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* {{Download|Sim_Meth_I_T2_ 11_12.pdf| Worksheet for T2 }} <br />
* {{Download|Sim_Meth_I_T2_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2011 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2011 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* {{Download|Sim_Meth_I_T3_11_12.pdf|Worksheet for T3 }}<br />
* {{Download|Sim_Meth_I_T3_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2011 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2011 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2011 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2012 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2012 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2012 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2012 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2012 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10701Simulation Methods in Physics I 11 122011-12-09T09:10:46Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.00, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids, LJ Units || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_031111(3).pdf Lecture Notes 03.11.2011]<br />
|-<br />
| 10.11.2011 || Stat Mech in a Nutshell, efficiency considerations, Simple MD Program || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_101111(4).pdf Lecture Notes 10.11.2011]<br />
|-<br />
| 17.11.2011 || Observables in MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_171111(5).pdf Lecture Notes 17.11.2011]<br />
|-<br />
| 24.11.2011 || Diffusion, Brownian motion, RDF || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111_(6)Simulating_Brownian_Motion.pdf Presentation 24.11.2011] [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111(6).pdf Lecture Notes 24.11.2011]<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_011211(7).pdf Lecture Notes 01.12.2011]<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_081211(8).pdf Lecture Notes 08.12.2011]<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs ||<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP ||<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. ||<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena ||<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2011 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2011 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* {{Download|Sim_Meth_I_T1_ 11_12.pdf| Worksheet for T1 }} (Update2)<br />
* {{Download|Sim_Meth_I_T1_11_12_Code.tar.gz|Source code for download|tar}} (Update1: bugfix)<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2011 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2011 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* {{Download|Sim_Meth_I_T2_ 11_12.pdf| Worksheet for T2 }} <br />
* {{Download|Sim_Meth_I_T2_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2011 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2011 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* {{Download|Sim_Meth_I_T3_11_12.pdf|Worksheet for T3 }}<br />
* {{Download|Sim_Meth_I_T3_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2011 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2011 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2011 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2012 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2012 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2012 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2012 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2012 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10700Simulation Methods in Physics I 11 122011-12-09T09:08:26Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.00, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids, LJ Units || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_031111(3).pdf Lecture Notes 03.11.2011]<br />
|-<br />
| 10.11.2011 || Stat Mech in a Nutshell, efficiency considerations, Simple MD Program || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_101111(4).pdf Lecture Notes 10.11.2011]<br />
|-<br />
| 17.11.2011 || Observables in MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_171111(5).pdf Lecture Notes 17.11.2011]<br />
|-<br />
| 24.11.2011 || Diffusion, Brownian motion, RDF || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111_(6)Simulating_Brownian_Motion.pdf Lecture Notes 24.11.2011]<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_011211(7).pdf Lecture Notes 01.12.2011]<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_081211(8).pdf Lecture Notes 08.12.2011]<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs ||<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP ||<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. ||<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena ||<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2011 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2011 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* {{Download|Sim_Meth_I_T1_ 11_12.pdf| Worksheet for T1 }} (Update2)<br />
* {{Download|Sim_Meth_I_T1_11_12_Code.tar.gz|Source code for download|tar}} (Update1: bugfix)<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2011 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2011 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* {{Download|Sim_Meth_I_T2_ 11_12.pdf| Worksheet for T2 }} <br />
* {{Download|Sim_Meth_I_T2_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2011 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2011 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* {{Download|Sim_Meth_I_T3_11_12.pdf|Worksheet for T3 }}<br />
* {{Download|Sim_Meth_I_T3_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2011 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2011 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2011 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2012 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2012 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2012 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2012 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2012 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10667Simulation Methods in Physics I 11 122011-12-08T09:18:26Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.00, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids, LJ Units || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_031111(3).pdf Lecture Notes 03.11.2011]<br />
|-<br />
| 10.11.2011 || Stat Mech in a Nutshell, efficiency considerations, Simple MD Program || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_101111(4).pdf Lecture Notes 10.11.2011]<br />
|-<br />
| 17.11.2011 || Observables in MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_171111(5).pdf Lecture Notes 17.11.2011]<br />
|-<br />
| 24.11.2011 || Diffusion, Brownian motion, RDF || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111_(6)Simulating_Brownian_Motion.pdf Lecture Notes 24.11.2011]<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble ||<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles ||<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs ||<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP ||<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. ||<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena ||<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2011 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2011 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* {{Download|Sim_Meth_I_T1_ 11_12.pdf| Worksheet for T1 }} (Update2)<br />
* {{Download|Sim_Meth_I_T1_11_12_Code.tar.gz|Source code for download|tar}} (Update1: bugfix)<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2011 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2011 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* {{Download|Sim_Meth_I_T2_ 11_12.pdf| Worksheet for T2 }} <br />
* {{Download|Sim_Meth_I_T2_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2011 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2011 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* {{Download|Sim_Meth_I_T3_11_12.pdf|Worksheet for T3 }}<br />
* {{Download|Sim_Meth_I_T3_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2011 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2011 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2011 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2012 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2012 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2012 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2012 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2012 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10666Simulation Methods in Physics I 11 122011-12-08T09:17:38Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.00, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids, LJ Units || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_031111(3).pdf Lecture Notes 03.11.2011]<br />
|-<br />
| 10.11.2011 || Stat Mech in a Nutshell, efficiency considerations, Simple MD Program || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_101111(4).pdf Lecture Notes 10.11.2011]<br />
|-<br />
| 17.11.2011 || Observables in MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_171111(5).pdf Lecture Notes 17.11.2011]<br />
|-<br />
| 24.11.2011 || Diffusion, Brownian motion, RDF || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241111_(6)Simulating Brownian Motion.pdf Lecture Notes 24.11.2011]<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble ||<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles ||<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs ||<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP ||<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. ||<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena ||<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2011 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2011 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* {{Download|Sim_Meth_I_T1_ 11_12.pdf| Worksheet for T1 }} (Update2)<br />
* {{Download|Sim_Meth_I_T1_11_12_Code.tar.gz|Source code for download|tar}} (Update1: bugfix)<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2011 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2011 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* {{Download|Sim_Meth_I_T2_ 11_12.pdf| Worksheet for T2 }} <br />
* {{Download|Sim_Meth_I_T2_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2011 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2011 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* {{Download|Sim_Meth_I_T3_11_12.pdf|Worksheet for T3 }}<br />
* {{Download|Sim_Meth_I_T3_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2011 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2011 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2011 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2012 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2012 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2012 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2012 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2012 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10665Simulation Methods in Physics I 11 122011-12-08T09:17:03Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.00, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids, LJ Units || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_031111(3).pdf Lecture Notes 03.11.2011]<br />
|-<br />
| 10.11.2011 || Stat Mech in a Nutshell, efficiency considerations, Simple MD Program || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_101111(4).pdf Lecture Notes 10.11.2011]<br />
|-<br />
| 17.11.2011 || Observables in MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_171111(5).pdf Lecture Notes 17.11.2011]<br />
|-<br />
| 24.11.2011 || Diffusion, Brownian motion, RDF || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_241211(6).pdf Lecture Notes 24.11.2011]<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble ||<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles ||<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs ||<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP ||<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. ||<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena ||<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2011 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2011 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* {{Download|Sim_Meth_I_T1_ 11_12.pdf| Worksheet for T1 }} (Update2)<br />
* {{Download|Sim_Meth_I_T1_11_12_Code.tar.gz|Source code for download|tar}} (Update1: bugfix)<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2011 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2011 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* {{Download|Sim_Meth_I_T2_ 11_12.pdf| Worksheet for T2 }} <br />
* {{Download|Sim_Meth_I_T2_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2011 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2011 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* {{Download|Sim_Meth_I_T3_11_12.pdf|Worksheet for T3 }}<br />
* {{Download|Sim_Meth_I_T3_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2011 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2011 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2011 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2012 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2012 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2012 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2012 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2012 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10429Simulation Methods in Physics I 11 122011-11-18T08:41:29Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.0, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids, LJ Units || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_031111(3).pdf Lecture Notes 03.11.2011]<br />
|-<br />
| 10.11.2011 || Stat Mech in a Nutshell, efficiency considerations, Simple MD Program || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_101111(4).pdf Lecture Notes 10.11.2011]<br />
|-<br />
| 17.11.2011 || Observables in MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_171111(5).pdf Lecture Notes 17.11.2011]<br />
|-<br />
| 24.11.2011 || Diffusion, Brownian motion, RDF ||<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble ||<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles ||<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs ||<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP ||<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. ||<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena ||<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2010 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2010 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* {{Download|Sim_Meth_I_T1_ 11_12.pdf| Worksheet for T1 }} (Update2)<br />
* {{Download|Sim_Meth_I_T1_11_12_Code.tar.gz|Source code for download|tar}} (Update1: bugfix)<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2010 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2010 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* {{Download|Sim_Meth_I_T2_ 11_12.pdf| Worksheet for T2 }} <br />
* {{Download|Sim_Meth_I_T2_11_12_Code.tar.gz|Source code for download|tar}}<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2010 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2010 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2010 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2010 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2010 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2011 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2011 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2011 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2011 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2011 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10342Simulation Methods in Physics I 11 122011-11-04T08:06:49Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.0, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_031111(3).pdf Lecture Notes 03.11.2011]<br />
|-<br />
| 10.11.2011 ||LJ Units, Simple MD Program ||<br />
|-<br />
| 17.11.2011 || Stat Mech in a Nutshell, Observables in MD ||<br />
|-<br />
| 24.11.2011 || Observables in MD, Diffusion, Brownian motion, RDF ||<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble ||<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles ||<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs ||<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP ||<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. ||<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena ||<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2010 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2010 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* {{Download|Sim_Meth_I_T1_ 11_12.pdf| Worksheet for T1 }} (Update1)<br />
* {{Download|Sim_Meth_I_T1_10_11_Code.tar.gz|Source code for download|tar}} (same as last year)<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2010 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2010 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2010 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2010 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2010 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2010 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2010 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2011 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2011 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2011 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2011 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2011 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10321Simulation Methods in Physics I 11 122011-10-31T10:00:41Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.0, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_271011.pdf Lecture Notes 27.10.2011]<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids ||<br />
|-<br />
| 10.11.2011 ||LJ Units, Simple MD Program ||<br />
|-<br />
| 17.11.2011 || Stat Mech in a Nutshell, Observables in MD ||<br />
|-<br />
| 24.11.2011 || Observables in MD, Diffusion, Brownian motion, RDF ||<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble ||<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles ||<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs ||<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP ||<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. ||<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena ||<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2010 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2010 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* Worksheet is being updated. We make it available soon before the tutorial<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2010 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2010 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2010 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2010 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2010 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2010 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2010 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2011 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2011 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2011 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2011 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2011 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10311Simulation Methods in Physics I 11 122011-10-28T10:19:59Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.0, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD ||<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids ||<br />
|-<br />
| 10.11.2011 ||LJ Units, Simple MD Program ||<br />
|-<br />
| 17.11.2011 || Stat Mech in a Nutshell, Observables in MD ||<br />
|-<br />
| 24.11.2011 || Observables in MD, Diffusion, Brownian motion, RDF ||<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble ||<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles ||<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs ||<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP ||<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg. ||<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena ||<br />
|-<br />
| 26.01.2012 || Finite Size Scaling ||<br />
|-<br />
| 02.02.2012 || Error Analysis ||<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics ||<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2010 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2010 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* Worksheet is being updated. We make it available soon before the tutorial<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2010 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2010 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2010 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2010 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2010 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2010 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2010 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2011 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2011 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2011 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2011 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2011 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10310Simulation Methods in Physics I 11 122011-10-28T10:19:04Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.0, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course) !! Downloads<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction || [http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids<br />
|-<br />
| 10.11.2011 ||LJ Units, Simple MD Program<br />
|-<br />
| 17.11.2011 || Stat Mech in a Nutshell, Observables in MD<br />
|-<br />
| 24.11.2011 || Observables in MD, Diffusion, Brownian motion, RDF<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg.<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena<br />
|-<br />
| 26.01.2012 || Finite Size Scaling<br />
|-<br />
| 02.02.2012 || Error Analysis<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2010 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2010 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* Worksheet is being updated. We make it available soon before the tutorial<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2010 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2010 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2010 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2010 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2010 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2010 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2010 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2011 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2011 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2011 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2011 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2011 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10309Simulation Methods in Physics I 11 122011-10-28T09:28:56Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.0, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course)<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids<br />
|-<br />
| 10.11.2011 ||LJ Units, Simple MD Program<br />
|-<br />
| 17.11.2011 || Stat Mech in a Nutshell, Observables in MD<br />
|-<br />
| 24.11.2011 || Observables in MD, Diffusion, Brownian motion, RDF<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg.<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena<br />
|-<br />
| 26.01.2012 || Finite Size Scaling<br />
|-<br />
| 02.02.2012 || Error Analysis<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics<br />
|}<br />
[http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_intro.pdf Lecture Notes 20.10.2011]<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2010 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2010 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* Worksheet is being updated. We make it available soon before the tutorial<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2010 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2010 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2010 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2010 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2010 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2010 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2010 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2011 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2011 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2011 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2011 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2011 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10308Simulation Methods in Physics I 11 122011-10-28T09:22:30Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.0, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course)<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids<br />
|-<br />
| 10.11.2011 ||LJ Units, Simple MD Program<br />
|-<br />
| 17.11.2011 || Stat Mech in a Nutshell, Observables in MD<br />
|-<br />
| 24.11.2011 || Observables in MD, Diffusion, Brownian motion, RDF<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg.<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena<br />
|-<br />
| 26.01.2012 || Finite Size Scaling<br />
|-<br />
| 02.02.2012 || Error Analysis<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics<br />
|}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2010 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2010 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* Worksheet is being updated. We make it available soon before the tutorial<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2010 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2010 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2010 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2010 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2010 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2010 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2010 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2011 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2011 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2011 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2011 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2011 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10307Simulation Methods in Physics I 11 122011-10-28T09:22:16Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.0, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course)<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids<br />
|-<br />
| 10.11.2011 ||LJ Units, Simple MD Program<br />
|-<br />
| 17.11.2011 || Stat Mech in a Nutshell, Observables in MD<br />
|-<br />
| 24.11.2011 || Observables in MD, Diffusion, Brownian motion, RDF<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg.<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena<br />
|-<br />
| 26.01.2012 || Finite Size Scaling<br />
|-<br />
| 02.02.2012 || Error Analysis<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics<br />
|}<br />
* {{Download|http://www.icp.uni-stuttgart.de/~icp/html/teaching/2011-sum/Vorlesung_SM1_Intro.pdf|Lecture Notes 20.10.2011}}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2010 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2010 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* Worksheet is being updated. We make it available soon before the tutorial<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2010 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2010 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2010 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2010 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2010 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2010 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2010 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2011 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2011 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2011 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2011 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2011 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michelhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_11_12&diff=10306Simulation Methods in Physics I 11 122011-10-28T09:20:09Z<p>Michel: /* Lecture */</p>
<hr />
<div><!-- ==Simulationsmethoden in der Physik I== --><br />
<!-- ==Simulation Methods in Physics I == --><br />
<br />
<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
: <br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]] (Lecture); [[Marcello Sega]] and [[Peter Košovan]] (Tutorials)<br />
;Course language<br />
:Deutsch oder Englisch, wie gewünscht - German or English, by vote<br />
;Lectures<br />
:Time: Thursdays, 11:30 - 13:00, Room V 57.06 <br />
;Tutorials<br />
:Time: Wednesday afternoon, 14.00-15.30 and 17:30-19.0, Room V27.U104<br />
<br />
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
<br />
==Scope==<br />
<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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. In more detail, the<br />
lecture will consist of:<br />
<br />
'''1. Molecular Dynamics'''<br />
<br />
The first problem that comes to mind when thinking about simulating<br />
physics is solving Newtons equations of motion for some particles with<br />
given interactions. From that perspective, we first introduce the most<br />
common numerical integrators. This approach quickly leads us to<br />
Molecular Dynamics (MD) simulations. Many of the complex problems of<br />
practical importance require us to take a closer look at statistical<br />
properties, ensembles and the macroscopic observables.<br />
<br />
The goal is to be able to set up and run real MD simulations for<br />
different ensembles and understand and interpret the output.<br />
<br />
'''2. Partial Differential Equations'''<br />
<br />
Some of the most common physical problems today can be formulated with<br />
Partial Differential Equations (PDEs). We want to think about what kinds<br />
of physical problems can be dealt with PDEs and what methods we<br />
have to solve them numerically. <br />
<br />
The goal is to get to know the problems you run into when solving these<br />
simple-looking equations and to get an overview on the methods available.<br />
<br />
'''3. Quantum mechanical systems'''<br />
<br />
It is obvious that solving quantum mechanical systems analytically is not possible and we need numerical help. We want to introduce various methods like (post-)Hartree-Fock, Density Functional Theory, and Car-Parrinello-Molecular dynamics. We also want to examine the possibilities to simulate the quantum chromodynamics PDEs on a lattice (lattice gauge theory).<br />
<br />
The goal is to get an overview on the methods to treat quantum<br />
mechanical systems and know about some of the advantages and<br />
disadvantages of each method. <br />
<br />
'''4. Monte Carlo Simulations'''<br />
<br />
Since their invention, the importance of Monte Carlo (MC) sampling has<br />
grown constantly. Nowadays it is applied to a wide class of problems in modern<br />
computational physics. We want to present the general idea and theory<br />
behind MC simulations and show some more properties using simple toy models<br />
like the Ising-model.<br />
<br />
== Prerequisites ==<br />
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 (preferably C or C++).<br />
<br />
== Prerequisites for the examination ==<br />
# Attendance of the exercise classes<br />
# Obtaining 50% of the possible marks in the hand-in exercises<br />
(In German: USL -V )<br />
<br />
There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II and the exercise of Simulation Methods I) determined at the end of lecture Simulation Methods II.<br />
The grade will be determined in the following way :<br />
There is an oral examination (60 minutes) performed at (or after) the end of the course Simulation Methods II (SS 2012), where the dates are to be settled with the lecturer.<br />
<br />
People taking other modules where this course is part of should contact the lecturer for optional other examinations.<br />
<br />
== Lecture ==<br />
{| class="prettytable"<br />
|-valign="top"<br />
!Date !! Topics (subject may change during the course)<br />
|-<br />
| 20.10.2011 || Course Content, Organisation,Introduction<br />
|-<br />
| 27.10.2011 ||Equation of Motion and simple Integrators for Classical MD<br />
|-<br />
| 03.11.2011 ||Integrators cont., simple Potentials for Liquids<br />
|-<br />
| 10.11.2011 ||LJ Units, Simple MD Program<br />
|-<br />
| 17.11.2011 || Stat Mech in a Nutshell, Observables in MD<br />
|-<br />
| 24.11.2011 || Observables in MD, Diffusion, Brownian motion, RDF<br />
|-<br />
| 01.12.2011 || Green-Kubo relations, temperature fluctuations in NVE ensemble<br />
|-<br />
| 08.12.2011 || Thermostats and different ensembles<br />
|-<br />
| 15.12.2011 || Finite differencing techniques, solving PDEs<br />
|-<br />
| 22.12.2011 || Overview over research topics at the ICP<br />
|-<br />
| 12.01.2012 || Introduction to Monte Carlo Methods, Metropolis Alg.<br />
|-<br />
| 19.01.2012 || Phase transitions, critical phenomena<br />
|-<br />
| 26.01.2012 || Finite Size Scaling<br />
|-<br />
| 02.02.2012 || Error Analysis<br />
|-<br />
| 09.02.2012 || Single particle Quantum Mechanics<br />
|}<br />
* {{Download|Vorlesung_SM1_Intro.pdf|Lecture Notes 20.10.2011}}<br />
<br />
== Tutorials (U 104)==<br />
<br />
;Scheduling of tutorials<br />
:First tutorial is an introductory one and does not contain any graded homework. Starting from the second tutorial, a new worksheet is handed out every second week. 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 tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.<br />
<br />
<br />
{| class="prettytable"<br />
|-valign="top"<br />
! Week || Date || Topic and files to download || Responsible tutor<br />
|-<br />
| 1. || 26.10.2010 || T0: First steps with Linux and C <br />
* {{Download|Sim_Meth_I_T0_ 11_12.pdf| Worksheet for T0 }}<br />
* [[T0_10_11| T0 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 2. || 2.11.2010 || Discussion of T0 <br />
T1: Equations of motion and integrators<br />
* Worksheet is being updated. We make it available soon before the tutorial<br />
* [[T1_10_11| T1 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 3. || 9.11.2010 || Working on problems from T1 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 4. || 16.11.2010 || Discussion of T1 <br />
T2: Molecular Dynamics: Lennard-Jones liquid<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T2_10_11| T2 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 5. || 23.11.2010 || Working on problems from T2 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 6. || 30.11.2010 || Discussion of T2<br />
T3: MD in NVE and NVT ensembles; implementing different thermostats<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T3_10_11| T3 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 7. || 7.12.2010 || Working on problems from T3 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 8. || 14.12.2010 || Discussion of T3<br />
T4: The finite Difference and Finite element methods<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T4_10_11| T4 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 9. || 21.12.2010 || Working on problems from T4 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 10. || 11.1.2011 || Discussion of T4<br />
T5: Simple and importance sampling. Random walks.<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T5_10_11| T5 from last year]]<br />
|| [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 11. || 18.1.2011 || Working on problems from T5 || [[Marcello Sega|Marcello Sega]]<br />
|-<br />
| 12. || 25.1.2011 || Discussion of T5 <br />
T6: Monte Carlo-Ising model<br />
* Worksheet is being updated. We make it available before the tutorial.<br />
* [[T6_10_11| T6 from last year]]<br />
|| [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 13. || 1.2.2011 || Working on problems from T6 || [[Peter Košovan|Peter Košovan]]<br />
|-<br />
| 14. || 8.2.2011 || Discussion of T6, end of the tutorials <br />
|| [[Peter Košovan|Peter Košovan]]<br />
[[Marcello Sega|Marcello Sega]]<br />
|-<br />
|}<br />
<br />
== Assessment of the tutorials ==<br />
Each task within the tutorial is assigned a given number of points. In total, every tutorial comprises 10 points. This means that there is a total maximum of 60 points and 30 are required to pass.<br />
<br />
;Obtaining extra points<br />
:Most tutorials contain some extra tasks. These constitute bonus points. typically there are two bonus points per worksheet.<br />
:First person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. Same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints but these are not awarded extra points.<br />
:If you have a brilliant idea about an extra task which could be done in addition to what is requested in the worksheet, first ask the tutor to approve it. He will also tell you how many points you can get for it.<br />
<br />
== Guidelines for submitting the reports ==<br />
<br />
Homework for the tutorials should be submitted in the form of a report. It has to be submitted via e-mail as a '''single pdf document'''. Submission of handwritten reports is discouraged, but will also be accepted. Source code should always be sent via e-mail in a separate file, if needed. If the code concerns only a few lines, it may be a part of the report. Reports clearly not meeting these requirements may be rejected without evaluation.<br />
<br />
Reports obviously copied from someone else will be rejected without evaluation. It is encouraged to help each other and discuss your results, but each report has to be an original work.<br />
<br />
If you have a technical problem on the CIP pool computers, e.g. a missing program or library or something else which does not allow you to perform a certain task, ask the tutor for assistance.<br />
<br />
If you are not able for any reason to get the expected results, you should at least describe in the report your attempts to obtain them and/or to understand the origin of the problem. Saying in your report "I was not able to run program XXX, therefore I do not provide answer to Task YY." will not be accepted.<br />
<br />
In your communications by email, always send the message to both tutors.<br />
<br />
;Deadline<br />
:Every other Monday morning, that is, two days before the next task is handed out. <br />
:A delayed submission is penalized -1 point for each day of the delay.<br />
:The deadline can be postponed if there is a good reason, but it must be decided together with the tutors during the last tutorial before the deadline. The tutor has a right to accept or reject the request and will announce it to all students.<br />
:In case of special circumstances (illness, accident, ...) contact the tutors immediately via e-mail to agree on an individual deadline.<br />
<br />
;Text of the report<br />
:Has to contain author name, student ID and date.<br />
:Should be subdivided into sections, each section being clearly related to one task of the homework.<br />
:Must be written in sentences, not points like in a presentation. <br />
:All conclusions must be explained and when appropriate, supported by data (plots, tables). In case a derivation is required, all intermediate steps have to be clearly understandable or explained in the text.<br />
:For each simulation, it has to be clear, what were the input parameters, so that it can be re-run.<br />
:There is no upper or lower size limit on the report. Use common sense.<br />
<br />
;Figures and plots<br />
:Each figure has to have a number and a caption or title saying what is in the figure.<br />
:In text, refer to figures by the number or title, so that it is clear which figure you are referring to.<br />
:Each plot has to have labels on axes with font size comparable to other text. Plots without labels will not be considered.<br />
:Data points should fill a major part of plot area. The point size, x- and y-scales have to be chosen appropriately so that all important features can be seen.<br />
:All figures have to be included in the report. Figures sent as separate files will not be considered.<br />
:You may optionally provide the data files. If there is a problem in your work, it may help the tutor understand where you made a mistake.<br />
<br />
;Source files<br />
:Remember that someone has to read your code, understand it and check that it is correct.<br />
:Provide all files in which you made changes!<br />
:Use variables with intuitively understandable names. If not, at least put a comment saying what it means.<br />
:If the code is more complex, add comments to it. Especially to parts which may not be easy to read.<br />
:We recommend that you indent your code for better readability.<br />
<br />
== Recommended literature ==<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a</bibentry><br />
<br />
<br />
== Useful online resources ==<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}<br />
<br />
* [http://www.icp.uni-stuttgart.de/~icp/Computergrundlagen_WS_2010 Computer basics lectures (in german)]<br />
<br />
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749 A guide to Monte Carlo Simulations in Statistical Physics]<br />
<br />
* 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]<br />
<br />
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics]<br />
<br />
* Becareful when using Wiki-type of resources. They may contain a lot of useful information, but also a lot of nonsense, because anyone can write into them.</div>Michel