https://www2.icp.uni-stuttgart.de/~icp/mediawiki/api.php?action=feedcontributions&user=Holm&feedformat=atomICPWiki - User contributions [en]2020-11-27T03:56:54ZUser contributionsMediaWiki 1.31.10https://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2020/2021&diff=25175Simulation Methods in Physics I WS 2020/20212020-11-03T11:09:14Z<p>Holm: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00&ndash;15:30; online: via [https://unistuttgart.webex.com/meet/christian.holm webex]<br />
:'''Tutorials''': TBA ([[Samuel Tovey]]); TBA ([[Christoph Lohrmann]])<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place via webex (details will follow). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Course material ==<br />
<br />
All course material (general info, lecture recordings, worksheets, ...) will be distributed via ILIAS (you join the ILIAS groups upon registration through C@MPUS) <br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents in second order phase transitions<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
! !! Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|1||2020-11-05 || Organization, Introduction, MD Basics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2||2020-11-12 || Integrators Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|3||2020-11-19 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|4||2020-11-26 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|5||2020-12-03 || Observables, Brownian Motion, Diffusion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|6||2020-12-10 || Diffusion, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|7||2020-12-17 || Thermostats part 1 || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|8||2021-01-07 || Error analysis || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|9||2021-01-14 || Thermostat part2 + Intro Monte Carlo || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|10||2021-01-21 || Monte-Carlo Method and critical phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|11||2021-01-28 || Critical Exponents || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|12||2021-02-04 || Finite Size Scaling || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|13||2021-02-11 || Reweighting || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|}<br />
--><br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script, please send an email to [[Christoph Lohrmann]] or [[Samuel Tovey]].<br />
--><br />
<!--<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
* Monte Carlo Simulations: W. Janke, [https://link.springer.com/chapter/10.1007/978-3-642-85238-1_3 <i>Monte Carlo</i>], Monte Carlo Simulations of Spin Systems, Computational Physics pp 10-43<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
--><br />
<br />
== Tutorials ==<br />
<br />
<!--<br />
--><br />
<br />
<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
<!--<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
--><br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Samuel Tovey]] or [[Christoph Lohrmann]]).<br />
* Each task within the tutorial is assigned a given number of points. Each student should have 50 % of the points from each tutorial as a prerequisite for the oral examination.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
== Getting ready for the exercises ==<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) &ndash; the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ &ndash; the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} &ndash; the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ &ndash; the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} &ndash; Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python3 python3-numpy python3-scipy \<br />
python3-matplotlib ipython ipython-notebook gcc g++<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python36 py36-numpy py36-scipy \<br />
py36-matplotlib py36-ipython py36-jupyter<br />
sudo port select python python36<br />
sudo port select ipython py36-ipython<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the programme you are enrolled in, Simulation Methods is part of different modules that award different numbers of credits after different kinds of exams. Please have a look at [[File:SimMethModuleOverview.pdf]], which also explains how you can take Advanced Simulation Methods.<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [https://campus.uni-stuttgart.de/cusonline/ee/ui/ca2/app/desktop/#/slc.tm.cp/student/courses/269105?$ctx=design=ca;lang=de C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in winter semester 2020 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' &ndash; but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2020 if they intend to enroll in the master programme (starting in fall 2021) and take Advanced Simulation Methods (in summer 2022). All students will need to present their ''"Schein"'' at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2020/2021&diff=25174Simulation Methods in Physics I WS 2020/20212020-11-03T11:01:56Z<p>Holm: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00&ndash;15:30; online: via [https://unistuttgart.webex.com/meet/christian.holm webex]<br />
:'''Tutorials''': TBA ([[Samuel Tovey]]); TBA ([[Christoph Lohrmann]])<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place via webex (details will follow). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Course material ==<br />
<br />
All course material (general info, lecture recordings, worksheets, ...) will be distributed via ILIAS (you join the ILIAS groups upon registration through C@MPUS) <br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents in second order phase transitions<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
! !! Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|1||2020-11-05 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2||2020-11-12 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|3||2020-11-19 || Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|4||2020-11-26 || Basics of Statistical Mechanics, Chaos || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|5||2020-12-03 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|6||2020-12-10 || Observables, Brownian Motion, Diffusion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|7||2019-12-17 || Diffusion, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|8||2021-01-07 || Thermostats part 1 || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|9||2021-01-14 || Error analysis || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|10||2021-01-21 ||Thermostat part2 + Intro Monte Carlo|| [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|11||2021-01-28 || Monte-Carlo Method and critical phenomena|| [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|12||2021-02-04 ||Critical Exponents || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|13||2021-02-11 || Finite Size Scaling || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|14||2020-01-30 || Reweighting || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture15_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|15||2020-02-06 || Research @ICP and thesis topics|| [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
|}<br />
--><br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script, please send an email to [[Christoph Lohrmann]] or [[Samuel Tovey]].<br />
--><br />
<!--<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
* Monte Carlo Simulations: W. Janke, [https://link.springer.com/chapter/10.1007/978-3-642-85238-1_3 <i>Monte Carlo</i>], Monte Carlo Simulations of Spin Systems, Computational Physics pp 10-43<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
--><br />
<br />
== Tutorials ==<br />
<br />
<!--<br />
--><br />
<br />
<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
<!--<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
--><br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Samuel Tovey]] or [[Christoph Lohrmann]]).<br />
* Each task within the tutorial is assigned a given number of points. Each student should have 50 % of the points from each tutorial as a prerequisite for the oral examination.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
== Getting ready for the exercises ==<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) &ndash; the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ &ndash; the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} &ndash; the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ &ndash; the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} &ndash; Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python3 python3-numpy python3-scipy \<br />
python3-matplotlib ipython ipython-notebook gcc g++<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python36 py36-numpy py36-scipy \<br />
py36-matplotlib py36-ipython py36-jupyter<br />
sudo port select python python36<br />
sudo port select ipython py36-ipython<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the programme you are enrolled in, Simulation Methods is part of different modules that award different numbers of credits after different kinds of exams. Please have a look at [[File:SimMethModuleOverview.pdf]], which also explains how you can take Advanced Simulation Methods.<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [https://campus.uni-stuttgart.de/cusonline/ee/ui/ca2/app/desktop/#/slc.tm.cp/student/courses/269105?$ctx=design=ca;lang=de C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in winter semester 2020 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' &ndash; but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2020 if they intend to enroll in the master programme (starting in fall 2021) and take Advanced Simulation Methods (in summer 2022). All students will need to present their ''"Schein"'' at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2020/2021&diff=25173Simulation Methods in Physics I WS 2020/20212020-11-03T10:59:23Z<p>Holm: /* Script */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00&ndash;15:30; online: via [https://unistuttgart.webex.com/meet/christian.holm webex]<br />
:'''Tutorials''': TBA ([[Samuel Tovey]]); TBA ([[Christoph Lohrmann]])<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place via webex (details will follow). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Course material ==<br />
<br />
All course material (general info, lecture recordings, worksheets, ...) will be distributed via ILIAS (you join the ILIAS groups upon registration through C@MPUS) <br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents in second order phase transitions<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
! !! Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|1||2019-10-17 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2||2019-10-24 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|3||2019-11-07 || Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|4||2019-10-31 || Basics of Statistical Mechanics, Chaos || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|5||2019-11-14 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|6||2019-11-21 || Observables, Brownian Motion, Diffusion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|7||2019-11-28 || Diffusion, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|8||2019-12-05 || Thermostats part 1 || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|9||2019-12-12 || Error analysis || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|10||2019-12-19 ||Thermostat part2 + Intro Monte Carlo|| [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|11||2020-01-09 || Monte-Carlo Method and critical phenomena|| [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|12||2020-01-16 ||Critical Exponents || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|13||2020-01-23 || Finite Size Scaling || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|14||2020-01-30 || Reweighting || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture15_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|15||2020-02-06 || Research @ICP and thesis topics|| [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
|}<br />
--><br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script, please send an email to [[Christoph Lohrmann]] or [[Samuel Tovey]].<br />
--><br />
<!--<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
* Monte Carlo Simulations: W. Janke, [https://link.springer.com/chapter/10.1007/978-3-642-85238-1_3 <i>Monte Carlo</i>], Monte Carlo Simulations of Spin Systems, Computational Physics pp 10-43<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
--><br />
<br />
== Tutorials ==<br />
<br />
<!--<br />
--><br />
<br />
<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
<!--<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
--><br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Samuel Tovey]] or [[Christoph Lohrmann]]).<br />
* Each task within the tutorial is assigned a given number of points. Each student should have 50 % of the points from each tutorial as a prerequisite for the oral examination.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
== Getting ready for the exercises ==<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) &ndash; the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ &ndash; the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} &ndash; the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ &ndash; the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} &ndash; Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python3 python3-numpy python3-scipy \<br />
python3-matplotlib ipython ipython-notebook gcc g++<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python36 py36-numpy py36-scipy \<br />
py36-matplotlib py36-ipython py36-jupyter<br />
sudo port select python python36<br />
sudo port select ipython py36-ipython<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the programme you are enrolled in, Simulation Methods is part of different modules that award different numbers of credits after different kinds of exams. Please have a look at [[File:SimMethModuleOverview.pdf]], which also explains how you can take Advanced Simulation Methods.<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [https://campus.uni-stuttgart.de/cusonline/ee/ui/ca2/app/desktop/#/slc.tm.cp/student/courses/269105?$ctx=design=ca;lang=de C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in winter semester 2020 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' &ndash; but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2020 if they intend to enroll in the master programme (starting in fall 2021) and take Advanced Simulation Methods (in summer 2022). All students will need to present their ''"Schein"'' at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2020/2021&diff=25172Simulation Methods in Physics I WS 2020/20212020-11-03T10:58:49Z<p>Holm: /* Lecture */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00&ndash;15:30; online: via [https://unistuttgart.webex.com/meet/christian.holm webex]<br />
:'''Tutorials''': TBA ([[Samuel Tovey]]); TBA ([[Christoph Lohrmann]])<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place via webex (details will follow). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Course material ==<br />
<br />
All course material (general info, lecture recordings, worksheets, ...) will be distributed via ILIAS (you join the ILIAS groups upon registration through C@MPUS) <br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents in second order phase transitions<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
! !! Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|1||2019-10-17 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2||2019-10-24 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|3||2019-11-07 || Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|4||2019-10-31 || Basics of Statistical Mechanics, Chaos || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|5||2019-11-14 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|6||2019-11-21 || Observables, Brownian Motion, Diffusion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|7||2019-11-28 || Diffusion, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|8||2019-12-05 || Thermostats part 1 || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|9||2019-12-12 || Error analysis || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|10||2019-12-19 ||Thermostat part2 + Intro Monte Carlo|| [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|11||2020-01-09 || Monte-Carlo Method and critical phenomena|| [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|12||2020-01-16 ||Critical Exponents || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|13||2020-01-23 || Finite Size Scaling || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|14||2020-01-30 || Reweighting || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture15_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|15||2020-02-06 || Research @ICP and thesis topics|| [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
|}<br />
--><br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script, please send an email to [[Patrick Kreissl]] or [[Kai Szuttor]].<br />
--><br />
<!--<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
* Monte Carlo Simulations: W. Janke, [https://link.springer.com/chapter/10.1007/978-3-642-85238-1_3 <i>Monte Carlo</i>], Monte Carlo Simulations of Spin Systems, Computational Physics pp 10-43<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
--><br />
<br />
== Tutorials ==<br />
<br />
<!--<br />
--><br />
<br />
<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
<!--<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
--><br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Samuel Tovey]] or [[Christoph Lohrmann]]).<br />
* Each task within the tutorial is assigned a given number of points. Each student should have 50 % of the points from each tutorial as a prerequisite for the oral examination.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
== Getting ready for the exercises ==<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) &ndash; the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ &ndash; the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} &ndash; the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ &ndash; the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} &ndash; Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python3 python3-numpy python3-scipy \<br />
python3-matplotlib ipython ipython-notebook gcc g++<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python36 py36-numpy py36-scipy \<br />
py36-matplotlib py36-ipython py36-jupyter<br />
sudo port select python python36<br />
sudo port select ipython py36-ipython<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the programme you are enrolled in, Simulation Methods is part of different modules that award different numbers of credits after different kinds of exams. Please have a look at [[File:SimMethModuleOverview.pdf]], which also explains how you can take Advanced Simulation Methods.<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [https://campus.uni-stuttgart.de/cusonline/ee/ui/ca2/app/desktop/#/slc.tm.cp/student/courses/269105?$ctx=design=ca;lang=de C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in winter semester 2020 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' &ndash; but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2020 if they intend to enroll in the master programme (starting in fall 2021) and take Advanced Simulation Methods (in summer 2022). All students will need to present their ''"Schein"'' at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Christian_Holm&diff=24786Christian Holm2020-01-10T10:29:33Z<p>Holm: /* Publications */</p>
<hr />
<div>{{Person<br />
|name=Holm, Christian<br />
|title=Prof. Dr.<br />
|status=Director<br />
|phone=63701<br />
|fax=53701<br />
|room=1.046<br />
|email=holm<br />
|image=Christian_Holm.jpg<br />
|researcherid=C-2134-2009<br />
|category=holm<br />
|topical=active<br />
|topical2=atomistics<br />
|topical3=gel<br />
|topical4=nanopore<br />
|topical6=hydrodynamics<br />
|ordering=1<br />
}}<br />
<br />
==Research==<br />
<br />
My scientific interests are especially the study of complex charged and magnetic soft matter by means of computer simulations, and the development of simple theoretical models to describe them. More precisely I am currently working on the solution properties and association behavior of flexible and semi-flexible polyelectrolytes in various solvents and under various salt concentrations and salt types. In addition I am interested in the effective pair interactions of charged colloidal particles and their phase behavior. This includes simple DNA models, and DNA protein interactions, as well as developing coarse grained models for DNA-Histone complexes. We also investigate in depth polyelectrolyte hydrogels and magnetically interacting ferrogels, as well as pure ferrofluids, where special attention is given to the structure of the solution and the magnetic response functions. Another interest is the applicability of mean-field models for the description of models with long range interactions, and possible improvements beyond the mean-field approach. This include local density functional methods based on the Poisson-Boltzmann functional, as well as strong coupling theories such as Wigner-crystal methods. In addition I am interested in the development of fast methods for the computation of long range interactions. These include pure Coulomb as well as dipolar interactions in various geometries (3D-1D), and under various boundary conditions. And least but not last, we are interested in developing fast methods to deal with fluid-structure couplings using various coupling schemes of particles to a lattice-boltzmann fluid. These can be charged fluids, as well as fluids that undergo reactions at boundaries, such as needed for active Janus-Colloids,or for catalytic particles. We also are interested to apply machine learning algorithms for the development of force-fields with almost DFT precision. <br />
<br />
Some of our research is part of collaborative research centres such as:<br />
<br />
==Member of collaborative research centers== <br />
'''SFB 716''' [http://www.sfb716.uni-stuttgart.de sfb716.uni-stuttgart.de] <br />
<br />
'''SFB 1313''' [http://www.sfb1313.uni-stuttgart.de/ sfb1313.uni-stuttgart.de] <br />
<br />
'''SFB 1333''' [http://www.crc1333.uni-stuttgart.de/ crc1333.uni-stuttgart.de] <br />
<br />
'''SimTech''' [http://www.simtech.uni-stuttgart.de SimTech Cluster of Excellence]<br />
<br />
==Publications==<br />
ResearcherID: [https://publons.com/researcher/2862679/christian-holm/ C-2134-2009]<br />
<span id="badgeCont90"><script type="text/javascript" src="https://publons.com/mashlets?el=badgeCont90&rid=C-2134-2009"></script></span><br />
<br />
<br />
===2019===<br />
<bibentry pdflink="yes"><br />
sanchez19a<br />
landsgesell19c<br />
arens19a<br />
zeman19a,<br />
landsgesell19b,<br />
lee19a,<br />
weik19b,<br />
holm19a,<br />
weik19a,<br />
landsgesell19a,<br />
sean19a,<br />
kuron19a,<br />
kuron19b<br />
</bibentry><br />
<br />
===2018===<br />
<bibentry pdflink="yes"><br />
krishnamoorthy18c,<br />
michalowsky18a,<br />
krishnamoorthy18b,<br />
krishnamoorthy18a,<br />
kuron18a,<br />
smiatek18a,<br />
weeber18b,<br />
uhlig18a,<br />
weyman18a,<br />
weeber18a<br />
</bibentry><br />
<br />
===2017===<br />
<bibentry pdflink="yes"><br />
sean17a<br />
uhlig17a,<br />
roy17b,<br />
roy17a,<br />
szuttor17a,<br />
richter17a,<br />
bauer17a,<br />
landsgesell17b,<br />
landsgesell17a,<br />
chung17a,<br />
rau17a,<br />
rud17a,<br />
michalowsky17a,<br />
niu17a,<br />
brown17a,<br />
rempfer17a<br />
landsgesell17b<br />
landsgesell17a<br />
</bibentry><br />
<br />
===2016===<br />
<bibentry pdflink="yes"><br />
micciulla16a,<br />
lesch16a,<br />
huang16a,<br />
kreissl16a,<br />
sanchez16a,<br />
degraaf16a,<br />
degraaf16b,<br />
rempfer16a,<br />
rempfer16b,<br />
breitsprecher16a,<br />
bordin16a,<br />
ilse16a,<br />
burt16a,<br />
krishnamoorthy16a,<br />
weik16a,<br />
kuron16a<br />
</bibentry><br />
<br />
===2015===<br />
<bibentry pdflink="yes"><br />
bauer15a,<br />
breitsprecher15a,<br />
fischer15a,<br />
degraaf15b,<br />
degraaf15c,<br />
fahrenberger15b,<br />
fahrenberger15c,<br />
holm15a,<br />
kosovan15a,<br />
lesch15a,<br />
lesch15b,<br />
pessot15a,<br />
raafatnia15a,<br />
ryzhkov15a,<br />
vogele15a,<br />
vogele15b,<br />
weeber15a,<br />
weeber15c<br />
</bibentry><br />
<br />
===2014===<br />
<bibentry pdflink="yes"><br />
breitsprecher14a,<br />
breitsprecher14b,<br />
dommert14a,<br />
ertl14a,<br />
fahrenberger14a,<br />
fahrenberger14b,<br />
hickey14a,<br />
kesselheim14a,<br />
krishnamoorthy14a,<br />
micciulla14a,<br />
raafatnia14a,<br />
raafatnia14b,<br />
sega14a,<br />
smiatek14a,<br />
smiatek14d,<br />
vagias14a<br />
</bibentry><br />
<br />
===2013===<br />
<bibentry pdflink="yes"><br />
arnold13a,<br />
arnold13b,<br />
arnold13c,<br />
cerda13a,<br />
chakrabarti13a,<br />
dommert12b,<br />
dommert13a,<br />
hickey13a,<br />
hoepfner13b,<br />
klinkigt13a,<br />
kosovan13a,<br />
samin13a,<br />
sanchez13b,<br />
sega13a,<br />
semenov13a,<br />
vagias13a,<br />
vagias13b,<br />
weeber13a<br />
</bibentry><br />
<br />
===2012===<br />
<bibentry pdflink="yes"><br />
kesselheim12a,<br />
bachthaler12a,<br />
dellesite12a,<br />
cerda12a,<br />
weeber12a,<br />
dommert12a,<br />
wendler12a,<br />
ballenegger12a<br />
</bibentry><br />
<br />
===2011===<br />
<bibentry pdflink="yes"><br />
qiao11b,<br />
qiao11a,<br />
gribova11a,<br />
mann11a,<br />
hickey11a,<br />
wendler11b,<br />
kantorovich11b,<br />
cerda11c,<br />
cerda11b,<br />
klinkigt11b,<br />
tabatabaei11a,<br />
sanchez11a,<br />
pyanzina11a,<br />
prokopyeva11a,<br />
kesselheim11a,<br />
kantorovich11a,<br />
cerda11a,<br />
ballenegger11a,<br />
luigi11a<br />
</bibentry><br />
<br />
===2010===<br />
<bibentry pdflink="yes"><br />
neelov10a,<br />
grass10a,<br />
krekeler10a,<br />
tyagi10a,<br />
schmidt10a,<br />
dommert10a,<br />
wang10a,<br />
sayar10a,<br />
qiao10a,<br />
hickey10a,<br />
cerda10a<br />
</bibentry><br />
<br />
===2009===<br />
<bibentry pdflink="yes"><br />
dommert09a,<br />
suezen09a,<br />
pyanzina09a,<br />
prokopieva09a,<br />
smiatek09a,<br />
claudio09a,<br />
pyanzina09a,<br />
cerda09b,<br />
cerda09c,<br />
slater09a,<br />
grass09a,<br />
grass09b<br />
</bibentry><br />
<br />
===2008===<br />
<bibentry pdflink="yes">cerda08d,cerda08e,cerda08a,grass08a,qiao08a,kantorovich08a,lenz08a,ballenegger08a,tyagi08a</bibentry><br />
<br />
===2007===<br />
<bibentry pdflink="yes">tyagi07a,ivanov07a,lobaskin07a,antypov07a, hess07a, sayar07a</bibentry><br />
<br />
===2006===<br />
<bibentry pdflink="yes">antypov07b,holm06a, holm06b, antypov06a, arnold06a, hess06a, hess06b, limbach06a, mann06a, muehlbacher06a, muehlbacher06b, stukan06a</bibentry><br />
<br />
===2005===<br />
<bibentry pdflink="yes">antypov05a, arnold05a, arnold05b, holm05a, holm05b, huang05a, huang05b, limbach05a, mann05a</bibentry><br />
<br />
===2004===<br />
<bibentry pdflink="yes">barbosa04a, espresso03a, holm04a, holm04b, holm04c, huang04a, ivanov04a, limbach04a, limbach04b, lobaskin04b, mann04a, messina04a, naji04b</bibentry><br />
<br />
===2003===<br />
<bibentry pdflink="yes">deserno02b, holm03a, jimenez03a, limbach03a, messina03a, wang03a, wang03b, wang03c</bibentry><br />
<br />
===2002===<br />
<bibentry pdflink="yes">arnold02a, arnold02b, arnold02c, arnold02d, dejoannis02a, deserno02a, holm02a, limbach02a, limbach02c, messina02a, messina02c, messina02d, messina02e, wang02a</bibentry><br />
<br />
===2001===<br />
<bibentry pdflink="yes">deserno00c, deserno01a, deserno01b, deserno01c, holm01b, holm01c, limbach01a, messina01a, messina01b, wang01a</bibentry><br />
<br />
===2000===<br />
<bibentry pdflink="yes">barbosa00a, deserno00a, deserno99b, messina00a, messina00b</bibentry><br />
<br />
===1999===<br />
<bibentry pdflink="yes">holm99a, holm99b, bittner99a, bittner99b, micka99a</bibentry><br />
<br />
===1998 and before===<br />
<bibentry pdflink="yes"><br />
holm98a, holm98b, bittner98a, bittner98b, deserno98a, deserno98b,<br />
holm97a, holm97c, holm97d, holm97e,<br />
holm96a, holm96b, holm96c, holm95c,<br />
holm95a, holm95b, <br />
holm94a, holm94b, holm94c, holm93d,<br />
holm93a, holm93b, holm93c, adler93a,<br />
holm91a, holm91b,<br />
holm90a, holm90b, holm90c, <br />
holm89a, finkelstein89a,<br />
holm88a, holm88b,<br />
holm87a, finkelstein87a,<br />
holm86a, eidson86a, finkelstein86a,<br />
holm85a</bibentry></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2019/2020&diff=24741Simulation Methods in Physics I WS 2019/20202019-12-09T15:44:45Z<p>Holm: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00&ndash;15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu, 15:45&ndash;17:15 ([[Patrick Kreissl]]); Fri, 14:00&ndash;15:30 ([[Kai Szuttor]])<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents in second order phase transitions<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
! !! Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|1||2019-10-17 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2||2019-10-24 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|3||2019-11-07 || Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|4||2019-10-31 || Basics of Statistical Mechanics, Chaos || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|5||2019-11-14 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|6||2019-11-21 || Observables, Brownian Motion, Diffusion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|7||2019-11-28 || Diffusion, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|8||2019-12-05 || Thermostats part 1 || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|9||2019-12-12 || Error analysis || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|10||2019-12-19 ||Thermostat part2 + Intro Monte Carlo|| [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|11||2020-01-09 || Monte-Carlo Method and critical phenomena|| [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|12||2020-01-16 ||Critical Exponents || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|13||2020-01-23 || Finite Size Scaling || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|14||2020-01-30 || Reweighting || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture15_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|15||2020-02-06 || Research @ICP and thesis topics|| [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|}<br />
<!--<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
--><br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
* Monte Carlo Simulations: W. Janke, [https://link.springer.com/chapter/10.1007/978-3-642-85238-1_3 <i>Monte Carlo</i>], Monte Carlo Simulations of Spin Systems, Computational Physics pp 10-43<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.<br />
<br />
== Tutorials ==<br />
<br />
<!--<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) <!--on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[Michael Kuron]]<br />
** Fridays 14:00-15:30 (Tutor: [[Kartik Jain]])--><br />
<!--* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.--><br />
<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Online on !! Deadline !! Files<br />
<br />
|-<br />
<br />
|-<br />
| 1. Integrators || 2019-10-25 || 2019-11-10 midnight || [[:Media:Worksheet_01.tar.gz|Worksheet 1]]<br />
|-<br />
| 2. Statistical Mechanics and Molecular Dynamics || 2019-11-08 || 2019-11-24 midnight || [[:Media:Worksheet_02.tar.gz|Worksheet 2]]<br />
|-<br />
| 3. Molecular Dynamics 2 and Observables|| 2019-11-25 || 2019-12-09 midnight || [[:Media:Worksheet_03.tar.gz|Worksheet 3]]<br />
|-<br />
| 4. Thermostats || 2019-12-09 || 2019-12-23 midnight ||[[:Media:Worksheet_04.tar.gz|Worksheet 4]]<br />
|-<br />
| 5. || 2019-12-20 || 2019-01-19 midnight ||<br />
|-<br />
| 6. || 2019-01-17 || 2019-02-02 midnight ||<br />
<br />
|}<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|txt}}.<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email.<br />
* Participants need 50&thinsp;% of the points of the hands-in exercises on each worksheet to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) &ndash; the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ &ndash; the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} &ndash; the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ &ndash; the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} &ndash; Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the programme you are enrolled in, Simulation Methods is part of different modules that award different numbers of credits after different kinds of exams. Please have a look at [[File:SimMethModuleOverview.pdf]], which also explains how you can take Advanced Simulation Methods.<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [https://campus.uni-stuttgart.de/cusonline/wbLv.wbShowLVDetail?pStpSpNr=208686 C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2020 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' &ndash; but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2020 if they intend to enroll in the master programme (starting in fall 2020) and take Advanced Simulation Methods (in summer 2021). All students will need to present their ''"Schein"'' at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2019/2020&diff=24688Simulation Methods in Physics I WS 2019/20202019-11-21T16:57:03Z<p>Holm: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00&ndash;15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu, 15:45&ndash;17:15 ([[Patrick Kreissl]]); Fri, 14:00&ndash;15:30 ([[Kai Szuttor]])<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents in second order phase transitions<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
! !! Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|1||2019-10-17 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2||2019-10-24 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|3||2019-11-07 || Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|4||2019-10-31 || Basics of Statistical Mechanics, Chaos || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|5||2019-11-14 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|6||2019-11-21 || Observables, Brownian Motion, Diffusion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|7||2019-11-28 || Diffusion, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|8||2019-12-05 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|9||2019-12-12 || Error analysis || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|10||2019-12-19 ||B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|11||2020-01-09 || Monte-Carlo Method || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|12||2020-01-16 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|13||2020-01-23 || Critical Exponent || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|14||2020-01-30 || Finite Size Scaling || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|15||2020-02-06 || Reweighting || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture15_notes.pdf Lecture Notes] ||<br />
<br />
|}<br />
<!--<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
--><br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
* Monte Carlo Simulations: W. Janke, [https://link.springer.com/chapter/10.1007/978-3-642-85238-1_3 <i>Monte Carlo</i>], Monte Carlo Simulations of Spin Systems, Computational Physics pp 10-43<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.<br />
<br />
== Tutorials ==<br />
<br />
<!--<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) <!--on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[Michael Kuron]]<br />
** Fridays 14:00-15:30 (Tutor: [[Kartik Jain]])--><br />
<!--* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.--><br />
<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Online on !! Deadline !! Files<br />
<br />
|-<br />
<br />
|-<br />
| 1. Integrators || 2019-10-25 || 2019-11-10 midnight || [[:Media:Worksheet_01.tar.gz|Worksheet 1]]<br />
|-<br />
| 2. Statistical Mechanics and Molecular Dynamics || 2019-11-08 || 2019-11-24 midnight || [[:Media:Worksheet_02.tar.gz|Worksheet 2]]<br />
|-<br />
| 3. || 2019-11-22 || 2019-12-08 midnight ||<br />
|-<br />
| 4. || 2019-12-06 || 2019-12-22 midnight ||<br />
|-<br />
| 5. || 2019-12-20 || 2019-01-19 midnight ||<br />
|-<br />
| 6. || 2019-01-17 || 2019-02-02 midnight ||<br />
<br />
|}<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|txt}}.<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email.<br />
* Participants need 50&thinsp;% of the points of the hands-in exercises on each worksheet to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) &ndash; the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ &ndash; the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} &ndash; the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ &ndash; the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} &ndash; Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the programme you are enrolled in, Simulation Methods is part of different modules that award different numbers of credits after different kinds of exams. Please have a look at [[File:SimMethModuleOverview.pdf]], which also explains how you can take Advanced Simulation Methods.<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [https://campus.uni-stuttgart.de/cusonline/wbLv.wbShowLVDetail?pStpSpNr=208686 C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2020 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' &ndash; but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2020 if they intend to enroll in the master programme (starting in fall 2020) and take Advanced Simulation Methods (in summer 2021). All students will need to present their ''"Schein"'' at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2019/2020&diff=24579Simulation Methods in Physics I WS 2019/20202019-11-01T10:26:32Z<p>Holm: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00&ndash;15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu, 15:45&ndash;17:15 ([[Patrick Kreissl]]); Fri, 14:00&ndash;15:30 ([[Kai Szuttor]])<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents in second order phase transitions<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
! !! Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|1||2019-10-17 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2||2019-10-24 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|3||2019-11-07 || Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|4||2019-10-31 || Basics of Statistical Mechanics, Chaos || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
<br />
|-<br />
|5||2019-11-14 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|6||2019-11-21 || Observables, Brownian Motion, Diffusion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|7||2019-11-28 || Diffusion, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|8||2019-12-05 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|9||2019-12-12 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|10||2019-12-19 || Error analysis, B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|11||2020-01-09 || Monte-Carlo Method || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|12||2020-01-16 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|13||2020-01-23 || Critical Exponent || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|14||2020-01-30 || Finite Size Scaling || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|15||2020-02-06 || Reweighting || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2019-ws-sim_methods/lecture15_notes.pdf Lecture Notes] ||<br />
<br />
|}<br />
<!--<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
--><br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
* Monte Carlo Simulations: W. Janke, [https://link.springer.com/chapter/10.1007/978-3-642-85238-1_3 <i>Monte Carlo</i>], Monte Carlo Simulations of Spin Systems, Computational Physics pp 10-43<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.<br />
<br />
== Tutorials ==<br />
<br />
<!--<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) <!--on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[Michael Kuron]]<br />
** Fridays 14:00-15:30 (Tutor: [[Kartik Jain]])--><br />
<!--* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.--><br />
<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Online on !! Deadline !! Files<br />
<br />
|-<br />
<br />
|-<br />
| 1. Integrators || 2019-10-25 || 2019-11-10 midnight || [[:Media:Worksheet_01.tar.gz|Worksheet 1]]<br />
|-<br />
| 2. || 2019-11-08 || 2019-11-24 midnight ||<br />
|-<br />
| 3. || 2019-11-22 || 2019-12-08 midnight ||<br />
|-<br />
| 4. || 2019-12-06 || 2019-12-22 midnight ||<br />
|-<br />
| 5. || 2019-12-20 || 2019-01-19 midnight ||<br />
|-<br />
| 6. || 2019-01-17 || 2019-02-02 midnight ||<br />
<br />
|}<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|txt}}.<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email.<br />
* Participants need 50&thinsp;% of the points of the hands-in exercises on each worksheet to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) &ndash; the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ &ndash; the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} &ndash; the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ &ndash; the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} &ndash; Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the programme you are enrolled in, Simulation Methods is part of different modules that award different numbers of credits after different kinds of exams. Please have a look at [[File:SimMethModuleOverview.pdf]], which also explains how you can take Advanced Simulation Methods.<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [https://campus.uni-stuttgart.de/cusonline/wbLv.wbShowLVDetail?pStpSpNr=208686 C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2020 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' &ndash; but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2020 if they intend to enroll in the master programme (starting in fall 2020) and take Advanced Simulation Methods (in summer 2021). All students will need to present their ''"Schein"'' at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2019/2020&diff=24534Simulation Methods in Physics I WS 2019/20202019-10-16T16:18:15Z<p>Holm: /* Hand-in-exercises */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00&ndash;15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': ([[Patrick Kreissl]] and [[Kai Szuttor]])<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents in second order phase transitions<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<!--<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
! !! Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|1||2018-10-18 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture01_slides.pdf Slides] [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture01_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2||2018-10-25 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
| ||2018-11-01 || public holiday, no lecture || ||<br />
<br />
|-<br />
|3||2018-11-08 || Basics of Statistical Mechanics, Chaos || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|4||2018-11-15 || Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|5||2018-11-22 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|6||2018-11-29 || Observables, Brownian Motion, Diffusion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|7||2018-12-06 || Diffusion, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|8||2018-12-13 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|9||2018-12-20 || Error analysis, B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|10||2019-01-10 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture10_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|11||2019-01-17 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|12||2019-01-24 || Critical Exponent ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|13||2019-01-31 || Finite Size Scaling ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|14||2019-02-07 ||Reweighting || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture14_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
--><br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
* Monte Carlo Simulations: W. Janke, [https://link.springer.com/chapter/10.1007/978-3-642-85238-1_3 <i>Monte Carlo</i>], Monte Carlo Simulations of Spin Systems, Computational Physics pp 10-43<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.<br />
<br />
== Tutorials ==<br />
<br />
<!--<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) <!--on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[Michael Kuron]]<br />
** Fridays 14:00-15:30 (Tutor: [[Kartik Jain]])--><br />
<!--* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.--><br />
<br />
<!--<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators (lectures 1-2) || 2018-11-12 12:00 || {{Download|WS_2018_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics (lectures 2-4) || 2018-11-26 12:00 || {{Download|WS_2018_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables (lectures 4-5) || 2018-12-10 12:00 || {{Download|WS_2018_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion (lectures 6-8) || 2019-01-07 12:00 || {{Download|WS_2018_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2018_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo (lectures 10-11) || 2019-01-21 12:00 || {{Download|WS_2018_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling (lectures 11-13) || 2019-02-04 12:00 || {{Download|WS_2018_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<br />
|}<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|txt}}.<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email.<br />
* Participants need 50&thinsp;% of the points of the hands-in exercises on each worksheet to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) &ndash; the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ &ndash; the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} &ndash; the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ &ndash; the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} &ndash; Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the programme you are enrolled in, Simulation Methods is part of different modules that award different numbers of credits after different kinds of exams. Please have a look at [[File:SimMethModuleOverview.pdf]], which also explains how you can take Advanced Simulation Methods.<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [https://campus.uni-stuttgart.de/cusonline/wbLv.wbShowLVDetail?pStpSpNr=208686 C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2020 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' &ndash; but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2020 if they intend to enroll in the master programme (starting in fall 2020) and take Advanced Simulation Methods (in summer 2021). All students will need to present their ''"Schein"'' at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2019/2020&diff=24533Simulation Methods in Physics I WS 2019/20202019-10-16T16:14:28Z<p>Holm: /* Lecture */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00&ndash;15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': ([[Patrick Kreissl]] and [[Kai Szuttor]])<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents in second order phase transitions<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<!--<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
! !! Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|1||2018-10-18 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture01_slides.pdf Slides] [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture01_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2||2018-10-25 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
| ||2018-11-01 || public holiday, no lecture || ||<br />
<br />
|-<br />
|3||2018-11-08 || Basics of Statistical Mechanics, Chaos || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|4||2018-11-15 || Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|5||2018-11-22 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|6||2018-11-29 || Observables, Brownian Motion, Diffusion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|7||2018-12-06 || Diffusion, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|8||2018-12-13 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|9||2018-12-20 || Error analysis, B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|10||2019-01-10 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture10_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|11||2019-01-17 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|12||2019-01-24 || Critical Exponent ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|13||2019-01-31 || Finite Size Scaling ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|14||2019-02-07 ||Reweighting || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture14_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
--><br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
* Monte Carlo Simulations: W. Janke, [https://link.springer.com/chapter/10.1007/978-3-642-85238-1_3 <i>Monte Carlo</i>], Monte Carlo Simulations of Spin Systems, Computational Physics pp 10-43<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.<br />
<br />
== Tutorials ==<br />
<br />
<!--<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) <!--on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[Michael Kuron]]<br />
** Fridays 14:00-15:30 (Tutor: [[Kartik Jain]])--><br />
<!--* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.--><br />
<br />
<!--<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators (lectures 1-2) || 2018-11-12 12:00 || {{Download|WS_2018_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics (lectures 2-4) || 2018-11-26 12:00 || {{Download|WS_2018_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables (lectures 4-5) || 2018-12-10 12:00 || {{Download|WS_2018_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion (lectures 6-8) || 2019-01-07 12:00 || {{Download|WS_2018_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2018_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo (lectures 10-11) || 2019-01-21 12:00 || {{Download|WS_2018_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling (lectures 11-13) || 2019-02-04 12:00 || {{Download|WS_2018_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<br />
|}<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|txt}}.<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email.<br />
* Most participants need 50&thinsp;% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) &ndash; the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ &ndash; the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} &ndash; the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ &ndash; the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} &ndash; Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the programme you are enrolled in, Simulation Methods is part of different modules that award different numbers of credits after different kinds of exams. Please have a look at [[File:SimMethModuleOverview.pdf]], which also explains how you can take Advanced Simulation Methods.<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [https://campus.uni-stuttgart.de/cusonline/wbLv.wbShowLVDetail?pStpSpNr=208686 C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2020 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' &ndash; but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2020 if they intend to enroll in the master programme (starting in fall 2020) and take Advanced Simulation Methods (in summer 2021). All students will need to present their ''"Schein"'' at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Advanced_Simulation_Methods_SS_2019&diff=24349Advanced Simulation Methods SS 20192019-06-20T20:36:50Z<p>Holm: /* Report */</p>
<hr />
<div><br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students should send an email to [[Maria Fyta]] until April 1st 2019.<br />
<br><br />
First meeting: Friday, April 12 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).</b>}}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture and Tutorials (2 SWS in total)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]], JP. Dr. [[Maria Fyta]]<br />
;Course language<br />
:English or German<br />
;Location<br />
:ICP, Allmandring 3; Room: ICP Meeting Room<br />
;Time<br />
:(see below)<br />
The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]] and JP. Dr. [[Maria Fyta]]. It will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules.<br />
The students can work in groups. All groups should write a report of about 10 pages on each module, which they should submit to the responsible person for each module by the deadline set for each module.<br />
<br />
<br />
<br />
== Module 1: [[Maria Fyta]], [[Frank Maier]], Inter-atomic interactions modeled with quantum mechanical simulations ==<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday, April 12 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<br />
<br />
Final meeting and presentation: Friday, May 10 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<br />
<br />
Tutorials: Fridays 11:30-13:00 in the ICP CIP-Pool. The first tutorial will take place on Wed. April 17 at 15:00-16:30.<br />
<br />
Deadline for reports: Mai 08, 2019<br />
<br />
=== Description ===<br />
<br />
This module focuses on the influence of using quantum mechanical simulations. The quantum mechanical schemes which will be applied in this module are based on density functional theory (DFT). This method allows the investigation of the electronic properties of a system. An understanding of the method, an analysis of the results from the simulations is the main goal of this module. The analysis of the simulations should be written up in a report. The talk will be a presentation of a DFT-related journal paper. For this, one of the following papers can be chosen:<br />
<br />
* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J. Klimeš and A. Michaelides, The Journal of Chemical Physics 137, 120901 (2012); doi: 10.1063/1.4754130<br />
* Challenges for Density Functional Theory, A.J. Cohen, P. Mori-Sanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.<br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module please do not hesitate to contact [[Maria Fyta]]. For practical guidance regarding the simulations [[Frank Uhlig]].<br />
<br />
=== Density functional theory and exchange-correlation functionals ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the density functional theory (DFT) method. A scheme which has revolutionarized the way materials and their properties are studied. The students should focus on this method and understand how it works and which its capabilities are. A specific focus would be the different levels of approximations that can be made in this method. For this, the choice of the exchange-correlation functional mapping the interactions of a system is crucial. To this end, the discussion in this module will be directed. The report should contain an introduction to the exchange-correlation functionals in DFT in the context of the simulations and the analysis of the simulations in the tutorial.<br />
<br />
Overall, a variety of DFT exchange correlation functionals have been developed. Some of these often fail in describe complex interactions. For example, only very advanced and quite recent density functionals are able to describe the long-range dispersion interactions [2]. Hence, effective methods based on pair potentials have been developed. These methods can achieve<br />
comparable accuracy to more ab initio methods while coming at a signifcantly lower computational effort [2,3].<br />
<br />
[1] https://dx.doi.org/10.1063/1.4754130<br />
<br />
[2] https://dx.doi.org/10.1103/PhysRevLett.102.073005<br />
<br />
[3] https://dx.doi.org/10.1063/1.3382344<br />
<br />
==== Tutorial ====<br />
<br />
In this exercise you will test different exchange correlation functionals for two systems (silicon and graphite) and analyze the results. All simulations will be performed with the software package [https://departments.icmab.es/leem/siesta/ SIESTA]. A thorough analysis of the stability and energetics of the two system is expected. Tutorial files and brief instructions can be found in ?. The software is installed on our CIP pool machines under /group/allatom/.<br />
<br />
<b> Files </b>{{Download|AdvSimMethoMod1.zip| AdvSimMethoMod1.zip}}<br />
<br />
<br />
Pseudopotential for LMKLL-VDW {{Download|C_VDW.psf| C_VDW.psf}} (rename it to C.psf in order to use it in SIESTA)<br />
<br />
[[Media:Graphene.png]]<br />
<br />
[[Media:Graphene_layers.png]]<br />
<br />
[[Media:Graphite.png]]<br />
<br />
[[Media:Graphite_layers.png]]<br />
<br />
==== Literature ====<br />
<br />
* A bird's-eye view of density-functional theory, Klaus Capelle, arXiv:cond-mat/0211443 (2002).<br />
* Self-Consistent Equations Including Exchange and Correlation Effects, W. Kohn and L.J. Sham, , Phys. Rev. (140), A1133 (1965).<br />
* Understanding and Reducing Errors in Density Functional Calculations, Min-Cheol Kim, Eunji Sim, and Kieron Burke, Phys. Rev. Lett. 111, 073003 (2013).<br />
* Impact of the electron-electron correlation on phonon dispersion: Failure of LDA and GGA DFT functionals in graphene and graphite, Michele Lazzeri, Claudio Attaccalite, Ludger Wirtz, and Francesco Mauri, Phys. Rev. B 78, 081406(R) (2008). <br />
* Electronic properties of nano-graphene sheets calculated using quantum chemical DFT<br />
* Sangam Banerjeea, , Dhananjay Bhattacharyya, Computational Materials Science, 44, 41–45 (2008).<br />
* Dependence of band structures on stacking and field in layered graphene, Masato Aoki, , Hiroshi Amawashi, Solid State Communications 142, 123–127 (2007).<br />
* Graphite Interplanar Bonding: Electronic Delocalization and van der Waals Interaction, J.-C. Charlier, X. Gonze and J.-P. Michenaud, Europhysics Letters), 28 , 403 (1994).<br />
<br />
==== Further reading (if interested) ====<br />
<br />
* An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases, V.R. Cooper, T. Thonhauser, and D.C. Langreth, J. Chem. Phys. 128, 204102 (2008).<br />
* On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit, B. Santra, A. Michaelides, and M. Scheffler, J. Chem. Phys. 127, 184104 (2007).<br />
* On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level, I. Dąbkowska, P. Jurečka, and P. Hobza, J. Chem. Phys. 122, 204322 (2005).<br />
<br />
<b> Lecture Notes </b>{{Download|advSimMeth_module1_XCfunct.pdf| Module 1}}<br />
<br />
== Module 2: [[Maria Fyta]], [[Takeshi Kobayashi]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday May 10 at 13:00 in the ICP meeting room. <br />
<br />
Final meeting and presentation: Friday, June 07 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<br />
<br />
Tutorials: Fridays 11:30-13:00 in the ICP CIP-Pool.<br />
<br />
Deadline for reports: June 05, 2019<br />
<br />
=== Description ===<br />
<br />
This module focuses on atomistic Molecular Dynamics simulations and the study of biological co-solutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological co-solutes, often also called osmolytes are omnipresent in biological cells. A main function of these small-weight organic <br />
molecules is given by the protection of protein structures under harsh environmental conditions (protein stabilizers) or the denaturation of proteins (protein denaturants). The underlying mechanism leading to these effects is still unknown. It has been often discussed that osmolytes have a significant impact on the aqueous solution.<br />
The module consists of model development, simulation, analysis and oral and written presentation part. <br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Takeshi Kobayashi]].<br />
<br />
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the Kirkwood-Buff theory which can be well applied to computer simulations.<br />
The students should study the literature given below and present their findings. The presentation should at a minimum contain an introduction to Kirkwood-Buff theory in the context of the simulations.<br />
<br />
==== Literature ====<br />
<br />
* D. R. Canchi and A. E. Garcia, "Co-solvent effects on protein stability", Ann. Rev. Phys. Chem. 64. 273 (2013)<br />
* J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951) <br />
* V. Pierce, M. Kang, M. Aburi, S. Weerasinghe and P. E. Smith, "Recent applications of Kirkwood–Buff theory to biological systems", Cell Biochem. Biophys. 50, 1 (2008)<br />
* S. Weerasinghe and P. E. Smith, "A Kirkwood–Buff derived force field for sodium chloride in water", The Journal of Chemical Physics 119, 11342 (2003).<br />
* J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)<br />
* J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)<br />
* T. Kobayashi <i>et al</i>, "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches", Phys.Chem.Chem.Phys. 19, 18924 (2017)<br />
<br />
=== Part 2: Simulations ===<br />
<br />
==== Description ====<br />
<br />
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will perform the simulations of ionic liquids(IL)-water mixtures at different water concentration in combination with the SPC/E water model and OPLSAA force field for EMImBF4. To generate the initial configuration of the simulation boxes, the software package Packmol [http://www.ime.unicamp.br/~martinez/packmol] will be used.<br />
<br />
First the students simulate pure water and pure IL, and analyze the output data. Following properties will be calculated. The Kirkwood-Buff theory will be used to calculate the Kirkwood-Buff integrals. The student perform the different simulation box size to estimate the proper box size for calculating the properties.<br />
* Kirkwood-Buff integrals<br />
* diffusion coefficients<br />
* mass densities<br />
In addition to above, for water<br />
* hydrogen bond life times and number of hydrogen bonds for water-water pairs<br />
* water mean relaxation times<br />
<br />
Next the student perform the IL-water mixtures at different water concentrations. After energy minimization and warm up, run 500 ns simulations with GROMACS for water mole fractions between X_H2O = 0 - 0.30.<br />
<br />
In comparison to pure water/pure IL, the students will analyze several properties stated above and elucidate their water concentration dependent behavior.<br />
Interpret the corresponding results with regard to the findings in Phys.Chem.Chem.Phys. 19, 18924 (2017). <br />
<br />
All the data needed for the exercise can be found in /group/sm/2019/Advsm_part2 <br />
<br />
<!--<br />
==== Force Fields for IL(EMImBF4) ====<br />
<br />
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}<br />
* {{Download| hectoinzwittmp2.gro |gro-File for Hydroxyectoine}}<br />
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}<br />
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}<br />
--><br />
<br />
<!--1. Implement the developed force fields for the osmolytes (urea, ectoine and hydroxyectoine) in combination with the SPC/E water model. After energy minimization and warm up, run 20-30 ns simulations with GROMACS for osmolyte concentrations between c = 0 - 6 M.<br />
<br />
2. Study the following properties for the different osmolytes and concentrations:<br />
* diffusion coefficients<br />
* hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs<br />
* water mean relaxation times<br />
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?<br />
<br />
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.<br />
Use this information to compute the<br />
<br />
* derivatives of the chemical activity<br />
* derivatives of the activity coefficient<br />
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004). <br />
<br />
==== Literature ====<br />
<br />
* D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media", J. Phys. Chem. B 110, 4393 (2006)<br />
* J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem. 25, 1157 (2004)<br />
--><br />
<br />
== Module 3: [[Christian Holm]], [[Rudolph Weeber]] Electrostatics, Lattice Boltzmann, and Electrokinetics==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: June 21 at 11:30 in the ICP meeting room. <br />
<br />
Final meeting and presentation: Friday, July 19 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<br />
<br />
Tutorials: Fridays 11:30-13:00 in the ICP CIP-Pool.<br />
<br />
Deadline for reports: July 17, 2019<br />
<br />
=== Description ===<br />
<br />
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people.<br />
It consists of one lecture on electrostatic algorithms, simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation<br />
and hand in one report. The Module 3 consists of three parts:<br />
<br />
=== Contact ===<br />
If you have any questions regarding the organisation or content of this module please do not hesitate to contact [[Christian Holm]].<br />
For questions regarding the practical part of the module and technical help contact [[Rudolf Weeber]].<br />
<br />
=== Part 1: Electrostatics ===<br />
==== Description ====<br />
This part is about the theory of electrostatic algorithms for molecular dynamics simulations.<br />
It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald<br />
methods. To this end the students should read the referenced literature. [[Christian Holm]] will give an hour long lecture. Afterwards we will discuss the content and try to resolve open questions. The presentation should foster the students understanding of the P3M method as well<br />
as give them an overview of its performance compared to other modern electrostatics methods.<br />
<br />
==== Literature ====<br />
:* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''. <br /> [[Media:longrange.pdf|[PDF]]] (15.4 MB) <br /><br />
<bibentry>deserno98a,arnold13b,arnold05a</bibentry><br />
<br />
=== Part 2: Electro-Osmotic Flow ===<br />
==== Description ====<br />
[[File:Slitpore.png|550px|right|Electroosmotic flow in a slit pore]]<br />
This part is practical. It is concerned with the movement of ions in an charged slit pore.<br />
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]<br />
which is recommended reading. A slit pore consists of two infinite charge walls as shown<br />
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].<br />
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented<br />
by charge Week-Chandler-Anderson spheres.<br />
In addition to the charge on the walls, the ions are also subject to an external electrical field parallel to the walls.<br />
Electrostatics should be handled by the P3M algorithm with ELC.<br />
A set of realistic parameters and an more in detail description of the system can be found in the<br />
thesis.<br />
You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit<br />
pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high<br />
salt limit (Debye-Hueckel-Limit).<br />
Calculate the ion profiles in one or both of these cases and compare the results with the simulation.<br />
<br />
===== Worksheet =====<br />
<br />
{{Download|adv_sm_mod3_EOF.pdf|Detailed worksheet}}<br />
<br />
==== Literature ====<br />
<br />
Some ESPResSo tutorials can be helpful.<br />
* General part and parts 4 & 6 of [https://github.com/espressomd/espresso/blob/python/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann.pdf the Lattice-Boltzmann tutorial] <br />
* Part 7 of the [https://github.com/espressomd/espresso/blob/python/doc/tutorials/02-charged_system/02-charged_system.pdf charged systems tutorial] to see how to setup proper electrostatics in quasi-2D geometry.<br />
<br />
* Georg Rempfer, {{Download|BSc_thesis_rempfer.pdf|"Lattice-Boltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart<br />
<br />
=== Part 3: Electrophoresis of Polyelectrolytes ===<br />
==== Description ====<br />
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions.<br />
Set up a system consisting of a charged polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled with <br />
the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer<br />
for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and<br />
experimental results (see literature).<br />
<br />
<br />
==== Worksheet ====<br />
{{Download|adv_sm_mod3_elpho.pdf|Detailed worksheet}}<br />
<br />
==== Instructions and Literature ====<br />
General part and part 5 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
<bibentry>grass08a, grass09c</bibentry><br />
<br />
=== Report ===<br />
<br />
At the final meeting day of this module, one group will give a presentation about the learned and performed work. In addition, they write a report of about 5 pages containing and discussing the obtained results and hand it in together with the reports of the other modules at the end of the course (see above).<br />
<br />
The final report is due electronically July 17, TBA<br />
<br />
<br />
<br />
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.--></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Advanced_Simulation_Methods_SS_2019&diff=24348Advanced Simulation Methods SS 20192019-06-20T20:34:54Z<p>Holm: /* Contact */</p>
<hr />
<div><br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students should send an email to [[Maria Fyta]] until April 1st 2019.<br />
<br><br />
First meeting: Friday, April 12 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).</b>}}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture and Tutorials (2 SWS in total)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]], JP. Dr. [[Maria Fyta]]<br />
;Course language<br />
:English or German<br />
;Location<br />
:ICP, Allmandring 3; Room: ICP Meeting Room<br />
;Time<br />
:(see below)<br />
The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]] and JP. Dr. [[Maria Fyta]]. It will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules.<br />
The students can work in groups. All groups should write a report of about 10 pages on each module, which they should submit to the responsible person for each module by the deadline set for each module.<br />
<br />
<br />
<br />
== Module 1: [[Maria Fyta]], [[Frank Maier]], Inter-atomic interactions modeled with quantum mechanical simulations ==<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday, April 12 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<br />
<br />
Final meeting and presentation: Friday, May 10 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<br />
<br />
Tutorials: Fridays 11:30-13:00 in the ICP CIP-Pool. The first tutorial will take place on Wed. April 17 at 15:00-16:30.<br />
<br />
Deadline for reports: Mai 08, 2019<br />
<br />
=== Description ===<br />
<br />
This module focuses on the influence of using quantum mechanical simulations. The quantum mechanical schemes which will be applied in this module are based on density functional theory (DFT). This method allows the investigation of the electronic properties of a system. An understanding of the method, an analysis of the results from the simulations is the main goal of this module. The analysis of the simulations should be written up in a report. The talk will be a presentation of a DFT-related journal paper. For this, one of the following papers can be chosen:<br />
<br />
* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J. Klimeš and A. Michaelides, The Journal of Chemical Physics 137, 120901 (2012); doi: 10.1063/1.4754130<br />
* Challenges for Density Functional Theory, A.J. Cohen, P. Mori-Sanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.<br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module please do not hesitate to contact [[Maria Fyta]]. For practical guidance regarding the simulations [[Frank Uhlig]].<br />
<br />
=== Density functional theory and exchange-correlation functionals ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the density functional theory (DFT) method. A scheme which has revolutionarized the way materials and their properties are studied. The students should focus on this method and understand how it works and which its capabilities are. A specific focus would be the different levels of approximations that can be made in this method. For this, the choice of the exchange-correlation functional mapping the interactions of a system is crucial. To this end, the discussion in this module will be directed. The report should contain an introduction to the exchange-correlation functionals in DFT in the context of the simulations and the analysis of the simulations in the tutorial.<br />
<br />
Overall, a variety of DFT exchange correlation functionals have been developed. Some of these often fail in describe complex interactions. For example, only very advanced and quite recent density functionals are able to describe the long-range dispersion interactions [2]. Hence, effective methods based on pair potentials have been developed. These methods can achieve<br />
comparable accuracy to more ab initio methods while coming at a signifcantly lower computational effort [2,3].<br />
<br />
[1] https://dx.doi.org/10.1063/1.4754130<br />
<br />
[2] https://dx.doi.org/10.1103/PhysRevLett.102.073005<br />
<br />
[3] https://dx.doi.org/10.1063/1.3382344<br />
<br />
==== Tutorial ====<br />
<br />
In this exercise you will test different exchange correlation functionals for two systems (silicon and graphite) and analyze the results. All simulations will be performed with the software package [https://departments.icmab.es/leem/siesta/ SIESTA]. A thorough analysis of the stability and energetics of the two system is expected. Tutorial files and brief instructions can be found in ?. The software is installed on our CIP pool machines under /group/allatom/.<br />
<br />
<b> Files </b>{{Download|AdvSimMethoMod1.zip| AdvSimMethoMod1.zip}}<br />
<br />
<br />
Pseudopotential for LMKLL-VDW {{Download|C_VDW.psf| C_VDW.psf}} (rename it to C.psf in order to use it in SIESTA)<br />
<br />
[[Media:Graphene.png]]<br />
<br />
[[Media:Graphene_layers.png]]<br />
<br />
[[Media:Graphite.png]]<br />
<br />
[[Media:Graphite_layers.png]]<br />
<br />
==== Literature ====<br />
<br />
* A bird's-eye view of density-functional theory, Klaus Capelle, arXiv:cond-mat/0211443 (2002).<br />
* Self-Consistent Equations Including Exchange and Correlation Effects, W. Kohn and L.J. Sham, , Phys. Rev. (140), A1133 (1965).<br />
* Understanding and Reducing Errors in Density Functional Calculations, Min-Cheol Kim, Eunji Sim, and Kieron Burke, Phys. Rev. Lett. 111, 073003 (2013).<br />
* Impact of the electron-electron correlation on phonon dispersion: Failure of LDA and GGA DFT functionals in graphene and graphite, Michele Lazzeri, Claudio Attaccalite, Ludger Wirtz, and Francesco Mauri, Phys. Rev. B 78, 081406(R) (2008). <br />
* Electronic properties of nano-graphene sheets calculated using quantum chemical DFT<br />
* Sangam Banerjeea, , Dhananjay Bhattacharyya, Computational Materials Science, 44, 41–45 (2008).<br />
* Dependence of band structures on stacking and field in layered graphene, Masato Aoki, , Hiroshi Amawashi, Solid State Communications 142, 123–127 (2007).<br />
* Graphite Interplanar Bonding: Electronic Delocalization and van der Waals Interaction, J.-C. Charlier, X. Gonze and J.-P. Michenaud, Europhysics Letters), 28 , 403 (1994).<br />
<br />
==== Further reading (if interested) ====<br />
<br />
* An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases, V.R. Cooper, T. Thonhauser, and D.C. Langreth, J. Chem. Phys. 128, 204102 (2008).<br />
* On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit, B. Santra, A. Michaelides, and M. Scheffler, J. Chem. Phys. 127, 184104 (2007).<br />
* On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level, I. Dąbkowska, P. Jurečka, and P. Hobza, J. Chem. Phys. 122, 204322 (2005).<br />
<br />
<b> Lecture Notes </b>{{Download|advSimMeth_module1_XCfunct.pdf| Module 1}}<br />
<br />
== Module 2: [[Maria Fyta]], [[Takeshi Kobayashi]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday May 10 at 13:00 in the ICP meeting room. <br />
<br />
Final meeting and presentation: Friday, June 07 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<br />
<br />
Tutorials: Fridays 11:30-13:00 in the ICP CIP-Pool.<br />
<br />
Deadline for reports: June 05, 2019<br />
<br />
=== Description ===<br />
<br />
This module focuses on atomistic Molecular Dynamics simulations and the study of biological co-solutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological co-solutes, often also called osmolytes are omnipresent in biological cells. A main function of these small-weight organic <br />
molecules is given by the protection of protein structures under harsh environmental conditions (protein stabilizers) or the denaturation of proteins (protein denaturants). The underlying mechanism leading to these effects is still unknown. It has been often discussed that osmolytes have a significant impact on the aqueous solution.<br />
The module consists of model development, simulation, analysis and oral and written presentation part. <br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Takeshi Kobayashi]].<br />
<br />
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the Kirkwood-Buff theory which can be well applied to computer simulations.<br />
The students should study the literature given below and present their findings. The presentation should at a minimum contain an introduction to Kirkwood-Buff theory in the context of the simulations.<br />
<br />
==== Literature ====<br />
<br />
* D. R. Canchi and A. E. Garcia, "Co-solvent effects on protein stability", Ann. Rev. Phys. Chem. 64. 273 (2013)<br />
* J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951) <br />
* V. Pierce, M. Kang, M. Aburi, S. Weerasinghe and P. E. Smith, "Recent applications of Kirkwood–Buff theory to biological systems", Cell Biochem. Biophys. 50, 1 (2008)<br />
* S. Weerasinghe and P. E. Smith, "A Kirkwood–Buff derived force field for sodium chloride in water", The Journal of Chemical Physics 119, 11342 (2003).<br />
* J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)<br />
* J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)<br />
* T. Kobayashi <i>et al</i>, "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches", Phys.Chem.Chem.Phys. 19, 18924 (2017)<br />
<br />
=== Part 2: Simulations ===<br />
<br />
==== Description ====<br />
<br />
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will perform the simulations of ionic liquids(IL)-water mixtures at different water concentration in combination with the SPC/E water model and OPLSAA force field for EMImBF4. To generate the initial configuration of the simulation boxes, the software package Packmol [http://www.ime.unicamp.br/~martinez/packmol] will be used.<br />
<br />
First the students simulate pure water and pure IL, and analyze the output data. Following properties will be calculated. The Kirkwood-Buff theory will be used to calculate the Kirkwood-Buff integrals. The student perform the different simulation box size to estimate the proper box size for calculating the properties.<br />
* Kirkwood-Buff integrals<br />
* diffusion coefficients<br />
* mass densities<br />
In addition to above, for water<br />
* hydrogen bond life times and number of hydrogen bonds for water-water pairs<br />
* water mean relaxation times<br />
<br />
Next the student perform the IL-water mixtures at different water concentrations. After energy minimization and warm up, run 500 ns simulations with GROMACS for water mole fractions between X_H2O = 0 - 0.30.<br />
<br />
In comparison to pure water/pure IL, the students will analyze several properties stated above and elucidate their water concentration dependent behavior.<br />
Interpret the corresponding results with regard to the findings in Phys.Chem.Chem.Phys. 19, 18924 (2017). <br />
<br />
All the data needed for the exercise can be found in /group/sm/2019/Advsm_part2 <br />
<br />
<!--<br />
==== Force Fields for IL(EMImBF4) ====<br />
<br />
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}<br />
* {{Download| hectoinzwittmp2.gro |gro-File for Hydroxyectoine}}<br />
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}<br />
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}<br />
--><br />
<br />
<!--1. Implement the developed force fields for the osmolytes (urea, ectoine and hydroxyectoine) in combination with the SPC/E water model. After energy minimization and warm up, run 20-30 ns simulations with GROMACS for osmolyte concentrations between c = 0 - 6 M.<br />
<br />
2. Study the following properties for the different osmolytes and concentrations:<br />
* diffusion coefficients<br />
* hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs<br />
* water mean relaxation times<br />
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?<br />
<br />
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.<br />
Use this information to compute the<br />
<br />
* derivatives of the chemical activity<br />
* derivatives of the activity coefficient<br />
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004). <br />
<br />
==== Literature ====<br />
<br />
* D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media", J. Phys. Chem. B 110, 4393 (2006)<br />
* J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem. 25, 1157 (2004)<br />
--><br />
<br />
== Module 3: [[Christian Holm]], [[Rudolph Weeber]] Electrostatics, Lattice Boltzmann, and Electrokinetics==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: June 21 at 11:30 in the ICP meeting room. <br />
<br />
Final meeting and presentation: Friday, July 19 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<br />
<br />
Tutorials: Fridays 11:30-13:00 in the ICP CIP-Pool.<br />
<br />
Deadline for reports: July 17, 2019<br />
<br />
=== Description ===<br />
<br />
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people.<br />
It consists of one lecture on electrostatic algorithms, simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation<br />
and hand in one report. The Module 3 consists of three parts:<br />
<br />
=== Contact ===<br />
If you have any questions regarding the organisation or content of this module please do not hesitate to contact [[Christian Holm]].<br />
For questions regarding the practical part of the module and technical help contact [[Rudolf Weeber]].<br />
<br />
=== Part 1: Electrostatics ===<br />
==== Description ====<br />
This part is about the theory of electrostatic algorithms for molecular dynamics simulations.<br />
It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald<br />
methods. To this end the students should read the referenced literature. [[Christian Holm]] will give an hour long lecture. Afterwards we will discuss the content and try to resolve open questions. The presentation should foster the students understanding of the P3M method as well<br />
as give them an overview of its performance compared to other modern electrostatics methods.<br />
<br />
==== Literature ====<br />
:* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''. <br /> [[Media:longrange.pdf|[PDF]]] (15.4 MB) <br /><br />
<bibentry>deserno98a,arnold13b,arnold05a</bibentry><br />
<br />
=== Part 2: Electro-Osmotic Flow ===<br />
==== Description ====<br />
[[File:Slitpore.png|550px|right|Electroosmotic flow in a slit pore]]<br />
This part is practical. It is concerned with the movement of ions in an charged slit pore.<br />
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]<br />
which is recommended reading. A slit pore consists of two infinite charge walls as shown<br />
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].<br />
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented<br />
by charge Week-Chandler-Anderson spheres.<br />
In addition to the charge on the walls, the ions are also subject to an external electrical field parallel to the walls.<br />
Electrostatics should be handled by the P3M algorithm with ELC.<br />
A set of realistic parameters and an more in detail description of the system can be found in the<br />
thesis.<br />
You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit<br />
pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high<br />
salt limit (Debye-Hueckel-Limit).<br />
Calculate the ion profiles in one or both of these cases and compare the results with the simulation.<br />
<br />
===== Worksheet =====<br />
<br />
{{Download|adv_sm_mod3_EOF.pdf|Detailed worksheet}}<br />
<br />
==== Literature ====<br />
<br />
Some ESPResSo tutorials can be helpful.<br />
* General part and parts 4 & 6 of [https://github.com/espressomd/espresso/blob/python/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann.pdf the Lattice-Boltzmann tutorial] <br />
* Part 7 of the [https://github.com/espressomd/espresso/blob/python/doc/tutorials/02-charged_system/02-charged_system.pdf charged systems tutorial] to see how to setup proper electrostatics in quasi-2D geometry.<br />
<br />
* Georg Rempfer, {{Download|BSc_thesis_rempfer.pdf|"Lattice-Boltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart<br />
<br />
=== Part 3: Electrophoresis of Polyelectrolytes ===<br />
==== Description ====<br />
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions.<br />
Set up a system consisting of a charged polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled with <br />
the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer<br />
for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and<br />
experimental results (see literature).<br />
<br />
<br />
==== Worksheet ====<br />
{{Download|adv_sm_mod3_elpho.pdf|Detailed worksheet}}<br />
<br />
==== Instructions and Literature ====<br />
General part and part 5 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
<bibentry>grass08a, grass09c</bibentry><br />
<br />
=== Report ===<br />
<br />
At the final meeting day of this module, one group will give a presentation about the learned and performed work. In addition, they write a report of about 5 pages containing and discussing the obtained results and hand it in together with the reports of the other modules at the end of the course (see above).<br />
<br />
The final report is due electronically Friday night, TBA<br />
<br />
<br />
<br />
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.--></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Christian_Holm&diff=24104Christian Holm2019-04-16T12:55:22Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|name=Holm, Christian<br />
|title=Prof. Dr.<br />
|status=Director<br />
|phone=63701<br />
|fax=53701<br />
|room=1.046<br />
|email=holm<br />
|image=Christian_Holm.jpg<br />
|researcherid=C-2134-2009<br />
|category=holm<br />
|topical=electrokinetics<br />
|topical2=atomistics<br />
|topical3=gel<br />
|topical4=nanopore<br />
|topical5=ionic_liquids<br />
|ordering=1<br />
}}<br />
<br />
==Research==<br />
<br />
My scientific interests are especially the study of complex charged and magnetic soft matter by means of computer simulations, and the development of simple theoretical models to describe them. More precisely I am currently working on the solution properties and association behavior of flexible and semi-flexible polyelectrolytes in various solvents and under various salt concentrations and salt types. In addition I am interested in the effective pair interactions of charged colloidal particles and their phase behavior. This includes simple DNA models, and DNA protein interactions, as well as developing coarse grained models for DNA-Histone complexes. We also investigate in depth polyelectrolyte hydrogels and magnetically interacting ferrogels, as well as pure ferrofluids, where special attention is given to the structure of the solution and the magnetic response functions. Another interest is the applicability of mean-field models for the description of models with long range interactions, and possible improvements beyond the mean-field approach. This include local density functional methods based on the Poisson-Boltzmann functional, as well as strong coupling theories such as Wigner-crystal methods. In addition I am interested in the development of fast methods for the computation of long range interactions. These include pure Coulomb as well as dipolar interactions in various geometries (3D-1D), and under various boundary conditions. And least but not last, we are interested in developing fast methods to deal with fluid-structure couplings using various coupling schemes of particles to a lattice-boltzmann fluid. These can be charged fluids, as well as fluids that undergo reactions at boundaries, such as needed for active Janus-Colloids,or for catalytic particles. We also are interested to apply machine learning algorithms for the development of force-fields with almost DFT precision. <br />
<br />
Some of our research is part of collaborative research centres such as:<br />
<br />
==Member of collaborative research centers== <br />
'''SFB 716''' [http://www.sfb716.uni-stuttgart.de sfb716.uni-stuttgart.de] <br />
<br />
'''SFB 1313''' [http://www.sfb1313.uni-stuttgart.de/ sfb1313.uni-stuttgart.de] <br />
<br />
'''SFB 1333''' [http://www.crc1333.uni-stuttgart.de/ crc1333.uni-stuttgart.de] <br />
<br />
'''SimTech''' [http://www.simtech.uni-stuttgart.de SimTech Cluster of Excellence]<br />
<br />
==Publications==<br />
<span id="badgeCont471"><script type="text/javascript" src="https://publons.com/mashlets?el=badgeCont471&rid=C-2134-2009"></script></span><br />
<br />
<!--<br />
Publications only on Publications-Site!! the <pubentries> statement import the publications vrom Publications-Site<br />
--><br />
<br />
<!--<br />
Falls das Badge hier hin soll auskommentierung und den Text hier wegmachen<br />
<div style="float:right;"><researcherID>C-2134-2009</researcherID></div><br />
--><br />
<br />
===2019===<br />
<bibentry pdflink="yes"><br />
weik19b,<br />
holm19a,<br />
weik19a,<br />
landsgesell19a,<br />
sean19a<br />
</bibentry><br />
<br />
===2018===<br />
<bibentry pdflink="yes"><br />
krishnamoorthy18c,<br />
michalowsky18a,<br />
krishnamoorthy18b,<br />
krishnamoorthy18a,<br />
smiatek18a,<br />
weeber18b,<br />
uhlig18a,<br />
weyman18a,<br />
weeber18a<br />
</bibentry><br />
<br />
===2017===<br />
<bibentry pdflink="yes"><br />
sean17a<br />
uhlig17a,<br />
roy17b,<br />
roy17a,<br />
szuttor17a,<br />
richter17a,<br />
bauer17a,<br />
landsgesell17b,<br />
landsgesell17a,<br />
chung17a,<br />
rau17a,<br />
rud17a,<br />
michalowsky17a,<br />
niu17a,<br />
brown17a,<br />
rempfer17a<br />
landsgesell17b<br />
landsgesell17a<br />
</bibentry><br />
<br />
===2016===<br />
<bibentry pdflink="yes"><br />
micciulla16a,<br />
lesch16a,<br />
huang16a,<br />
kreissl16a,<br />
sanchez16a,<br />
degraaf16a,<br />
degraaf16b,<br />
rempfer16a,<br />
rempfer16b,<br />
bauer16a,<br />
breitsprecher16a,<br />
bordin16a,<br />
ilse16a,<br />
burt16a,<br />
krishnamoorthy16a,<br />
weik16a,<br />
kuron16a<br />
</bibentry><br />
<br />
===2015===<br />
<bibentry pdflink="yes"><br />
bauer15a,<br />
breitsprecher15a,<br />
fischer15a,<br />
degraaf15b,<br />
degraaf15c,<br />
fahrenberger15b,<br />
fahrenberger15c,<br />
holm15a,<br />
kosovan15a,<br />
lesch15a,<br />
lesch15b,<br />
pessot15a,<br />
raafatnia15a,<br />
ryzhkov15a,<br />
vogele15a,<br />
vogele15b,<br />
weeber15a,<br />
weeber15c<br />
</bibentry><br />
<br />
===2014===<br />
<bibentry pdflink="yes"><br />
breitsprecher14a,<br />
breitsprecher14b,<br />
dommert14a,<br />
ertl14a,<br />
fahrenberger14a,<br />
fahrenberger14b,<br />
hickey14a,<br />
kesselheim14a,<br />
krishnamoorthy14a,<br />
micciulla14a,<br />
raafatnia14a,<br />
raafatnia14b,<br />
sega14a,<br />
smiatek14a,<br />
smiatek14d,<br />
vagias14a<br />
</bibentry><br />
<br />
===2013===<br />
<bibentry pdflink="yes"><br />
arnold13a,<br />
arnold13b,<br />
arnold13c,<br />
cerda13a,<br />
chakrabarti13a,<br />
dommert12b,<br />
dommert13a,<br />
hickey13a,<br />
hoepfner13b,<br />
klinkigt13a,<br />
kosovan13a,<br />
samin13a,<br />
sanchez13b,<br />
sega13a,<br />
semenov13a,<br />
vagias13a,<br />
vagias13b,<br />
weeber13a<br />
</bibentry><br />
<br />
===2012===<br />
<bibentry pdflink="yes"><br />
kesselheim12a,<br />
bachthaler12a,<br />
dellesite12a,<br />
cerda12a,<br />
weeber12a,<br />
dommert12a,<br />
wendler12a,<br />
ballenegger12a<br />
</bibentry><br />
<br />
===2011===<br />
<bibentry pdflink="yes"><br />
qiao11b,<br />
qiao11a,<br />
gribova11a,<br />
mann11a,<br />
hickey11a,<br />
wendler11b,<br />
kantorovich11b,<br />
cerda11c,<br />
cerda11b,<br />
klinkigt11b,<br />
tabatabaei11a,<br />
sanchez11a,<br />
pyanzina11a,<br />
prokopyeva11a,<br />
kesselheim11a,<br />
kantorovich11a,<br />
cerda11a,<br />
ballenegger11a,<br />
luigi11a<br />
</bibentry><br />
<br />
===2010===<br />
<bibentry pdflink="yes"><br />
neelov10a,<br />
grass10a,<br />
krekeler10a,<br />
tyagi10a,<br />
schmidt10a,<br />
dommert10a,<br />
wang10a,<br />
sayar10a,<br />
qiao10a,<br />
hickey10a,<br />
cerda10a<br />
</bibentry><br />
<br />
===2009===<br />
<bibentry pdflink="yes"><br />
dommert09a,<br />
suezen09a,<br />
pyanzina09a,<br />
prokopieva09a,<br />
smiatek09a,<br />
claudio09a,<br />
pyanzina09a,<br />
cerda09b,<br />
cerda09c,<br />
slater09a,<br />
grass09a,<br />
grass09b<br />
</bibentry><br />
<br />
===2008===<br />
<bibentry pdflink="yes">cerda08d,cerda08e,cerda08a,grass08a,qiao08a,kantorovich08a,lenz08a,ballenegger08a,tyagi08a</bibentry><br />
<br />
===2007===<br />
<bibentry pdflink="yes">tyagi07a,ivanov07a,lobaskin07a,antypov07a, hess07a, sayar07a</bibentry><br />
<br />
===2006===<br />
<bibentry pdflink="yes">antypov07b,holm06a, holm06b, antypov06a, arnold06a, hess06a, hess06b, limbach06a, mann06a, muehlbacher06a, muehlbacher06b, stukan06a</bibentry><br />
<br />
===2005===<br />
<bibentry pdflink="yes">antypov05a, arnold05a, arnold05b, holm05a, holm05b, huang05a, huang05b, limbach05a, mann05a</bibentry><br />
<br />
===2004===<br />
<bibentry pdflink="yes">barbosa04a, espresso03a, holm04a, holm04b, holm04c, huang04a, ivanov04a, limbach04a, limbach04b, lobaskin04b, mann04a, messina04a, naji04b</bibentry><br />
<br />
===2003===<br />
<bibentry pdflink="yes">deserno02b, holm03a, jimenez03a, limbach03a, messina03a, wang03a, wang03b, wang03c</bibentry><br />
<br />
===2002===<br />
<bibentry pdflink="yes">arnold02a, arnold02b, arnold02c, arnold02d, dejoannis02a, deserno02a, holm02a, limbach02a, limbach02c, messina02a, messina02c, messina02d, messina02e, wang02a</bibentry><br />
<br />
===2001===<br />
<bibentry pdflink="yes">deserno00c, deserno01a, deserno01b, deserno01c, holm01b, holm01c, limbach01a, messina01a, messina01b, wang01a</bibentry><br />
<br />
===2000===<br />
<bibentry pdflink="yes">barbosa00a, deserno00a, deserno99b, messina00a, messina00b</bibentry><br />
<br />
===1999===<br />
<bibentry pdflink="yes">holm99a, holm99b, bittner99a, bittner99b, micka99a</bibentry><br />
<br />
===1998 and before===<br />
<bibentry pdflink="yes"><br />
holm98a, holm98b, bittner98a, bittner98b, deserno98a, deserno98b,<br />
holm97a, holm97c, holm97d, holm97e,<br />
holm96a, holm96b, holm96c, holm95c,<br />
holm95a, holm95b, <br />
holm94a, holm94b, holm94c, holm93d,<br />
holm93a, holm93b, holm93c, adler93a,<br />
holm91a, holm91b,<br />
holm90a, holm90b, holm90c, <br />
holm89a, finkelstein89a,<br />
holm88a, holm88b,<br />
holm87a, finkelstein87a,<br />
holm86a, eidson86a, finkelstein86a,<br />
holm85a</bibentry></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Christian_Holm&diff=24103Christian Holm2019-04-16T12:54:22Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|name=Holm, Christian<br />
|title=Prof. Dr.<br />
|status=Director<br />
|phone=63701<br />
|fax=53701<br />
|room=1.046<br />
|email=holm<br />
|image=Christian_Holm.jpg<br />
|researcherid=C-2134-2009<br />
|category=holm<br />
|topical=electrokinetics<br />
|topical2=atomistics<br />
|topical3=gel<br />
|topical4=nanopore<br />
|topical5=ionic_liquids<br />
|ordering=1<br />
}}<br />
<br />
==Research==<br />
<br />
My scientific interests are especially the study of complex charged and magnetic soft matter by means of computer simulations, and the development of simple theoretical models to describe them. More precisely I am currently working on the solution properties and association behavior of flexible and semi-flexible polyelectrolytes in various solvents and under various salt concentrations and salt types. In addition I am interested in the effective pair interactions of charged colloidal particles and their phase behavior. This includes simple DNA models, and DNA protein interactions, as well as developing coarse grained models for DNA-Histone complexes. We also investigate in depth polyelectrolyte hydrogels and magnetically interacting ferrogels, as well as pure ferrofluids, where special attention is given to the structure of the solution and the magnetic response functions. Another interest is the applicability of mean-field models for the description of models with long range interactions, and possible improvements beyond the mean-field approach. This include local density functional methods based on the Poisson-Boltzmann functional, as well as strong coupling theories such as Wigner-crystal methods. In addition I am interested in the development of fast methods for the computation of long range interactions. These include pure Coulomb as well as dipolar interactions in various geometries (3D-1D), and under various boundary conditions. And least but not last, we are interested in developing fast methods to deal with fluid-structure couplings using various coupling schemes of particles to a lattice-boltzmann fluid. These can be charged fluids, as well as fluids that undergo reactions at boundaries, such as needed for active Janus-Colloids,or for catalytic particles. We also are interested to apply machine learning algorithms for the development of force-fields with almost DFT precision. <br />
<br />
Some of our research is part of collaborative research centres such as:<br />
<br />
==Member of collaborative research centers== <br />
'''SFB 716''' [http://www.sfb716.uni-stuttgart.de sfb716.uni-stuttgart.de] <br />
<br />
'''SFB 1313''' [http://www.sfb1313.uni-stuttgart.de/ sfb1313.uni-stuttgart.de] <br />
<br />
'''SFB 1333''' [http://www.crc1333.uni-stuttgart.de/ crc1333.uni-stuttgart.de] <br />
<br />
'''SimTech''' [http://www.simtech.uni-stuttgart.de SimTech Cluster of Excellence]<br />
<br />
==Publications==<br />
<!--<br />
Publications only on Publications-Site!! the <pubentries> statement import the publications vrom Publications-Site<br />
--><br />
<br />
<!--<br />
Falls das Badge hier hin soll auskommentierung und den Text hier wegmachen<br />
<div style="float:right;"><researcherID>C-2134-2009</researcherID></div><br />
--><br />
<br />
===2019===<br />
<bibentry pdflink="yes"><br />
weik19b,<br />
holm19a,<br />
weik19a,<br />
landsgesell19a,<br />
sean19a<br />
</bibentry><br />
<br />
===2018===<br />
<bibentry pdflink="yes"><br />
krishnamoorthy18c,<br />
michalowsky18a,<br />
krishnamoorthy18b,<br />
krishnamoorthy18a,<br />
smiatek18a,<br />
weeber18b,<br />
uhlig18a,<br />
weyman18a,<br />
weeber18a<br />
</bibentry><br />
<br />
===2017===<br />
<bibentry pdflink="yes"><br />
sean17a<br />
uhlig17a,<br />
roy17b,<br />
roy17a,<br />
szuttor17a,<br />
richter17a,<br />
bauer17a,<br />
landsgesell17b,<br />
landsgesell17a,<br />
chung17a,<br />
rau17a,<br />
rud17a,<br />
michalowsky17a,<br />
niu17a,<br />
brown17a,<br />
rempfer17a<br />
landsgesell17b<br />
landsgesell17a<br />
</bibentry><br />
<br />
===2016===<br />
<bibentry pdflink="yes"><br />
micciulla16a,<br />
lesch16a,<br />
huang16a,<br />
kreissl16a,<br />
sanchez16a,<br />
degraaf16a,<br />
degraaf16b,<br />
rempfer16a,<br />
rempfer16b,<br />
bauer16a,<br />
breitsprecher16a,<br />
bordin16a,<br />
ilse16a,<br />
burt16a,<br />
krishnamoorthy16a,<br />
weik16a,<br />
kuron16a<br />
</bibentry><br />
<br />
===2015===<br />
<bibentry pdflink="yes"><br />
bauer15a,<br />
breitsprecher15a,<br />
fischer15a,<br />
degraaf15b,<br />
degraaf15c,<br />
fahrenberger15b,<br />
fahrenberger15c,<br />
holm15a,<br />
kosovan15a,<br />
lesch15a,<br />
lesch15b,<br />
pessot15a,<br />
raafatnia15a,<br />
ryzhkov15a,<br />
vogele15a,<br />
vogele15b,<br />
weeber15a,<br />
weeber15c<br />
</bibentry><br />
<br />
===2014===<br />
<bibentry pdflink="yes"><br />
breitsprecher14a,<br />
breitsprecher14b,<br />
dommert14a,<br />
ertl14a,<br />
fahrenberger14a,<br />
fahrenberger14b,<br />
hickey14a,<br />
kesselheim14a,<br />
krishnamoorthy14a,<br />
micciulla14a,<br />
raafatnia14a,<br />
raafatnia14b,<br />
sega14a,<br />
smiatek14a,<br />
smiatek14d,<br />
vagias14a<br />
</bibentry><br />
<br />
===2013===<br />
<bibentry pdflink="yes"><br />
arnold13a,<br />
arnold13b,<br />
arnold13c,<br />
cerda13a,<br />
chakrabarti13a,<br />
dommert12b,<br />
dommert13a,<br />
hickey13a,<br />
hoepfner13b,<br />
klinkigt13a,<br />
kosovan13a,<br />
samin13a,<br />
sanchez13b,<br />
sega13a,<br />
semenov13a,<br />
vagias13a,<br />
vagias13b,<br />
weeber13a<br />
</bibentry><br />
<br />
===2012===<br />
<bibentry pdflink="yes"><br />
kesselheim12a,<br />
bachthaler12a,<br />
dellesite12a,<br />
cerda12a,<br />
weeber12a,<br />
dommert12a,<br />
wendler12a,<br />
ballenegger12a<br />
</bibentry><br />
<br />
===2011===<br />
<bibentry pdflink="yes"><br />
qiao11b,<br />
qiao11a,<br />
gribova11a,<br />
mann11a,<br />
hickey11a,<br />
wendler11b,<br />
kantorovich11b,<br />
cerda11c,<br />
cerda11b,<br />
klinkigt11b,<br />
tabatabaei11a,<br />
sanchez11a,<br />
pyanzina11a,<br />
prokopyeva11a,<br />
kesselheim11a,<br />
kantorovich11a,<br />
cerda11a,<br />
ballenegger11a,<br />
luigi11a<br />
</bibentry><br />
<br />
===2010===<br />
<bibentry pdflink="yes"><br />
neelov10a,<br />
grass10a,<br />
krekeler10a,<br />
tyagi10a,<br />
schmidt10a,<br />
dommert10a,<br />
wang10a,<br />
sayar10a,<br />
qiao10a,<br />
hickey10a,<br />
cerda10a<br />
</bibentry><br />
<br />
===2009===<br />
<bibentry pdflink="yes"><br />
dommert09a,<br />
suezen09a,<br />
pyanzina09a,<br />
prokopieva09a,<br />
smiatek09a,<br />
claudio09a,<br />
pyanzina09a,<br />
cerda09b,<br />
cerda09c,<br />
slater09a,<br />
grass09a,<br />
grass09b<br />
</bibentry><br />
<br />
===2008===<br />
<bibentry pdflink="yes">cerda08d,cerda08e,cerda08a,grass08a,qiao08a,kantorovich08a,lenz08a,ballenegger08a,tyagi08a</bibentry><br />
<br />
===2007===<br />
<bibentry pdflink="yes">tyagi07a,ivanov07a,lobaskin07a,antypov07a, hess07a, sayar07a</bibentry><br />
<br />
===2006===<br />
<bibentry pdflink="yes">antypov07b,holm06a, holm06b, antypov06a, arnold06a, hess06a, hess06b, limbach06a, mann06a, muehlbacher06a, muehlbacher06b, stukan06a</bibentry><br />
<br />
===2005===<br />
<bibentry pdflink="yes">antypov05a, arnold05a, arnold05b, holm05a, holm05b, huang05a, huang05b, limbach05a, mann05a</bibentry><br />
<br />
===2004===<br />
<bibentry pdflink="yes">barbosa04a, espresso03a, holm04a, holm04b, holm04c, huang04a, ivanov04a, limbach04a, limbach04b, lobaskin04b, mann04a, messina04a, naji04b</bibentry><br />
<br />
===2003===<br />
<bibentry pdflink="yes">deserno02b, holm03a, jimenez03a, limbach03a, messina03a, wang03a, wang03b, wang03c</bibentry><br />
<br />
===2002===<br />
<bibentry pdflink="yes">arnold02a, arnold02b, arnold02c, arnold02d, dejoannis02a, deserno02a, holm02a, limbach02a, limbach02c, messina02a, messina02c, messina02d, messina02e, wang02a</bibentry><br />
<br />
===2001===<br />
<bibentry pdflink="yes">deserno00c, deserno01a, deserno01b, deserno01c, holm01b, holm01c, limbach01a, messina01a, messina01b, wang01a</bibentry><br />
<br />
===2000===<br />
<bibentry pdflink="yes">barbosa00a, deserno00a, deserno99b, messina00a, messina00b</bibentry><br />
<br />
===1999===<br />
<bibentry pdflink="yes">holm99a, holm99b, bittner99a, bittner99b, micka99a</bibentry><br />
<br />
===1998 and before===<br />
<bibentry pdflink="yes"><br />
holm98a, holm98b, bittner98a, bittner98b, deserno98a, deserno98b,<br />
holm97a, holm97c, holm97d, holm97e,<br />
holm96a, holm96b, holm96c, holm95c,<br />
holm95a, holm95b, <br />
holm94a, holm94b, holm94c, holm93d,<br />
holm93a, holm93b, holm93c, adler93a,<br />
holm91a, holm91b,<br />
holm90a, holm90b, holm90c, <br />
holm89a, finkelstein89a,<br />
holm88a, holm88b,<br />
holm87a, finkelstein87a,<br />
holm86a, eidson86a, finkelstein86a,<br />
holm85a</bibentry></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Christian_Holm&diff=24102Christian Holm2019-04-16T12:53:50Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|name=Holm, Christian<br />
|title=Prof. Dr.<br />
|status=Director<br />
|phone=63701<br />
|fax=53701<br />
|room=1.046<br />
|email=holm<br />
|image=Christian_Holm.jpg<br />
|researcherid=C-2134-2009<br />
|category=holm<br />
|topical=electrokinetics<br />
|topical2=atomistics<br />
|topical3=gel<br />
|topical4=nanopore<br />
|topical5=ionic_liquids<br />
|ordering=1<br />
}}<br />
<br />
==Research==<br />
<br />
My scientific interests are especially the study of complex charged and magnetic soft matter by means of computer simulations, and the development of simple theoretical models to describe them. More precisely I am currently working on the solution properties and association behavior of flexible and semi-flexible polyelectrolytes in various solvents and under various salt concentrations and salt types. In addition I am interested in the effective pair interactions of charged colloidal particles and their phase behavior. This includes simple DNA models, and DNA protein interactions, as well as developing coarse grained models for DNA-Histone complexes. We also investigate in depth polyelectrolyte hydrogels and magnetically interacting ferrogels, as well as pure ferrofluids, where special attention is given to the structure of the solution and the magnetic response functions. Another interest is the applicability of mean-field models for the description of models with long range interactions, and possible improvements beyond the mean-field approach. This include local density functional methods based on the Poisson-Boltzmann functional, as well as strong coupling theories such as Wigner-crystal methods. In addition I am interested in the development of fast methods for the computation of long range interactions. These include pure Coulomb as well as dipolar interactions in various geometries (3D-1D), and under various boundary conditions. And least but not last, we are interested in developing fast methods to deal with fluid-structure couplings using various coupling schemes of particles to a lattice-boltzmann fluid. These can be charged fluids, as well as fluids that undergo reactions at boundaries, such as needed for active Janus-Colloids,or for catalytic particles. We also are interested to apply machine learning algorithms for the development of force-fields with almost DFT precision. <br />
<br />
Some of our research is part of collaborative research centres such as:<br />
<br />
==Member of collaborative research centers== <br />
'''SFB 716''' [http://www.sfb716.uni-stuttgart.de sfb716.uni-stuttgart.de] <br />
<br />
'''SFB 1313''' [http://www.sfb1313.uni-stuttgart.de/ sfb1313.uni-stuttgart.de] <br />
<br />
'''SFB 1333''' [http://www.crc1333.uni-stuttgart.de/ crc1333.uni-stuttgart.de] <br />
<br />
'''SimTech''' [http://www.simtech.uni-stuttgart.de SimTech Cluster of Excellence]<br />
<br />
==Publications==<br />
<br />
<span id="badgeCont471"><script type="text/javascript" src="https://publons.com/mashlets?el=badgeCont471&rid=C-2134-2009"></script></span><br />
<br />
<!--<br />
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--><br />
<br />
<br />
<!--<br />
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<div style="float:right;"><researcherID>C-2134-2009</researcherID></div><br />
--><br />
<br />
===2019===<br />
<bibentry pdflink="yes"><br />
weik19b,<br />
holm19a,<br />
weik19a,<br />
landsgesell19a,<br />
sean19a<br />
</bibentry><br />
<br />
===2018===<br />
<bibentry pdflink="yes"><br />
krishnamoorthy18c,<br />
michalowsky18a,<br />
krishnamoorthy18b,<br />
krishnamoorthy18a,<br />
smiatek18a,<br />
weeber18b,<br />
uhlig18a,<br />
weyman18a,<br />
weeber18a<br />
</bibentry><br />
<br />
===2017===<br />
<bibentry pdflink="yes"><br />
sean17a<br />
uhlig17a,<br />
roy17b,<br />
roy17a,<br />
szuttor17a,<br />
richter17a,<br />
bauer17a,<br />
landsgesell17b,<br />
landsgesell17a,<br />
chung17a,<br />
rau17a,<br />
rud17a,<br />
michalowsky17a,<br />
niu17a,<br />
brown17a,<br />
rempfer17a<br />
landsgesell17b<br />
landsgesell17a<br />
</bibentry><br />
<br />
===2016===<br />
<bibentry pdflink="yes"><br />
micciulla16a,<br />
lesch16a,<br />
huang16a,<br />
kreissl16a,<br />
sanchez16a,<br />
degraaf16a,<br />
degraaf16b,<br />
rempfer16a,<br />
rempfer16b,<br />
bauer16a,<br />
breitsprecher16a,<br />
bordin16a,<br />
ilse16a,<br />
burt16a,<br />
krishnamoorthy16a,<br />
weik16a,<br />
kuron16a<br />
</bibentry><br />
<br />
===2015===<br />
<bibentry pdflink="yes"><br />
bauer15a,<br />
breitsprecher15a,<br />
fischer15a,<br />
degraaf15b,<br />
degraaf15c,<br />
fahrenberger15b,<br />
fahrenberger15c,<br />
holm15a,<br />
kosovan15a,<br />
lesch15a,<br />
lesch15b,<br />
pessot15a,<br />
raafatnia15a,<br />
ryzhkov15a,<br />
vogele15a,<br />
vogele15b,<br />
weeber15a,<br />
weeber15c<br />
</bibentry><br />
<br />
===2014===<br />
<bibentry pdflink="yes"><br />
breitsprecher14a,<br />
breitsprecher14b,<br />
dommert14a,<br />
ertl14a,<br />
fahrenberger14a,<br />
fahrenberger14b,<br />
hickey14a,<br />
kesselheim14a,<br />
krishnamoorthy14a,<br />
micciulla14a,<br />
raafatnia14a,<br />
raafatnia14b,<br />
sega14a,<br />
smiatek14a,<br />
smiatek14d,<br />
vagias14a<br />
</bibentry><br />
<br />
===2013===<br />
<bibentry pdflink="yes"><br />
arnold13a,<br />
arnold13b,<br />
arnold13c,<br />
cerda13a,<br />
chakrabarti13a,<br />
dommert12b,<br />
dommert13a,<br />
hickey13a,<br />
hoepfner13b,<br />
klinkigt13a,<br />
kosovan13a,<br />
samin13a,<br />
sanchez13b,<br />
sega13a,<br />
semenov13a,<br />
vagias13a,<br />
vagias13b,<br />
weeber13a<br />
</bibentry><br />
<br />
===2012===<br />
<bibentry pdflink="yes"><br />
kesselheim12a,<br />
bachthaler12a,<br />
dellesite12a,<br />
cerda12a,<br />
weeber12a,<br />
dommert12a,<br />
wendler12a,<br />
ballenegger12a<br />
</bibentry><br />
<br />
===2011===<br />
<bibentry pdflink="yes"><br />
qiao11b,<br />
qiao11a,<br />
gribova11a,<br />
mann11a,<br />
hickey11a,<br />
wendler11b,<br />
kantorovich11b,<br />
cerda11c,<br />
cerda11b,<br />
klinkigt11b,<br />
tabatabaei11a,<br />
sanchez11a,<br />
pyanzina11a,<br />
prokopyeva11a,<br />
kesselheim11a,<br />
kantorovich11a,<br />
cerda11a,<br />
ballenegger11a,<br />
luigi11a<br />
</bibentry><br />
<br />
===2010===<br />
<bibentry pdflink="yes"><br />
neelov10a,<br />
grass10a,<br />
krekeler10a,<br />
tyagi10a,<br />
schmidt10a,<br />
dommert10a,<br />
wang10a,<br />
sayar10a,<br />
qiao10a,<br />
hickey10a,<br />
cerda10a<br />
</bibentry><br />
<br />
===2009===<br />
<bibentry pdflink="yes"><br />
dommert09a,<br />
suezen09a,<br />
pyanzina09a,<br />
prokopieva09a,<br />
smiatek09a,<br />
claudio09a,<br />
pyanzina09a,<br />
cerda09b,<br />
cerda09c,<br />
slater09a,<br />
grass09a,<br />
grass09b<br />
</bibentry><br />
<br />
===2008===<br />
<bibentry pdflink="yes">cerda08d,cerda08e,cerda08a,grass08a,qiao08a,kantorovich08a,lenz08a,ballenegger08a,tyagi08a</bibentry><br />
<br />
===2007===<br />
<bibentry pdflink="yes">tyagi07a,ivanov07a,lobaskin07a,antypov07a, hess07a, sayar07a</bibentry><br />
<br />
===2006===<br />
<bibentry pdflink="yes">antypov07b,holm06a, holm06b, antypov06a, arnold06a, hess06a, hess06b, limbach06a, mann06a, muehlbacher06a, muehlbacher06b, stukan06a</bibentry><br />
<br />
===2005===<br />
<bibentry pdflink="yes">antypov05a, arnold05a, arnold05b, holm05a, holm05b, huang05a, huang05b, limbach05a, mann05a</bibentry><br />
<br />
===2004===<br />
<bibentry pdflink="yes">barbosa04a, espresso03a, holm04a, holm04b, holm04c, huang04a, ivanov04a, limbach04a, limbach04b, lobaskin04b, mann04a, messina04a, naji04b</bibentry><br />
<br />
===2003===<br />
<bibentry pdflink="yes">deserno02b, holm03a, jimenez03a, limbach03a, messina03a, wang03a, wang03b, wang03c</bibentry><br />
<br />
===2002===<br />
<bibentry pdflink="yes">arnold02a, arnold02b, arnold02c, arnold02d, dejoannis02a, deserno02a, holm02a, limbach02a, limbach02c, messina02a, messina02c, messina02d, messina02e, wang02a</bibentry><br />
<br />
===2001===<br />
<bibentry pdflink="yes">deserno00c, deserno01a, deserno01b, deserno01c, holm01b, holm01c, limbach01a, messina01a, messina01b, wang01a</bibentry><br />
<br />
===2000===<br />
<bibentry pdflink="yes">barbosa00a, deserno00a, deserno99b, messina00a, messina00b</bibentry><br />
<br />
===1999===<br />
<bibentry pdflink="yes">holm99a, holm99b, bittner99a, bittner99b, micka99a</bibentry><br />
<br />
===1998 and before===<br />
<bibentry pdflink="yes"><br />
holm98a, holm98b, bittner98a, bittner98b, deserno98a, deserno98b,<br />
holm97a, holm97c, holm97d, holm97e,<br />
holm96a, holm96b, holm96c, holm95c,<br />
holm95a, holm95b, <br />
holm94a, holm94b, holm94c, holm93d,<br />
holm93a, holm93b, holm93c, adler93a,<br />
holm91a, holm91b,<br />
holm90a, holm90b, holm90c, <br />
holm89a, finkelstein89a,<br />
holm88a, holm88b,<br />
holm87a, finkelstein87a,<br />
holm86a, eidson86a, finkelstein86a,<br />
holm85a</bibentry></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Teaching&diff=23959Teaching2019-02-08T11:35:03Z<p>Holm: /* SS 2019 */</p>
<hr />
<div>Hier findet sich ein [[/Overview|Überblick über die Lehre am ICP]] {{german}}.<br />
<br />
== SS 2019 ==<br />
<br />
* [[Hauptseminar Soft Matter SS 2019|Hauptseminar "Theory and Simulation of Soft and Active Matter"]] <br/>Prof. Dr. Siegfried Dietrich (MPI-IS/ITP4), Prof. Dr. [[Christian Holm]] (ICP)<br />
<br />
* [[VL Advanced Simulation Methods SS 2019|VL "Advanced Simulation Methods"]] <br/>Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]] (ICP)<br />
<br />
== WS 2018/2019 ==<br />
<br />
* [//www.cecam.org/workshop-1605.html ESPResSo Summer School] <br />Prof. Dr. [[Christian Holm]] <br /> 2018-10-08 to 2018-10-12, daily 9:00&ndash;18:00 (ICP CIP-Pool 01.033/ ICP Seminar Room 1.079, Allmandring 3) '''Students who would like to attend this compact course should register under the Cecam Website [//www.cecam.org/workshop-1605.html ESPResSo Summer School] in advance.<br />
<br />
* [[Simulation Methods in Physics I WS 2018/2019|Simulation Methods in Physics I]] <br />Prof. Dr. [[Christian Holm]]<br> Lecture: Thu 14:00&ndash;15:30 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: TBA (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[Klassische Feldtheorie WS2018/19|Klassische Feldtheorie]] (Fortgeschrittene Kontinuumstheorie 1) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Mittwoch 9:45&ndash;11:15 (ICP Seminar Room 1.079, Allmandring 3) <br>Übungen: Mittwoch. 14:00&ndash;15:30 (ICP Seminar Room 01.079, Allmandring 3)<br />
<br />
* [[Statistische Kontinuumstheorie WS2018/19|Statistische Kontinuumstheorie]] (Ergänzungsvorlesung zu Fortgeschrittene Kontinuumstheorie 1) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Dienstag 11:30&ndash;13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Computergrundlagen WS 2018/2019|Computergrundlagen]] <br /> JP Dr. [[Maria Fyta]] <br />Lecture: Mittwoch 09:45&ndash;11:15 (V.57.02), Donnerstag (14tägig ab 25.10.2016) 14:00&ndash;15:30 (V.27.02); Übungen: im ICP CIP-Pool 01.033, Allmandring 3<br />
<br />
== SS 2018 ==<br />
<br />
<br />
* [[Allgemeine Relativitätstheorie_SS18|Allgemeine Relativitätstheorie]] (Relativitätstheorie II) (Kursvorlesung für B.Sc.,M.Sc.,Dipl.,LA,Ma.E.) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Vorlesung: Di 11:30-13:00 (Raum : ICP Seminarraum 1.079, Allmandring 3) <br />
<br />
* [[Allgemeine Relativitätstheorie_SS18|Allgemeine Relativitätstheorie]] (Relativitätstheorie II) (Übung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer], <br /> Übung: Mi 14:00-15:30 (Raum: ICP Seminarraum 1.079, Allmandring 3)<br />
<br />
* [[Simulation Methods in Physics II SS 2018|Simulation Methods in Physics II]] <br /> JP Dr. [[Maria Fyta]] (Lecture), Dr. [[Frank Uhlig]], and Dr. [[David Sean]] (Tutorials) <br> Lecture: Friday 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: tba (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[Advanced Simulation Methods SS 2018|Advanced Simulation Methods]] <br/> JP Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]], Dr. [[David Sean]] <br/> weekly during the summer semester 2018, Time: tba, (ICP Meeting Room 1.077, Allmandring 3) <br />
<br />
* [[Simulation Methods in Practice SS 2018|Simulation Methods in Practice]] <br/> Tutorials: Thursday 14:00-15:30 (ICP CIP-Pool 1.033)<br />
<br />
== WS 2017/2018 ==<br />
<br />
* [[Spezielle Relativitätstheorie_WS17|Spezielle Relativitätstheorie]] (Relativitätstheorie I) (Kursvorlesung für B.Sc.,M.Sc.,Dipl.,LA,Ma.E.) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Vorlesung: Di 11:30-13:00 (Raum : ICP Seminarraum 1.079, Allmandring 3) <br />
<br />
* [[Spezielle Relativitätstheorie_WS17|Spezielle Relativitätstheorie]] (Relativitätstheorie I) (Übung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer], <br /> Übung: Mi 14:00-15:30 (Raum: ICP Seminarraum 1.079, Allmandring 3)<br />
<br />
* [//www.cecam.org/workshop-1523.html ESPResSo Summer School] <br />Prof. Dr. [[Christian Holm]] <br /> 2017-10-09 to 2017-10-13, daily 9:00-18:00 (ICP CIP-Pool 01.033/ ICP Seminar Room 1.079, Allmandring 3) '''Students who would like to attend this compact course should register under the Cecam Website [//www.cecam.org/workshop-1523.html ESPResSo Summer School] in advance'''<br />
<br />
* [[Simulation Methods in Physics I WS 2017/2018|Simulation Methods in Physics I]] <br />Prof. Dr. [[Christian Holm]]<br> Lecture: Thu 14:00-15:30 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Wed 15:45–17:15, Fri 14:00-15:30 (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[Computergrundlagen WS 2017/2018|Computergrundlagen]] <br /> JP Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]]<br />Lecture: Mittwoch 09:45-11:15 (V.57.02), Donnerstag (14tägig ab 19.10.2016) 15:45-17:15 (V.53.01); Übungen: im ICP CIP-Pool 01.033, Allmandring 3<br />
<br />
== SS 2017 ==<br />
<br />
* [[Advanced Statistical Physics SS 2017|Advanced Statistical Physics]] <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Lecture: Thursday 8:00-9:30 and Friday 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorial: Monday 14:00-15:30 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Klassische Feldtheorie SS 17|Klassische Feldtheorie]] (Fortgeschrittene Kontinuumstheorie 2) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Mittwoch 9:45-11:15 (ICP Seminarraum 1.079, Allmandring 3) <br>Übungen: Mittwoch. 14:00-15:30 (ICP Seminarraum 1.079, Allmandring 3)<br />
<br />
* [[Hauptseminar Active Matter SS 2017|Hauptseminar "Active Matter"]] <br/>Prof. Dr. Clemens Bechinger (PI2), Prof. Dr. Siegfried Dietrich (MPI-IS/ITP4), Prof. Dr. [[Christian Holm]] (ICP) <br> Wed 17:30-19:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Simulation Methods in Physics II SS 2017|Simulation Methods in Physics II]] <br />Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]] (Lecture), Dr. [[Frank Uhlig]], and Dr. [[David Sean]] (Tutorials) <br> Lecture: Thu 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Thu 15:45–17:15 (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[Advanced Simulation Methods SS 2017|Advanced Simulation Methods]] <br/> Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP Dr. [[Maria Fyta]], <br/> weekly during the summer semester 2017, Time: tba, (ICP Meeting Room 1.077, Allmandring 3) <br />
<br />
* [[Physik auf dem Computer SS 2017|Physik auf dem Computer]] <br/> Dr. [[Jens Smiatek]], JP Dr. [[Maria Fyta]] <br/>Lecture: Wed 14:00-15:30 (V57.04), Thu 15:45-17:15 (biweekly, V57.05) <br/>Tutorials: Tue 15:45 - 17:15 (ICP CIP-Pool), Wed 15:45 - 17:15 (ICP CIP-Pool), Thu 14:00-15:30 (ICP CIP Pool)<br />
<br />
* [[Topologische Methoden der Physik SS17|Topologische Methoden der Physik]] (Vertiefung zu: Klassische Feldtheorie) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Dienstag 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Theorie poröser Medien SS17|Theorie poröser Medien]] (Vertiefung zu: Klassische Feldtheorie) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorbesprechung: Dienstag, 25.April 2017 13:05-13:45 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Simulationstechnik für Master-Studierende B|Simulationstechnik für Master-Studierende B (SimTech)]] <br/> JP Dr. [[Maria Fyta]] <br/>Lecture: Mi. 11:30-13:00 und Do. 14:00-15:30 von 03.05.2017-24.05.2017 im SimTech-Gebäude (Mi. im 1.015 und Do. im 1.009). <!--, Tutorials: n. V. (ICP CIP-Pool)--><br />
<br />
* [[Simulation Methods in Practice SS 2017|Simulation Methods in Practice]] <br/> Tutorials: Time tbd (ICP CIP-Pool 1.033)<br />
<br />
== WS 2016/2017 ==<br />
<br />
* [[Klassische Feldtheorie 16/17|Klassische Feldtheorie]] (Fortgeschrittene Kontinuumstheorie 1) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Mittwoch 9:45-11:15 (ICP Seminar Room 1.079, Allmandring 3) <br>Übungen: Mittwoch. 14:00-15:30 (ICP Seminarraum 01.079, Allmandring 3)<br />
<br />
* [[Topologische Methoden der Physik 16/17|Topologische Methoden der Physik]] (Vertiefung zu: Klassische Feldtheorie) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Dienstag 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Simulation Methods in Physics I WS 2016/2017|Simulation Methods in Physics I]] <br />Prof. Dr. [[Christian Holm]]<br> Lecture: Thu 14:00-15:30 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Thu 11:30-13:00 and Fri 14:00-15:30 (ICP Seminarraum 01.033, Allmandring 3)<br />
<br />
* [[ESPResSo Summer School WS 2016/2017|ESPResSo Summer School]] <br />Prof. Dr. [[Christian Holm]] <br /> 2016-10-10 to 2016-10-14, daily 9:00-18:00 (ICP CIP-Pool 01.033/ ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Computergrundlagen WS 2016/2017|Computergrundlagen]] <br /> JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]]<br />Lecture: Mittwoch 09:45-11:15 (V.57.02), Donnerstag (14tägig ab 27.10.2016) 14:00-15:30 (V.12.01); Übungen: im ICP CIP-Pool 01.033, Allmandring 3<br />
<br />
* [[ICP-Kolloquium WS 2015/2016|ICP-Kolloquium: Physik und Computeranwendungen]] <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer], Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]], Dr. [[Frank Uhlig]]<br /> Do 16:00-18:30 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* Oberseminar: [[Physik mit Höchstleistungsrechnern]] <br /> Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]], Dr. [[Frank Uhlig]]<br />Seminar: Mo 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
== SS 2016 ==<br />
* [[Klassische Feldtheorie 2]] (Fortgeschrittene Kontinuumstheorie 2) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Mittwoch 9:45-11:15 (ICP Seminar Room 1.079, Allmandring 3) <br>Übungen: Mittwoch. 14:00-15:30 (ICP CIP-Pool 01.079, Allmandring 3)<br />
<br />
* [[Topologische Methoden der Physik 2]] (Vertiefung zu: Fortgeschrittene Kontinuumstheorie 2) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Dienstag 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Hauptseminar Modern Simulation Methods for Structure and Properties of Charged Complex Molecules |Hauptseminar "Modern Simulation Methods for Structure and Properties of Charged Complex Molecules"]] <br/> Prof. Dr. [[Christian Holm]] (ICP), Dr. [[Jens Smiatek]], JP. Dr. [[Maria Fyta]]<br/>weekly during the summer semester 2016, Time: tba (room: tba)<br />
<br />
* [[Simulation Methods in Physics II SS 2016|Simulation Methods in Physics II]] <br />Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]] (Lecture), Dr. [[Frank Uhlig]], and [[Johannes Zeman]] (Tutorials) <br> Lecture: Thu 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Thu 14:00-15:30 (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[Advanced Simulation Methods SS 2016|Advanced Simulation Methods]] <br/> Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP Dr. [[Maria Fyta]], <br/> weekly during the summer semester 2015, Time: tba, ICP Meeting Room 1.077, Allmandring 3) <br />
<br />
* [[Physik auf dem Computer SS 2016|Physik auf dem Computer]] <br/> Dr. [[Jens Smiatek]], JP Dr. [[Maria Fyta]] <br/>Lecture: Wed 14:00-15:30 (V57.04), Fre 8:00-9:30 (biweekly, V57.05), Tutorials: Wed 15:45-17:15 (ICP CIP-Pool)<br />
<br />
* [[Simulation Methods in Practice SS 2016|Simulation Methods in Practice]] <br/> Tutorials: Time tbd (ICP CIP-Pool 1.033)<br />
<br />
* [[Simulationsmethoden fuer Master-Studierende B|Simulationsmethoden für Master-Studierende B (SimTech)]] <br/> Dr. [[Jens Smiatek]], JP Dr. [[Maria Fyta]] <br/>Lecture: n. V, Tutorials: n. V. (ICP CIP-Pool)<br />
<br />
== WS 2015/2016 ==<br />
* [[Simulation Methods in Physics I WS 2015/2016|Simulation Methods in Physics I]] <br />Prof. Dr. [[Christian Holm]], Dr. [[Gary Davies]] <br> Lecture: Thu 14:00-15:30 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Thu 11:30-13:00 and Fri 14:00-15:30 (ICP Seminarraum 01.033, Allmandring 3)<br />
<br />
* [[Klassische Feldtheorie]] (Fortgeschrittene Kontinuumstheorie 1) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Mittwoch 9:45-11:15 (ICP Seminar Room 1.079, Allmandring 3) <br>Übungen: Mittwoch. 14:00-15:30 (ICP CIP-Pool 01.079, Allmandring 3)<br />
<br />
* [[Topologische Methoden der Physik]] (Vertiefung zu: Fortgeschrittene Kontinuumstheorie) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Dienstag 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Computergrundlagen WS 2015|Computergrundlagen]] <br /> JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]]<br />Lecture: Mittwoch 09:45-11:15 (V.57.02), Freitag (14.tägig ab 23.10.2015) 14:00-15:30 (V.57.01), ab 15.12 wird der Freitag Termin mit Dienstag 09:45-11:15 (V.7.11) ersetzt; Übungen: am ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[ICP-Kolloquium WS 2015/2016|ICP-Kolloquium: Physik und Computeranwendungen]] <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer], Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]], Dr. [[Joost de Graaf]]<br /> Do 16:00-18:30 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* Oberseminar: [[Physik mit Höchstleistungsrechnern]] <br /> Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]], Dr. [[Gary Davies]]<br />Seminar: Mo 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Theoretische Physik ungeordneter Systeme]] <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Di 15:00-16:30 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[ESPResSo Summer School WS 2015/2016|ESPResSo Summer School]] <br />Prof. Dr. [[Christian Holm]],Dr. [[Joost de Graaf]], [[Florian Weik]] <br /> 2015-10-05 to 2015-10-09, daily 9:00-18:00 (ICP CIP-Pool 01.033/ ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* GS SimTech Seminar: [[Molecular Simulations]] <br />Dr. [[Jens Smiatek]], JP Dr. [http://www.itt.uni-stuttgart.de/institut/mitarbeiter/institutsleitung/hansen/ Niels Hansen] <br> Seminar: Donnerstag 14:00-15:30 (ICP Meeting Room 1.077, Allmandring 3)<br />
<br />
== SS 2015 ==<br />
<br />
* [[Simulation Methods in Physics II SS 2015|Simulation Methods in Physics II]] <br />Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]] (Lecture), [[Florian Weik]], and [[Johannes Zeman]] (Tutorials) <br> Lecture: Thu 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Thu 14:00-15:30 (Tutor: [[Bibek Adhikari]] and [[Johannes Zeman]]) (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[Relativitätstheorie]] 2 (Allgemeine Relativitätstheorie) (Vorlesung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Vorlesung: Di 11:30-13:00 (Raum : V57.05, Pfaffenwaldring 57) <br />
<br />
* Relativitätstheorie 2 (Allgemeine Relativitätstheorie) (Übung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] and [http://www.icp.uni-stuttgart.de/~icp/Christoph_Wolber Christoph Wolber], <br /> Übung: Mi 09:45-11:15, 14:00-15:30 (Raum: ICP Seminarraum 1.079, Allmandring 3)<br />
<br />
* Mathematische Quantentheorie 2 (Vorlesung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Do 09:30-11:30, (Raum: Seminarraum ICP 1.079, Allmandring 3) <br \>(1. Vorlesung, Do, 23.04.)<br />
<br />
* [[Simulation Methods in Practice SS 2015|Simulation Methods in Practice]] <br/>[[Bibek Adhikari]], [[Narayanan Krishnamoorthy Anand]] <br/> Tutorials: Time tbd (ICP CIP-Pool 1.033)<br />
<br />
* [[Hauptseminar Active Matter SS 2015|Hauptseminar "Active Matter"]] <br/>Prof. Dr. Clemens Bechinger (2. PI), Dr. Juan Ruben Gomez-Solano (2. PI), Prof. Dr. [[Christian Holm]] (ICP), Dr. [[Joost de Graaf]] (ICP)<br/>weekly during the summer semester 2015, time tab (room: tba)<br />
<br />
* [[Advanced Simulation Methods SS 2015|Advanced Simulation Methods]] <br/> Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], Dr. [[Joost de Graaf]], JP Dr. [[Maria Fyta]], <br/>weekly during the summer semester 2015, time tab (room: tba)<br />
<br />
== WS 2014/2015 ==<br />
* Weihnachtsvorlesung: Über Uhren, Altern und Zeit <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer], <br /> Zeit: Di, 30.12. 2014, 15:45-16:30, <br />Raum: ICP Seminarraum 1.079, Allmandring 3 <br /><br />
<br />
* [[Simulation Methods in Physics I WS 2014|Simulation Methods in Physics I]] <br />Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]] (Lecture), [[Florian Weik]], and [[Johannes Zeman]] (Tutorials) <br> Lecture: Thu 14:00-15:30 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Wed 15:45-17:15 (Tutor: [[Florian Weik]]) and Wed 17:30-19:00 (Tutor: [[Johannes Zeman]]) (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[RelativitätstheorieWS14_15|Relativitätstheorie]] 1 (Spezielle Relativitätstheorie) (Vorlesung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Vorlesung: Di 11:30-13:00 (Raum : V57.05, Pfaffenwaldring 57) <br />
<br />
* [[RelativitätstheorieWS14_15|Relativitätstheorie]] 1 (Spezielle Relativitätstheorie) (Übung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] and [http://www.icp.uni-stuttgart.de/~icp/Christoph_Wolber Christoph Wolber], <br /> Übung: Mi 11:30-13:00, 14:00-15:30 (Raum: ICP Seminarraum 1.079, Allmandring 3)<br />
<br />
* [[Computergrundlagen WS 2014|Computergrundlagen]] <br /> JP Dr. [[Axel Arnold]], Dr. [[Jens Smiatek]], and [[Tobias Richter]]<br />Lecture: Mi 9:45-11:15 (V57.06), Fr 14:00-15:30 (V38.01); Tutorials: Various dates (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* Mathematische Quantentheorie (Vorlesung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Do 11:30-13:45, (Raum: Seminarraum ICP 1.079, Allmandring 3) <br \>(1. Vorlesung, Do, 30.10.)<br />
<br />
* [[ICP-Kolloquium WS 2014/2015|ICP-Kolloquium: Physik und Computeranwendungen]] <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer], Prof. Dr. [[Christian Holm]], JP Dr. [[Axel Arnold]], JP Dr. [[Maria Fyta]], Dr. [[Olaf Lenz]]<br /> Do 16:00-18:30 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* Oberseminar: [[Physik mit Höchstleistungsrechnern]] <br /> Prof. Dr. [[Christian Holm]], Dr. [[Olaf Lenz]]<br />Seminar: Mo 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[ESPResSo Summer School WS 2014/20145|ESPResSo Summer School]] <br />DJP Dr. [[Axel Arnold]], Prof. Dr. [[Christian Holm]]<br /> 2014-10-06 to 2014-10-10, daily 9:00-18:00 (ICP CIP-Pool 01.033/ ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Hauptseminar Theorie und Simulation der weichen Materie WS 2014/2015|Hauptseminar "Theorie und Simulation der weichen Materie"]] <br/>Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], Dr. Matthias Krueger<br/> Blockseminar, 23.02.-25.03.2015 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Efficient Algorithms for Soft Matter WS 2014/2015|Efficient Algorithms for Soft Matter]] <br/> JP Dr. [[Axel Arnold]] <br/> Oberseminar, every second week Tu 10:30 (ICP Meeting Room 1.095, Allmandring 3)<br />
<br />
* [[Oberseminar WS 2014/2015|Oberseminar: Computational Biomaterials]] <br /> JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]]<br /> We 13:15-14:45 (ICP Meeting Room 1.095, Allmandring 3)<br />
<br />
* [[Theoretische Physik ungeordneter Systeme]] <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Di 15:00-16:30 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
== SS 2014 ==<br />
* [[Theoretische Physik III: Elektrodynamik SS 2014|Theoretische Physik III: Elektrodynamik]] (Vorlesung mit Übungen) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Vorlesung: Mi 11:30-13:00 & Do 8:00-9:30, V57.02 <br /> Übungen: Mi 15:45-17:15, V57.2.xxx & Allmandring 3, 1.079<br />
<br />
* [[Hauptseminar Theorie und Simulation der weichen Materie SS 2014|Hauptseminar "Theorie und Simulation der weichen Materie" (SS 2014)]] <br/> JP Dr. [[Axel Arnold]], Dr. [[Olaf Lenz]], Dr. [[Jens Smiatek]], Dr. Matthias Krüger (Max-Planck-Institut für Intelligente Systeme), Dr. Markus Bier (Max-Planck-Institut für Intelligente Systeme), Dr. Felix Höfling (Max-Planck-Institut für Intelligente Systeme)<br/> Tue, 14:00-15:30 (ICP Seminar Room 1.079)<br />
<br />
* [[Textsatz mit TeX/LaTeX SS 2014|Textsatz mit TeX/LaTeX &mdash; Typesetting with TeX/LaTeX]] <br/> JP Dr. [[Axel Arnold]], Dr. [[Olaf Lenz]], [[Henri Menke]]<br/>Block course, 21.07.2014 - 25.07.2014; Lecture: 9:00 - 13:00 (Seminar room ICP, Allmandring 3), Hands-on: 14:00 - 17:00 (ICP CIP-Pool 1.033)<br />
<br />
* [[Physics of Soft and Biological Matter 2 SS 2014|Physics of Soft and Biological Matter 2]] <br />Prof. Dr. Clemens Bechinger, Prof. Dr. [[Christian Holm]], Dr. [[Owen Hickey]]<br/>Lecture: Thu 14:00-15:30 (ICP Seminar room 1.079); Tutorials: Thu 08:00-09:30 (ICP CIP-Pool 1.033)<br />
<br />
* [[Simulation Methods in Physics II SS 2014|Simulation Methods in Physics II]] <br/>JP Dr. [[Maria Fyta]], Prof. Dr. [[Christian Holm]]<br/>Lecture: Thu 11:30-13:00 (ICP Seminar Room 1.079)<br />
<br />
* [[Simulation Methods in Practice SS 2014|Simulation Methods in Practice]] <br/>[[Bibek Adhikari]], [[Narayanan Krishnamoorthy Anand]] <br/> Tutorials: Time tbd (ICP CIP-Pool 1.033)<br />
<br />
* [[Advanced Simulation Methods SS 2014|Advanced Simulation Methods]] <br/>JP Dr. [[Axel Arnold]], JP Dr. [[Maria Fyta]], [[Stefan Kesselheim]], Dr. [[Olaf Lenz]], Dr. [[Jens Smiatek]]<br/>Wed 11:30-13:00 (Lecture: ICP Meeting room, Tutorials: ICP CIP-Pool 1.033)<br />
<br />
* [[Physik auf dem Computer SS 2014|Physik auf dem Computer]] <br/> JP Dr. [[Axel Arnold]], Dr. [[Olaf Lenz]]<br/>Lecture: Wed 9:45-11:15 (V57.05), Fre 9:45-11:15 (biweekly, V57.06), Tutorials: ''Time tbd'' (ICP CIP-Pool)<br />
<br />
== Lectures in Previous Terms ==<br />
<br />
* [[/2013|WS 2013/2014]]<br />
* [[/2012|WS 2012/2013 and SS 2013]]<br />
* [[/2011|WS 2011/2012 and SS 2012]]<br />
* [[/2010|WS 2010/2011 and SS 2011]]<br />
* [[/2009|WS 2009/2010 and SS 2010]]<br />
* [[/2008|WS 2008/2009 and SS 2009]]</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Christoph_Lohrmann&diff=23779Christoph Lohrmann2019-01-14T11:46:50Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|name=Lohrmann, Christoph<br />
|status=PhD Student<br />
|phone=63932<br />
|room=1.076<br />
|email=clohrmann<br />
|topical=electrokinetics<br />
|topical2=gel<br />
|topical3=hydrodynamics<br />
|category=holm<br />
}}</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Christoph_Lohrmann&diff=23778Christoph Lohrmann2019-01-14T11:45:13Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|name=Lohrmann, Christoph<br />
|status=PhD Student<br />
|phone=63932<br />
|room=1.076<br />
|email=clohrmann<br />
|topical=electrokinetics<br />
|topical2=gel<br />
|topical3=hydrodynamics<br />
|category=holm<br />
|topical=<br />
}}</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2018/2019&diff=23684Simulation Methods in Physics I WS 2018/20192018-12-12T17:50:12Z<p>Holm: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 15:45-17:15 ([[Kartik Jain]]), Fri 14:00-15:30 ([[Rudolf Weeber]])<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
! !! Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|1||2018-10-18 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture01_slides.pdf Slides] [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture01_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2||2018-10-25 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
| ||2018-11-01 || public holiday, no lecture || ||<br />
<br />
|-<br />
|3||2018-11-08 || Basics of Statistical Mechanics, Chaos || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|4||2018-11-15 || Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|5||2018-11-22 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|6||2018-11-29 || Observables, Brownian Motion, Diffusion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|7||2018-12-06 || Diffusion, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|8||2018-12-13 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|9||2018-12-20 || Error analysis, B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|10||2019-01-10 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture10_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|11||2019-01-17 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|12||2019-01-24 || Critical Exponent ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|13||2019-01-31 || Finite Size Scaling ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|14||2019-02-07 ||Reweighting || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2018-ws-sim_methods/lecture14_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) <!--on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[Michael Kuron]]<br />
** Fridays 14:00-15:30 (Tutor: [[Kartik Jain]])--><br />
<!--* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.--><br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators (lectures 1-2) || 2018-11-12 12:00 || {{Download|WS_2018_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics (lectures 2-4) || 2018-11-26 12:00 || {{Download|WS_2018_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables (lectures 4-5) || 2018-12-10 12:00 || {{Download|WS_2018_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion (lectures 6-8) || 2019-01-07 12:00 || {{Download|WS_2018_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo (lectures 10-11) || 2019-01-21 12:00 || {{Download|WS_2018_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling (lectures 11-13) || 2019-02-04 12:00 || {{Download|WS_2018_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<br />
|}<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|txt}}.<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the programme you are enrolled in, Simulation Methods is part of different modules that award different numbers of credits after different kinds of exams. Please have a look at [[File:SimMethModuleOverview.pdf]], which also explains how you can take Advanced Simulation Methods.<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [https://campus.uni-stuttgart.de/cusonline/wbLv.wbShowLVDetail?pStpSpNr=208686 C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2019 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2019 if they intend to enroll in the master programme (starting in fall 2019) and take Advanced Simulation Methods (in summer 2020). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Teaching&diff=23526Teaching2018-10-18T11:11:25Z<p>Holm: /* WS 2018/2019 */</p>
<hr />
<div>Hier findet sich ein [[/Overview|Überblick über die Lehre am ICP]] {{german}}.<br />
<br />
== WS 2018/2019 ==<br />
<br />
* [//www.cecam.org/workshop-1605.html ESPResSo Summer School] <br />Prof. Dr. [[Christian Holm]] <br /> 2018-10-08 to 2018-10-12, daily 9:00-18:00 (ICP CIP-Pool 01.033/ ICP Seminar Room 1.079, Allmandring 3) '''Students who would like to attend this compact course should register under the Cecam Website [//www.cecam.org/workshop-1605.html ESPResSo Summer School] in advance.<br />
<br />
* [[Simulation Methods in Physics I WS 2018/2019|Simulation Methods in Physics I]] <br />Prof. Dr. [[Christian Holm]]<br> Lecture: Thu 14:00-15:30 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: TBA (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[Klassische Feldtheorie WS2018/19|Klassische Feldtheorie]] (Fortgeschrittene Kontinuumstheorie 1) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Mittwoch 9:45-11:15 (ICP Seminar Room 1.079, Allmandring 3) <br>Übungen: Mittwoch. 14:00-15:30 (ICP Seminar Room 01.079, Allmandring 3)<br />
<br />
* [[Statistische Kontinuumstheorie WS2018/19|Statistische Kontinuumstheorie]] (Ergänzungsvorlesung zu Fortgeschrittene Kontinuumstheorie 1) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Dienstag 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Computergrundlagen WS 2018/2019|Computergrundlagen]] <br /> JP Dr. [[Maria Fyta]] <br />Lecture: Mittwoch 09:45-11:15 (V.57.02), Donnerstag (14tägig ab 25.10.2016) 14:00-15:30 (V.27.02); Übungen: im ICP CIP-Pool 01.033, Allmandring 3<br />
<br />
== SS 2018 ==<br />
<br />
<br />
* [[Allgemeine Relativitätstheorie_SS18|Allgemeine Relativitätstheorie]] (Relativitätstheorie II) (Kursvorlesung für B.Sc.,M.Sc.,Dipl.,LA,Ma.E.) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Vorlesung: Di 11:30-13:00 (Raum : ICP Seminarraum 1.079, Allmandring 3) <br />
<br />
* [[Allgemeine Relativitätstheorie_SS18|Allgemeine Relativitätstheorie]] (Relativitätstheorie II) (Übung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer], <br /> Übung: Mi 14:00-15:30 (Raum: ICP Seminarraum 1.079, Allmandring 3)<br />
<br />
* [[Simulation Methods in Physics II SS 2018|Simulation Methods in Physics II]] <br /> JP Dr. [[Maria Fyta]] (Lecture), Dr. [[Frank Uhlig]], and Dr. [[David Sean]] (Tutorials) <br> Lecture: Friday 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: tba (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[Advanced Simulation Methods SS 2018|Advanced Simulation Methods]] <br/> JP Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]], Dr. [[David Sean]] <br/> weekly during the summer semester 2018, Time: tba, (ICP Meeting Room 1.077, Allmandring 3) <br />
<br />
* [[Simulation Methods in Practice SS 2018|Simulation Methods in Practice]] <br/> Tutorials: Thursday 14:00-15:30 (ICP CIP-Pool 1.033)<br />
<br />
== WS 2017/2018 ==<br />
<br />
* [[Spezielle Relativitätstheorie_WS17|Spezielle Relativitätstheorie]] (Relativitätstheorie I) (Kursvorlesung für B.Sc.,M.Sc.,Dipl.,LA,Ma.E.) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Vorlesung: Di 11:30-13:00 (Raum : ICP Seminarraum 1.079, Allmandring 3) <br />
<br />
* [[Spezielle Relativitätstheorie_WS17|Spezielle Relativitätstheorie]] (Relativitätstheorie I) (Übung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer], <br /> Übung: Mi 14:00-15:30 (Raum: ICP Seminarraum 1.079, Allmandring 3)<br />
<br />
* [//www.cecam.org/workshop-1523.html ESPResSo Summer School] <br />Prof. Dr. [[Christian Holm]] <br /> 2017-10-09 to 2017-10-13, daily 9:00-18:00 (ICP CIP-Pool 01.033/ ICP Seminar Room 1.079, Allmandring 3) '''Students who would like to attend this compact course should register under the Cecam Website [//www.cecam.org/workshop-1523.html ESPResSo Summer School] in advance'''<br />
<br />
* [[Simulation Methods in Physics I WS 2017/2018|Simulation Methods in Physics I]] <br />Prof. Dr. [[Christian Holm]]<br> Lecture: Thu 14:00-15:30 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Wed 15:45–17:15, Fri 14:00-15:30 (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[Computergrundlagen WS 2017/2018|Computergrundlagen]] <br /> JP Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]]<br />Lecture: Mittwoch 09:45-11:15 (V.57.02), Donnerstag (14tägig ab 19.10.2016) 15:45-17:15 (V.53.01); Übungen: im ICP CIP-Pool 01.033, Allmandring 3<br />
<br />
== SS 2017 ==<br />
<br />
* [[Advanced Statistical Physics SS 2017|Advanced Statistical Physics]] <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Lecture: Thursday 8:00-9:30 and Friday 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorial: Monday 14:00-15:30 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Klassische Feldtheorie SS 17|Klassische Feldtheorie]] (Fortgeschrittene Kontinuumstheorie 2) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Mittwoch 9:45-11:15 (ICP Seminarraum 1.079, Allmandring 3) <br>Übungen: Mittwoch. 14:00-15:30 (ICP Seminarraum 1.079, Allmandring 3)<br />
<br />
* [[Hauptseminar Active Matter SS 2017|Hauptseminar "Active Matter"]] <br/>Prof. Dr. Clemens Bechinger (PI2), Prof. Dr. Siegfried Dietrich (MPI-IS/ITP4), Prof. Dr. [[Christian Holm]] (ICP) <br> Wed 17:30-19:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Simulation Methods in Physics II SS 2017|Simulation Methods in Physics II]] <br />Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]] (Lecture), Dr. [[Frank Uhlig]], and Dr. [[David Sean]] (Tutorials) <br> Lecture: Thu 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Thu 15:45–17:15 (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[Advanced Simulation Methods SS 2017|Advanced Simulation Methods]] <br/> Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP Dr. [[Maria Fyta]], <br/> weekly during the summer semester 2017, Time: tba, (ICP Meeting Room 1.077, Allmandring 3) <br />
<br />
* [[Physik auf dem Computer SS 2017|Physik auf dem Computer]] <br/> Dr. [[Jens Smiatek]], JP Dr. [[Maria Fyta]] <br/>Lecture: Wed 14:00-15:30 (V57.04), Thu 15:45-17:15 (biweekly, V57.05) <br/>Tutorials: Tue 15:45 - 17:15 (ICP CIP-Pool), Wed 15:45 - 17:15 (ICP CIP-Pool), Thu 14:00-15:30 (ICP CIP Pool)<br />
<br />
* [[Topologische Methoden der Physik SS17|Topologische Methoden der Physik]] (Vertiefung zu: Klassische Feldtheorie) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Dienstag 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Theorie poröser Medien SS17|Theorie poröser Medien]] (Vertiefung zu: Klassische Feldtheorie) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorbesprechung: Dienstag, 25.April 2017 13:05-13:45 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Simulationstechnik für Master-Studierende B|Simulationstechnik für Master-Studierende B (SimTech)]] <br/> JP Dr. [[Maria Fyta]] <br/>Lecture: Mi. 11:30-13:00 und Do. 14:00-15:30 von 03.05.2017-24.05.2017 im SimTech-Gebäude (Mi. im 1.015 und Do. im 1.009). <!--, Tutorials: n. V. (ICP CIP-Pool)--><br />
<br />
* [[Simulation Methods in Practice SS 2017|Simulation Methods in Practice]] <br/> Tutorials: Time tbd (ICP CIP-Pool 1.033)<br />
<br />
== WS 2016/2017 ==<br />
<br />
* [[Klassische Feldtheorie 16/17|Klassische Feldtheorie]] (Fortgeschrittene Kontinuumstheorie 1) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Mittwoch 9:45-11:15 (ICP Seminar Room 1.079, Allmandring 3) <br>Übungen: Mittwoch. 14:00-15:30 (ICP Seminarraum 01.079, Allmandring 3)<br />
<br />
* [[Topologische Methoden der Physik 16/17|Topologische Methoden der Physik]] (Vertiefung zu: Klassische Feldtheorie) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Dienstag 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Simulation Methods in Physics I WS 2016/2017|Simulation Methods in Physics I]] <br />Prof. Dr. [[Christian Holm]]<br> Lecture: Thu 14:00-15:30 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Thu 11:30-13:00 and Fri 14:00-15:30 (ICP Seminarraum 01.033, Allmandring 3)<br />
<br />
* [[ESPResSo Summer School WS 2016/2017|ESPResSo Summer School]] <br />Prof. Dr. [[Christian Holm]] <br /> 2016-10-10 to 2016-10-14, daily 9:00-18:00 (ICP CIP-Pool 01.033/ ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Computergrundlagen WS 2016/2017|Computergrundlagen]] <br /> JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]]<br />Lecture: Mittwoch 09:45-11:15 (V.57.02), Donnerstag (14tägig ab 27.10.2016) 14:00-15:30 (V.12.01); Übungen: im ICP CIP-Pool 01.033, Allmandring 3<br />
<br />
* [[ICP-Kolloquium WS 2015/2016|ICP-Kolloquium: Physik und Computeranwendungen]] <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer], Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]], Dr. [[Frank Uhlig]]<br /> Do 16:00-18:30 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* Oberseminar: [[Physik mit Höchstleistungsrechnern]] <br /> Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]], Dr. [[Frank Uhlig]]<br />Seminar: Mo 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
== SS 2016 ==<br />
* [[Klassische Feldtheorie 2]] (Fortgeschrittene Kontinuumstheorie 2) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Mittwoch 9:45-11:15 (ICP Seminar Room 1.079, Allmandring 3) <br>Übungen: Mittwoch. 14:00-15:30 (ICP CIP-Pool 01.079, Allmandring 3)<br />
<br />
* [[Topologische Methoden der Physik 2]] (Vertiefung zu: Fortgeschrittene Kontinuumstheorie 2) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Dienstag 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Hauptseminar Modern Simulation Methods for Structure and Properties of Charged Complex Molecules |Hauptseminar "Modern Simulation Methods for Structure and Properties of Charged Complex Molecules"]] <br/> Prof. Dr. [[Christian Holm]] (ICP), Dr. [[Jens Smiatek]], JP. Dr. [[Maria Fyta]]<br/>weekly during the summer semester 2016, Time: tba (room: tba)<br />
<br />
* [[Simulation Methods in Physics II SS 2016|Simulation Methods in Physics II]] <br />Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]] (Lecture), Dr. [[Frank Uhlig]], and [[Johannes Zeman]] (Tutorials) <br> Lecture: Thu 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Thu 14:00-15:30 (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[Advanced Simulation Methods SS 2016|Advanced Simulation Methods]] <br/> Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP Dr. [[Maria Fyta]], <br/> weekly during the summer semester 2015, Time: tba, ICP Meeting Room 1.077, Allmandring 3) <br />
<br />
* [[Physik auf dem Computer SS 2016|Physik auf dem Computer]] <br/> Dr. [[Jens Smiatek]], JP Dr. [[Maria Fyta]] <br/>Lecture: Wed 14:00-15:30 (V57.04), Fre 8:00-9:30 (biweekly, V57.05), Tutorials: Wed 15:45-17:15 (ICP CIP-Pool)<br />
<br />
* [[Simulation Methods in Practice SS 2016|Simulation Methods in Practice]] <br/> Tutorials: Time tbd (ICP CIP-Pool 1.033)<br />
<br />
* [[Simulationsmethoden fuer Master-Studierende B|Simulationsmethoden für Master-Studierende B (SimTech)]] <br/> Dr. [[Jens Smiatek]], JP Dr. [[Maria Fyta]] <br/>Lecture: n. V, Tutorials: n. V. (ICP CIP-Pool)<br />
<br />
== WS 2015/2016 ==<br />
* [[Simulation Methods in Physics I WS 2015/2016|Simulation Methods in Physics I]] <br />Prof. Dr. [[Christian Holm]], Dr. [[Gary Davies]] <br> Lecture: Thu 14:00-15:30 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Thu 11:30-13:00 and Fri 14:00-15:30 (ICP Seminarraum 01.033, Allmandring 3)<br />
<br />
* [[Klassische Feldtheorie]] (Fortgeschrittene Kontinuumstheorie 1) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Mittwoch 9:45-11:15 (ICP Seminar Room 1.079, Allmandring 3) <br>Übungen: Mittwoch. 14:00-15:30 (ICP CIP-Pool 01.079, Allmandring 3)<br />
<br />
* [[Topologische Methoden der Physik]] (Vertiefung zu: Fortgeschrittene Kontinuumstheorie) <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br> Vorlesung: Dienstag 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Computergrundlagen WS 2015|Computergrundlagen]] <br /> JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]]<br />Lecture: Mittwoch 09:45-11:15 (V.57.02), Freitag (14.tägig ab 23.10.2015) 14:00-15:30 (V.57.01), ab 15.12 wird der Freitag Termin mit Dienstag 09:45-11:15 (V.7.11) ersetzt; Übungen: am ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[ICP-Kolloquium WS 2015/2016|ICP-Kolloquium: Physik und Computeranwendungen]] <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer], Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]], Dr. [[Joost de Graaf]]<br /> Do 16:00-18:30 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* Oberseminar: [[Physik mit Höchstleistungsrechnern]] <br /> Prof. Dr. [[Christian Holm]], JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]], Dr. [[Gary Davies]]<br />Seminar: Mo 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Theoretische Physik ungeordneter Systeme]] <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Di 15:00-16:30 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[ESPResSo Summer School WS 2015/2016|ESPResSo Summer School]] <br />Prof. Dr. [[Christian Holm]],Dr. [[Joost de Graaf]], [[Florian Weik]] <br /> 2015-10-05 to 2015-10-09, daily 9:00-18:00 (ICP CIP-Pool 01.033/ ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* GS SimTech Seminar: [[Molecular Simulations]] <br />Dr. [[Jens Smiatek]], JP Dr. [http://www.itt.uni-stuttgart.de/institut/mitarbeiter/institutsleitung/hansen/ Niels Hansen] <br> Seminar: Donnerstag 14:00-15:30 (ICP Meeting Room 1.077, Allmandring 3)<br />
<br />
== SS 2015 ==<br />
<br />
* [[Simulation Methods in Physics II SS 2015|Simulation Methods in Physics II]] <br />Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]] (Lecture), [[Florian Weik]], and [[Johannes Zeman]] (Tutorials) <br> Lecture: Thu 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Thu 14:00-15:30 (Tutor: [[Bibek Adhikari]] and [[Johannes Zeman]]) (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[Relativitätstheorie]] 2 (Allgemeine Relativitätstheorie) (Vorlesung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Vorlesung: Di 11:30-13:00 (Raum : V57.05, Pfaffenwaldring 57) <br />
<br />
* Relativitätstheorie 2 (Allgemeine Relativitätstheorie) (Übung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] and [http://www.icp.uni-stuttgart.de/~icp/Christoph_Wolber Christoph Wolber], <br /> Übung: Mi 09:45-11:15, 14:00-15:30 (Raum: ICP Seminarraum 1.079, Allmandring 3)<br />
<br />
* Mathematische Quantentheorie 2 (Vorlesung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Do 09:30-11:30, (Raum: Seminarraum ICP 1.079, Allmandring 3) <br \>(1. Vorlesung, Do, 23.04.)<br />
<br />
* [[Simulation Methods in Practice SS 2015|Simulation Methods in Practice]] <br/>[[Bibek Adhikari]], [[Narayanan Krishnamoorthy Anand]] <br/> Tutorials: Time tbd (ICP CIP-Pool 1.033)<br />
<br />
* [[Hauptseminar Active Matter SS 2015|Hauptseminar "Active Matter"]] <br/>Prof. Dr. Clemens Bechinger (2. PI), Dr. Juan Ruben Gomez-Solano (2. PI), Prof. Dr. [[Christian Holm]] (ICP), Dr. [[Joost de Graaf]] (ICP)<br/>weekly during the summer semester 2015, time tab (room: tba)<br />
<br />
* [[Advanced Simulation Methods SS 2015|Advanced Simulation Methods]] <br/> Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], Dr. [[Joost de Graaf]], JP Dr. [[Maria Fyta]], <br/>weekly during the summer semester 2015, time tab (room: tba)<br />
<br />
== WS 2014/2015 ==<br />
* Weihnachtsvorlesung: Über Uhren, Altern und Zeit <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer], <br /> Zeit: Di, 30.12. 2014, 15:45-16:30, <br />Raum: ICP Seminarraum 1.079, Allmandring 3 <br /><br />
<br />
* [[Simulation Methods in Physics I WS 2014|Simulation Methods in Physics I]] <br />Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]] (Lecture), [[Florian Weik]], and [[Johannes Zeman]] (Tutorials) <br> Lecture: Thu 14:00-15:30 (ICP Seminar Room 1.079, Allmandring 3) <br>Tutorials: Wed 15:45-17:15 (Tutor: [[Florian Weik]]) and Wed 17:30-19:00 (Tutor: [[Johannes Zeman]]) (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* [[RelativitätstheorieWS14_15|Relativitätstheorie]] 1 (Spezielle Relativitätstheorie) (Vorlesung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Vorlesung: Di 11:30-13:00 (Raum : V57.05, Pfaffenwaldring 57) <br />
<br />
* [[RelativitätstheorieWS14_15|Relativitätstheorie]] 1 (Spezielle Relativitätstheorie) (Übung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] and [http://www.icp.uni-stuttgart.de/~icp/Christoph_Wolber Christoph Wolber], <br /> Übung: Mi 11:30-13:00, 14:00-15:30 (Raum: ICP Seminarraum 1.079, Allmandring 3)<br />
<br />
* [[Computergrundlagen WS 2014|Computergrundlagen]] <br /> JP Dr. [[Axel Arnold]], Dr. [[Jens Smiatek]], and [[Tobias Richter]]<br />Lecture: Mi 9:45-11:15 (V57.06), Fr 14:00-15:30 (V38.01); Tutorials: Various dates (ICP CIP-Pool 01.033, Allmandring 3)<br />
<br />
* Mathematische Quantentheorie (Vorlesung) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Do 11:30-13:45, (Raum: Seminarraum ICP 1.079, Allmandring 3) <br \>(1. Vorlesung, Do, 30.10.)<br />
<br />
* [[ICP-Kolloquium WS 2014/2015|ICP-Kolloquium: Physik und Computeranwendungen]] <br />Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer], Prof. Dr. [[Christian Holm]], JP Dr. [[Axel Arnold]], JP Dr. [[Maria Fyta]], Dr. [[Olaf Lenz]]<br /> Do 16:00-18:30 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* Oberseminar: [[Physik mit Höchstleistungsrechnern]] <br /> Prof. Dr. [[Christian Holm]], Dr. [[Olaf Lenz]]<br />Seminar: Mo 11:30-13:00 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[ESPResSo Summer School WS 2014/20145|ESPResSo Summer School]] <br />DJP Dr. [[Axel Arnold]], Prof. Dr. [[Christian Holm]]<br /> 2014-10-06 to 2014-10-10, daily 9:00-18:00 (ICP CIP-Pool 01.033/ ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Hauptseminar Theorie und Simulation der weichen Materie WS 2014/2015|Hauptseminar "Theorie und Simulation der weichen Materie"]] <br/>Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], Dr. Matthias Krueger<br/> Blockseminar, 23.02.-25.03.2015 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
* [[Efficient Algorithms for Soft Matter WS 2014/2015|Efficient Algorithms for Soft Matter]] <br/> JP Dr. [[Axel Arnold]] <br/> Oberseminar, every second week Tu 10:30 (ICP Meeting Room 1.095, Allmandring 3)<br />
<br />
* [[Oberseminar WS 2014/2015|Oberseminar: Computational Biomaterials]] <br /> JP Dr. [[Maria Fyta]], Dr. [[Jens Smiatek]]<br /> We 13:15-14:45 (ICP Meeting Room 1.095, Allmandring 3)<br />
<br />
* [[Theoretische Physik ungeordneter Systeme]] <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Di 15:00-16:30 (ICP Seminar Room 1.079, Allmandring 3)<br />
<br />
== SS 2014 ==<br />
* [[Theoretische Physik III: Elektrodynamik SS 2014|Theoretische Physik III: Elektrodynamik]] (Vorlesung mit Übungen) <br /> Prof. Dr. [http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br /> Vorlesung: Mi 11:30-13:00 & Do 8:00-9:30, V57.02 <br /> Übungen: Mi 15:45-17:15, V57.2.xxx & Allmandring 3, 1.079<br />
<br />
* [[Hauptseminar Theorie und Simulation der weichen Materie SS 2014|Hauptseminar "Theorie und Simulation der weichen Materie" (SS 2014)]] <br/> JP Dr. [[Axel Arnold]], Dr. [[Olaf Lenz]], Dr. [[Jens Smiatek]], Dr. Matthias Krüger (Max-Planck-Institut für Intelligente Systeme), Dr. Markus Bier (Max-Planck-Institut für Intelligente Systeme), Dr. Felix Höfling (Max-Planck-Institut für Intelligente Systeme)<br/> Tue, 14:00-15:30 (ICP Seminar Room 1.079)<br />
<br />
* [[Textsatz mit TeX/LaTeX SS 2014|Textsatz mit TeX/LaTeX &mdash; Typesetting with TeX/LaTeX]] <br/> JP Dr. [[Axel Arnold]], Dr. [[Olaf Lenz]], [[Henri Menke]]<br/>Block course, 21.07.2014 - 25.07.2014; Lecture: 9:00 - 13:00 (Seminar room ICP, Allmandring 3), Hands-on: 14:00 - 17:00 (ICP CIP-Pool 1.033)<br />
<br />
* [[Physics of Soft and Biological Matter 2 SS 2014|Physics of Soft and Biological Matter 2]] <br />Prof. Dr. Clemens Bechinger, Prof. Dr. [[Christian Holm]], Dr. [[Owen Hickey]]<br/>Lecture: Thu 14:00-15:30 (ICP Seminar room 1.079); Tutorials: Thu 08:00-09:30 (ICP CIP-Pool 1.033)<br />
<br />
* [[Simulation Methods in Physics II SS 2014|Simulation Methods in Physics II]] <br/>JP Dr. [[Maria Fyta]], Prof. Dr. [[Christian Holm]]<br/>Lecture: Thu 11:30-13:00 (ICP Seminar Room 1.079)<br />
<br />
* [[Simulation Methods in Practice SS 2014|Simulation Methods in Practice]] <br/>[[Bibek Adhikari]], [[Narayanan Krishnamoorthy Anand]] <br/> Tutorials: Time tbd (ICP CIP-Pool 1.033)<br />
<br />
* [[Advanced Simulation Methods SS 2014|Advanced Simulation Methods]] <br/>JP Dr. [[Axel Arnold]], JP Dr. [[Maria Fyta]], [[Stefan Kesselheim]], Dr. [[Olaf Lenz]], Dr. [[Jens Smiatek]]<br/>Wed 11:30-13:00 (Lecture: ICP Meeting room, Tutorials: ICP CIP-Pool 1.033)<br />
<br />
* [[Physik auf dem Computer SS 2014|Physik auf dem Computer]] <br/> JP Dr. [[Axel Arnold]], Dr. [[Olaf Lenz]]<br/>Lecture: Wed 9:45-11:15 (V57.05), Fre 9:45-11:15 (biweekly, V57.06), Tutorials: ''Time tbd'' (ICP CIP-Pool)<br />
<br />
== Lectures in Previous Terms ==<br />
<br />
* [[/2013|WS 2013/2014]]<br />
* [[/2012|WS 2012/2013 and SS 2013]]<br />
* [[/2011|WS 2011/2012 and SS 2012]]<br />
* [[/2010|WS 2010/2011 and SS 2011]]<br />
* [[/2009|WS 2009/2010 and SS 2010]]<br />
* [[/2008|WS 2008/2009 and SS 2009]]</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Publications&diff=23463Publications2018-09-30T12:00:47Z<p>Holm: /* 2015 */</p>
<hr />
<div>This page lists the publications of our working group.<br />
<br />
<div style="border:thin solid black; width:200px; background-color:#B1CED7; padding:10px; margin-bottom:2em">Visit the [[Special:ExternBibSearch|search engine]] for our database of relevant publications in the field (NOT WORKING).</div><br />
<br />
<br />
== Peer-reviewed articles ==<br />
<br />
=== 2018 ===<br />
<bibentry><br />
krishnamoorthy18c,<br />
michalowsky18a,<br />
krishnamoorthy18b,<br />
krishnamoorthy18a,<br />
smiatek18a,<br />
weeber18b,<br />
uhlig18a,<br />
weyman18a,<br />
weeber18a<br />
</bibentry><br />
<br />
=== 2017 ===<br />
<bibentry><br />
sean17a,<br />
sivaraman17b,<br />
datar17a,<br />
uhlig17a,<br />
roy17b,<br />
niskanen17a<br />
roy17a,<br />
kobayashi17a,<br />
szuttor17a,<br />
diddens17a,<br />
richter17a,<br />
bauer17a,<br />
smiatek17b,<br />
landsgesell17b,<br />
landsgesell17a,<br />
chung17a,<br />
rau17a,<br />
rud17a,<br />
michalowsky17a,<br />
niu17a,<br />
brown17a,<br />
smiatek17a,<br />
inci17a,<br />
rempfer17a<br />
</bibentry><br />
<br />
=== 2016 ===<br />
<bibentry><br />
adhikari16a,<br />
sivaraman16a,<br />
natterer16a,<br />
cruzleon16a,<br />
sivaraman16b,<br />
sivaraman16c,<br />
adhikari16b,<br />
fyta16a,<br />
schroer16a,<br />
weik16a,<br />
krishnamoorthy16a,<br />
burt16a,<br />
ilse16a,<br />
bordin16a,<br />
breitsprecher16a,<br />
lesch16b,<br />
hahn16a,<br />
degraaf16a,<br />
micciulla16a,<br />
lesch16a,<br />
sanchez16a,<br />
kreissl16a,<br />
degraaf16b,<br />
huang16a,<br />
rempfer16a,<br />
rempfer16b,<br />
kuron16a<br />
</bibentry><br />
<br />
=== 2015 ===<br />
<bibentry><br />
adhikari15a,<br />
vogele15b,<br />
hahn15a,<br />
fahrenberger15c,<br />
kosovan15a,<br />
lesch15b,<br />
pessot15a,<br />
weeber15c,<br />
fahrenberger15b,<br />
vogele15a,<br />
kratzer15a,<br />
kuron15a,<br />
lesch15a,<br />
minina15a,<br />
raafatnia15a,<br />
taudt15a,<br />
wohlfarth15a<br />
bauer15a,<br />
weeber15a,<br />
fischer15a<br />
</bibentry><br />
<br />
=== 2014 ===<br />
<bibentry><br />
adhikari14a,<br />
sivaraman14a,<br />
maier14a,<br />
fyta14a,<br />
sivaraman14b,<br />
maier14b,<br />
breitsprecher14a,<br />
breitsprecher14b,<br />
bohner14a,<br />
dommert14a,<br />
elshwishin14a,<br />
ertl14a,<br />
fahrenberger13c,<br />
fahrenberger14a,<br />
hickey14a,<br />
kesselheim14a,<br />
kratzer14a,<br />
krishnamoorthy14a,<br />
micciulla14a,<br />
minina14a,<br />
raafatnia14a,<br />
raafatnia14b,<br />
sega14a,<br />
smiatek14a,<br />
smiatek14b,<br />
smiatek14c,<br />
smiatek14d,<br />
vagias14a<br />
</bibentry><br />
<br />
=== 2013 ===<br />
<bibentry><br />
arnold13a,<br />
arnold13b,<br />
arnold13c,<br />
arnold13d,<br />
cerda13a,<br />
chakrabarti13a,<br />
dommert13a,<br />
dorozhko13a,<br />
fahrenberger13c,<br />
fyta13a,<br />
gunther13a,<br />
hecht13a,<br />
hickey13a,<br />
hoepfner13b,<br />
honig13a,<br />
klinkigt13a,<br />
koeddermann13a,<br />
kosovan13a,<br />
kratzer13a,<br />
krueger13a,<br />
mamatkulov13a,<br />
minina13a,<br />
novak13a,<br />
roehm13a,<br />
samin13a,<br />
sanchez13b,<br />
sega13a,<br />
semenov13a,<br />
smiatek13a,<br />
smiatek13b,<br />
vagias13a,<br />
vagias13b,<br />
weeber13a<br />
</bibentry><br />
<br />
=== 2012 ===<br />
<bibentry><br />
bachthaler12a,<br />
ballenegger12a,<br />
brandes12a,<br />
cerda12a,<br />
chakrabarti12a,<br />
dellesite12a,<br />
dommert12a,<br />
dorfler12a,<br />
doster12a,<br />
doster12b,<br />
fyta12a,<br />
fyta12b,<br />
hsu12a,<br />
hilfer12a,<br />
kesselheim12a,<br />
rohm12a,<br />
weeber12a,<br />
wendler12a<br />
</bibentry><br />
<br />
=== 2011 ===<br />
<bibentry><br />
gribova11a,<br />
hickey11a,<br />
wendler11b,<br />
kantorovich11b,<br />
cerda11c,<br />
klinkigt11b,<br />
sanchez11a,<br />
pyanzina11a,<br />
prokopyeva11a,<br />
kesselheim11a,<br />
luigi11a,<br />
cerda11b,<br />
cerda11a,<br />
qiao11b,<br />
mann11a,<br />
kantorovich11a,<br />
ballenegger11a,<br />
qiao11a,<br />
tabatabaei11a,<br />
kaoui11a,<br />
hyvaeluoma11a,<br />
janoschek11a,<br />
janoschek11b,<br />
gutsche11a,<br />
kunert11a,<br />
jansen11a,<br />
kalteh11a,<br />
schmieschek11a<br />
</bibentry><br />
<br />
=== 2010 ===<br />
<bibentry><br />
krekeler10a,<br />
sayar10a,<br />
hickey10a,<br />
cerda10a,<br />
qiao10a,<br />
neelov10a,<br />
grass10a,<br />
hecht10a,<br />
tyagi10a,<br />
wang10a,<br />
dommert10a,<br />
schmidt10a,<br />
schaefer10a,<br />
horsch10a,<br />
salazar10a,<br />
harting10a,<br />
narvaez10a,<br />
kunert10b,<br />
janoschek10a,<br />
hecht10b<br />
holm10a,<br />
ojedamay10a<br />
</bibentry><br />
<br />
=== 2009 ===<br />
<bibentry><br />
ahmed09c,<br />
hecht09b,<br />
dommert09a,<br />
ahmed09b,<br />
hecht09a,<br />
ahmed09a,<br />
suezen09a,<br />
prokopieva09a,<br />
smiatek09a,<br />
claudio09a<br />
ballenegger09a<br />
pyanzina09a<br />
cerda09a<br />
cerda09b<br />
cerda09c<br />
slater09a,<br />
grass09a,<br />
grass09b<br />
</bibentry><br />
<br />
=== 2008 ===<br />
<bibentry><br />
arnold08a,<br />
ballenegger08a,<br />
cerda08a,<br />
cerda08d,<br />
cerda08e,<br />
dommert08a,<br />
grass08a,<br />
gutsche08a,<br />
harting08a,<br />
harting08b,<br />
harting08c,<br />
harting08d,<br />
herrmann08a,<br />
hilfer08a,<br />
hyvaluoma08a,<br />
kantorovich08a,<br />
kunert08a,<br />
kunert08b,<br />
lenz08a,<br />
lind08a,<br />
lind08b,<br />
lind08c,<br />
pena08a,<br />
pena08b,<br />
qiao08a,<br />
seybold08a,<br />
tyagi08a<br />
</bibentry><br />
<br />
=== 2007 ===<br />
<bibentry><br />
antypov07a, <br />
biswal07a,<br />
burger07a,<br />
duran07a,<br />
duran07b,<br />
duran07c,<br />
gonzalez07a,<br />
harting07a,<br />
harting07b,<br />
harting07c,<br />
hecht07a,<br />
hecht07b,<br />
hecht07c,<br />
hecht07d,<br />
hess07a, <br />
ivanov07a,<br />
kunert07a,<br />
levin07a,<br />
lind07a,<br />
lind07b,<br />
lind07c,<br />
lind07d,<br />
lobaskin07a,<br />
parteli07a,<br />
parteli07b,<br />
parteli07c,<br />
sayar07a,<br />
tyagi07a<br />
holm06c<br />
</bibentry><br />
<br />
=== 2006 ===<br />
<bibentry><br />
almeida06a,<br />
alonso-marroquin06a,<br />
antypov06a, <br />
antypov07b,<br />
arcangelis06a,<br />
arnold06a, <br />
biswal06a,<br />
boettcher06a,<br />
burger06a,<br />
duran06a,<br />
duran06b,<br />
gerolymatou06a,<br />
gerolymatou06b,<br />
giupponi06a,<br />
gonzalez-segredo06a,<br />
gonzalez06a,<br />
gonzalez06b,<br />
gonzalez06c,<br />
gonzalez06d,<br />
gupta06a,<br />
harting06a,<br />
harting06b,<br />
harting06c,<br />
harting06d,<br />
harting06e,<br />
hecht06a,<br />
herrmann06a,<br />
herrmann06b,<br />
hess06a, <br />
hess06b, <br />
hilfer06a,<br />
hilfer06b,<br />
hilfer06c,<br />
hilfer06d,<br />
holm06a, <br />
holm06b, <br />
kun06a,<br />
kun06b,<br />
limbach06a, <br />
lind06a,<br />
luz-burgoa06a,<br />
mann06a, <br />
mcnamara06a,<br />
muehlbacher06a, <br />
muehlbacher06b, <br />
parteli06a,<br />
parteli06b,<br />
paula06a,<br />
raischel06a,<br />
raischel06b,<br />
raischel06c,<br />
schatz06a,<br />
schwammle06a,<br />
schwammle06b,<br />
schwammle06c,<br />
schwammle06d,<br />
schwammle06e,<br />
strauss06a,<br />
stukan06a, <br />
tyagi06a, <br />
tyagi06b<br />
</bibentry><br />
<br />
=== 2005 ===<br />
<bibentry><br />
alam05a,<br />
alonso-marroquin05a,<br />
alonso-marroquin05b,<br />
andrade05a,<br />
andradejr.05a,<br />
antypov05a, <br />
arnold05a, <br />
arnold05b, <br />
behera05a,<br />
behera05b,<br />
david05a,<br />
duran05a,<br />
duran05b,<br />
fonseca05a,<br />
gallas05a,<br />
garcia-rojo05a,<br />
garcia-rojo05b,<br />
garcia-rojo05c,<br />
gerolymatou05a,<br />
gonzalez05a,<br />
gonzalez05b,<br />
harting05a,<br />
hecht05a,<br />
herbst05a,<br />
herrmann05a,<br />
herrmann05b,<br />
herrmann05c,<br />
herrmann05d,<br />
herrmann05e,<br />
herrmann05f,<br />
herrmann05g,<br />
hidalgo05a,<br />
hilfer05a,<br />
hilfer05b,<br />
holm05a, <br />
holm05b, <br />
huang05a, <br />
huang05b, <br />
joseph05a,<br />
kun05a,<br />
lee05a,<br />
limbach05a, <br />
lind05a,<br />
lind05b,<br />
lind05c,<br />
luding05a,<br />
mahmoodi-baram05a,<br />
mann05a, <br />
mcnamara05a,<br />
mcnamara05b,<br />
osanloo05a,<br />
parteli05a,<br />
parteli05b,<br />
parteli05c,<br />
pena05a,<br />
raischel05a,<br />
raischel05b,<br />
rech05a,<br />
ribeiro05a,<br />
schatz05a,<br />
schwammle05a,<br />
schwammle05b,<br />
schwammle05c,<br />
schwammle05d,<br />
seybold05a,<br />
tyagi05a, <br />
tyagi05b,<br />
wackenhut05a,<br />
wackenhut05b,<br />
wackenhut05c,<br />
wittel05a<br />
</bibentry><br />
<br />
== Books ==<br />
<br />
<bibentry><br />
holm01a<br />
</bibentry><br />
[[Image:Cover-adv-com-simI.jpg|thumb|Advanced Computer Simulation Approaches for Soft Matter Sciences I]]<br />
<bibentry><br />
holm05c<br />
</bibentry><br />
[[Image:Cover-adv-com-simII.jpg|thumb|Advanced Computer Simulation Approaches for Soft Matter Sciences II]]<br />
<bibentry><br />
holm05d<br />
</bibentry><br />
[[Image:Cover-adv-com-simIII.jpg|thumb|Advanced Computer Simulation Approaches for Soft Matter Sciences III]]<br />
<bibentry><br />
holm09a<br />
</bibentry><br />
<br />
<br />
== Theses ==<br />
=== 2012 ===<br />
<bibentry><br />
dommert12c<br />
</bibentry><br />
<br />
=== 2011 ===<br />
<bibentry><br />
dietermann11a,<br />
doster11b<br />
</bibentry><br />
<br />
=== 2010 ===<br />
<bibentry><br />
kunert10a<br />
</bibentry></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Christian_Holm&diff=23461Christian Holm2018-09-28T09:15:22Z<p>Holm: /* Research */</p>
<hr />
<div>{{Person<br />
|name=Holm, Christian<br />
|title=Prof. Dr.<br />
|status=Director<br />
|phone=63701<br />
|fax=53701<br />
|room=1.046<br />
|email=holm<br />
|image=Christian_Holm.jpg<br />
|researcherid=C-2134-2009<br />
|category=holm<br />
|topical=electrokinetics<br />
|topical2=atomistics<br />
|topical3=gel<br />
|topical4=nanopore<br />
|topical5=ionic_liquids<br />
|ordering=1<br />
}}<br />
<br />
==Research==<br />
<br />
My scientific interests are especially the study of complex charged and magnetic soft matter by means of computer simulations, and the development of simple theoretical models to describe them. More precisely I am currently working on the solution properties and association behavior of flexible and semi-flexible polyelectrolytes in various solvents and under various salt concentrations and salt types. In addition I am interested in the effective pair interactions of charged colloidal particles and their phase behavior. This includes simple DNA models, and DNA protein interactions, as well as developing coarse grained models for DNA-Histone complexes. We also investigate in depth polyelectrolyte hydrogels and magnetically interacting ferrogels, as well as pure ferrofluids, where special attention is given to the structure of the solution and the magnetic response functions. Another interest is the applicability of mean-field models for the description of models with long range interactions, and possible improvements beyond the mean-field approach. This include local density functional methods based on the Poisson-Boltzmann functional, as well as strong coupling theories such as Wigner-crystal methods. In addition I am interested in the development of fast methods for the computation of long range interactions. These include pure Coulomb as well as dipolar interactions in various geometries (3D-1D), and under various boundary conditions. And least but not last, we are interested in developing fast methods to deal with fluid-structure couplings using various coupling schemes of particles to a lattice-boltzmann fluid. These can be charged fluids, as well as fluids that undergo reactions at boundaries, such as needed for active Janus-Colloids,or for catalytic particles. We also are interested to apply machine learning algorithms for the development of force-fields with almost DFT precision. <br />
<br />
Some of our research is part of collaborative research centres such as:<br />
<br />
==Member of collaborative research centers== <br />
'''SFB 716''' [http://www.sfb716.uni-stuttgart.de sfb716.uni-stuttgart.de] <br />
<br />
'''SFB 1313''' [http://www.sfb1313.uni-stuttgart.de/ sfb1313.uni-stuttgart.de] <br />
<br />
'''SFB 1333''' [http://www.crc1333.uni-stuttgart.de/ crc1333.uni-stuttgart.de] <br />
<br />
'''SimTech''' [http://www.simtech.uni-stuttgart.de SimTech Cluster of Excellence]<br />
<br />
==Publications==<br />
<!--<br />
Publications only on Publications-Site!! the <pubentries> statement import the publications vrom Publications-Site<br />
--><br />
<br />
<!--<br />
Falls das Badge hier hin soll auskommentierung und den Text hier wegmachen<br />
<div style="float:right;"><researcherID>C-2134-2009</researcherID></div><br />
--><br />
<br />
===2018===<br />
<bibentry pdflink="yes"><br />
michalowsky18a,<br />
krishnamoorthy18b,<br />
krishnamoorthy18a,<br />
smiatek18a,<br />
weeber18b,<br />
uhlig18a,<br />
weyman18a,<br />
weeber18a<br />
</bibentry><br />
<br />
===2017===<br />
<bibentry pdflink="yes"><br />
sean17a<br />
uhlig17a,<br />
roy17b,<br />
roy17a,<br />
szuttor17a,<br />
richter17a,<br />
bauer17a,<br />
landsgesell17b,<br />
landsgesell17a,<br />
chung17a,<br />
rau17a,<br />
rud17a,<br />
michalowsky17a,<br />
niu17a,<br />
brown17a,<br />
rempfer17a<br />
landsgesell17b<br />
landsgesell17a<br />
</bibentry><br />
<br />
===2016===<br />
<bibentry pdflink="yes"><br />
micciulla16a,<br />
lesch16a,<br />
huang16a,<br />
kreissl16a,<br />
sanchez16a,<br />
degraaf16a,<br />
degraaf16b,<br />
rempfer16a,<br />
rempfer16b,<br />
bauer16a,<br />
breitsprecher16a,<br />
bordin16a,<br />
ilse16a,<br />
burt16a,<br />
krishnamoorthy16a,<br />
weik16a,<br />
kuron16a<br />
</bibentry><br />
<br />
===2015===<br />
<bibentry pdflink="yes"><br />
bauer15a,<br />
breitsprecher15a,<br />
fischer15a,<br />
degraaf15b,<br />
degraaf15c,<br />
fahrenberger15b,<br />
fahrenberger15c,<br />
holm15a,<br />
kosovan15a,<br />
lesch15a,<br />
lesch15b,<br />
pessot15a,<br />
raafatnia15a,<br />
ryzhkov15a,<br />
vogele15a,<br />
vogele15b,<br />
weeber15a,<br />
weeber15c<br />
</bibentry><br />
<br />
===2014===<br />
<bibentry pdflink="yes"><br />
breitsprecher14a,<br />
breitsprecher14b,<br />
dommert14a,<br />
ertl14a,<br />
fahrenberger14a,<br />
fahrenberger14b,<br />
hickey14a,<br />
kesselheim14a,<br />
krishnamoorthy14a,<br />
micciulla14a,<br />
raafatnia14a,<br />
raafatnia14b,<br />
sega14a,<br />
smiatek14a,<br />
smiatek14d,<br />
vagias14a<br />
</bibentry><br />
<br />
===2013===<br />
<bibentry pdflink="yes"><br />
arnold13a,<br />
arnold13b,<br />
arnold13c,<br />
cerda13a,<br />
chakrabarti13a,<br />
dommert12b,<br />
dommert13a,<br />
hickey13a,<br />
hoepfner13b,<br />
klinkigt13a,<br />
kosovan13a,<br />
samin13a,<br />
sanchez13b,<br />
sega13a,<br />
semenov13a,<br />
vagias13a,<br />
vagias13b,<br />
weeber13a<br />
</bibentry><br />
<br />
===2012===<br />
<bibentry pdflink="yes"><br />
kesselheim12a,<br />
bachthaler12a,<br />
dellesite12a,<br />
cerda12a,<br />
weeber12a,<br />
dommert12a,<br />
wendler12a,<br />
ballenegger12a<br />
</bibentry><br />
<br />
===2011===<br />
<bibentry pdflink="yes"><br />
qiao11b,<br />
qiao11a,<br />
gribova11a,<br />
mann11a,<br />
hickey11a,<br />
wendler11b,<br />
kantorovich11b,<br />
cerda11c,<br />
cerda11b,<br />
klinkigt11b,<br />
tabatabaei11a,<br />
sanchez11a,<br />
pyanzina11a,<br />
prokopyeva11a,<br />
kesselheim11a,<br />
kantorovich11a,<br />
cerda11a,<br />
ballenegger11a,<br />
luigi11a<br />
</bibentry><br />
<br />
===2010===<br />
<bibentry pdflink="yes"><br />
neelov10a,<br />
grass10a,<br />
krekeler10a,<br />
tyagi10a,<br />
schmidt10a,<br />
dommert10a,<br />
wang10a,<br />
sayar10a,<br />
qiao10a,<br />
hickey10a,<br />
cerda10a<br />
</bibentry><br />
<br />
===2009===<br />
<bibentry pdflink="yes"><br />
dommert09a,<br />
suezen09a,<br />
pyanzina09a,<br />
prokopieva09a,<br />
smiatek09a,<br />
claudio09a,<br />
pyanzina09a,<br />
cerda09b,<br />
cerda09c,<br />
slater09a,<br />
grass09a,<br />
grass09b<br />
</bibentry><br />
<br />
===2008===<br />
<bibentry pdflink="yes">cerda08d,cerda08e,cerda08a,grass08a,qiao08a,kantorovich08a,lenz08a,ballenegger08a,tyagi08a</bibentry><br />
<br />
===2007===<br />
<bibentry pdflink="yes">tyagi07a,ivanov07a,lobaskin07a,antypov07a, hess07a, sayar07a</bibentry><br />
<br />
===2006===<br />
<bibentry pdflink="yes">antypov07b,holm06a, holm06b, antypov06a, arnold06a, hess06a, hess06b, limbach06a, mann06a, muehlbacher06a, muehlbacher06b, stukan06a</bibentry><br />
<br />
===2005===<br />
<bibentry pdflink="yes">antypov05a, arnold05a, arnold05b, holm05a, holm05b, huang05a, huang05b, limbach05a, mann05a</bibentry><br />
<br />
===2004===<br />
<bibentry pdflink="yes">barbosa04a, espresso03a, holm04a, holm04b, holm04c, huang04a, ivanov04a, limbach04a, limbach04b, lobaskin04b, mann04a, messina04a, naji04b</bibentry><br />
<br />
===2003===<br />
<bibentry pdflink="yes">deserno02b, holm03a, jimenez03a, limbach03a, messina03a, wang03a, wang03b, wang03c</bibentry><br />
<br />
===2002===<br />
<bibentry pdflink="yes">arnold02a, arnold02b, arnold02c, arnold02d, dejoannis02a, deserno02a, holm02a, limbach02a, limbach02c, messina02a, messina02c, messina02d, messina02e, wang02a</bibentry><br />
<br />
===2001===<br />
<bibentry pdflink="yes">deserno00c, deserno01a, deserno01b, deserno01c, holm01b, holm01c, limbach01a, messina01a, messina01b, wang01a</bibentry><br />
<br />
===2000===<br />
<bibentry pdflink="yes">barbosa00a, deserno00a, deserno99b, messina00a, messina00b</bibentry><br />
<br />
===1999===<br />
<bibentry pdflink="yes">holm99a, holm99b, bittner99a, bittner99b, micka99a</bibentry><br />
<br />
===1998 and before===<br />
<bibentry pdflink="yes"><br />
holm98a, holm98b, bittner98a, bittner98b, deserno98a, deserno98b,<br />
holm97a, holm97c, holm97d, holm97e,<br />
holm96a, holm96b, holm96c, holm95c,<br />
holm95a, holm95b, <br />
holm94a, holm94b, holm94c, holm93d,<br />
holm93a, holm93b, holm93c, adler93a,<br />
holm91a, holm91b,<br />
holm90a, holm90b, holm90c, <br />
holm89a, finkelstein89a,<br />
holm88a, holm88b,<br />
holm87a, finkelstein87a,<br />
holm86a, eidson86a, finkelstein86a,<br />
holm85a</bibentry></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Advanced_Simulation_Methods_SS_2018&diff=23281Advanced Simulation Methods SS 20182018-06-22T10:31:27Z<p>Holm: /* Literature */</p>
<hr />
<div><br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students should send an email to [[Maria Fyta]] as soon as possible.<br />
<br><br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).</b>}}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture and Tutorials (2 SWS in total)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]], JP. Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]], Dr. [[David Sean]]<br />
;Course language<br />
:English or German<br />
;Location<br />
:ICP, Allmandring 3; Room: ICP Meeting Room<br />
;Time<br />
:(see below)<br />
The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP. Dr. [[Maria Fyta]] and will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules.<br />
The students can work in groups. All groups should write a report on each module, which they should submit to the responsible person for each module by the deadline set for each module.<br />
<!-- [[Maria Fyta]] no later than Friday July 15, 2016. The report does not need to be longer than 20 pages.--><br />
<br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students write an Email to [[Maria Fyta]] until TBA.</b>}}<br />
<br />
== Module 1: [[Maria Fyta]], [[Frank Uhlig]], Inter-atomic interactions modeled with quantum mechanical simulations ==<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<!--ue 05.04.2016 at 14:00 in the ICP meeting room.--><br />
<br />
Tutorials: TBA in the ICP CIP-Pool.<br />
<br />
Talks: TBA am in the ICP meeting room.<br />
<br />
=== Description ===<br />
<br />
This module focuses on the influence of using quantum mechanical simulations. The quantum mechanical schemes which will be applied in this module are based on density functional theory (DFT). This method allows the investigation of the electronic properties of a system. An understanding of the method, an analysis of the results from the simulations is the main goal of this module. The analysis of the simulations should be written up in a report. The talk will be a presentation of a DFT-related journal paper. For this, one of the following papers can be chosen:<br />
<br />
* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J. Klimeš and A. Michaelides, The Journal of Chemical Physics 137, 120901 (2012); doi: 10.1063/1.4754130<br />
* Challenges for Density Functional Theory, A.J. Cohen, P. Mori-Sanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.<br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module please do not hesitate to contact [[Maria Fyta]]. For practical guidance regarding the simulations [[Frank Uhlig]].<br />
<br />
=== Density functional theory and exchange-correlation functionals ===<br />
<br />
==== Description ====<br />
<br />
Many modern catalyses are performed using noble metals. In particular at the<br />
surface of these catalysts, which come in a multitude of shapes and chemical<br />
composition. The overall catalysis is determined by many factors, including the<br />
actual reactivity of chemical species at the surface, adsorption of reactants<br />
and desorption of products, as well as kinetics of the diffusion on the surface.<br />
<br />
In this exercise you will look at the desorption behavior of hydrogen gas from<br />
the surface of noble metals. This process is important in the production of<br />
hydrogen gas for energy storage applications [1]. However, modeling this process<br />
using modern methods of quantum-mechanical density functional theory (DFT) is<br />
very challenging. Only very advanced and quite recent density functionals are<br />
able to describe the long-range dispersion interactions [2]. Hence, effective<br />
methods based on pair potentials have been developed. These methods can achieve<br />
comparable accuracy to more ab initio methods while coming at a signifcantly<br />
lower computational effort [3,4].<br />
<br />
Your task is to develop such a pair-wise dispersion correction for the<br />
interaction of hydrogen gas with a metal surface. The first step is to<br />
understand and document the metallic behavior of your metal substrate, followed<br />
by investigation of the performance of common DFT functionals for the desorption<br />
process, and finally developing a dispersion correction by determining<br />
individual dispersion coefficients for the involved species [5].<br />
<br />
[1] https://dx.doi.org/10.1038/ncomms6848<br />
<br />
[2] https://dx.doi.org/10.1063/1.4754130<br />
<br />
[3] https://dx.doi.org/10.1103/PhysRevLett.102.073005<br />
<br />
[4] https://dx.doi.org/10.1063/1.3382344<br />
<br />
[5] https://dx.doi.org/10.1063/1.2746031<br />
<br />
[6] [[:Media:Asm_2018_info.txt|ASM tutorial info links]]<br />
<br />
==== Literature ====<br />
<br />
* A bird's-eye view of density-functional theory, Klaus Capelle, arXiv:cond-mat/0211443 (2002).<br />
* Self-Consistent Equations Including Exchange and Correlation Effects, W. Kohn and L.J. Sham, , Phys. Rev. (140), A1133 (1965).<br />
* Understanding and Reducing Errors in Density Functional Calculations, Min-Cheol Kim, Eunji Sim, and Kieron Burke, Phys. Rev. Lett. 111, 073003 (2013).<br />
<!--* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J Klimeš, A Michaelides, J. Chem. Phys. 137, 120901 (2012).--><br />
* An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases, V.R. Cooper, T. Thonhauser, and D.C. Langreth, J. Chem. Phys. 128, 204102 (2008).<br />
* On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit, B. Santra, A. Michaelides, and M. Scheffler, J. Chem. Phys. 127, 184104 (2007).<br />
* On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level, I. Dąbkowska, P. Jurečka, and P. Hobza, J. Chem. Phys. 122, 204322 (2005).<br />
<br />
=== Report ===<br />
<br />
Please write a report 5-10 pages containing and discussing your results and hand it in by Friday TBA.<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 2: [[Maria Fyta]], [[Narayanan Krishnamoorthy Anand]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: 18.05.2018 in the ICP meeting room. <br />
<br />
Final meeting: 15.06.2018 in the ICP meeting room.<br />
<br />
Deadline for reports: 15.06.2018<br />
=== Description ===<br />
<br />
This module focuses on atomistic Molecular Dynamics simulations and the study of biological co-solutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological co-solutes, often also called osmolytes are omnipresent in biological cells. A main function of these small-weight organic <br />
molecules is given by the protection of protein structures under harsh environmental conditions (protein stabilizers) or the denaturation of proteins (protein denaturants). The underlying mechanism leading to these effects is still unknown. It has been often discussed that osmolytes have a significant impact on the aqueous solution.<br />
The module consists of model development, simulation, analysis and oral and written presentation part. <br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Narayanan Krishnamoorthy Anand]].<br />
<br />
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the Kirkwood-Buff theory which can be well applied to computer simulations.<br />
The students should study the literature given below and present their findings. The presentation should at a minimum contain an introduction to Kirkwood-Buff theory in the context of the simulations.<br />
<br />
==== Literature ====<br />
<br />
* D. R. Canchi and A. E. Garcia, "Co-solvent effects on protein stability", Ann. Rev. Phys. Chem. 64. 273 (2013)<br />
* J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951) <br />
* V. Pierce, M. Kang, M. Aburi, S. Weerasinghe and P. E. Smith, "Recent applications of Kirkwood–Buff theory to biological systems", Cell Biochem. Biophys. 50, 1 (2008)<br />
* S. Weerasinghe and P. E. Smith, "A Kirkwood–Buff derived force field for sodium chloride in water", The Journal of Chemical Physics 119, 11342 (2003).<br />
* J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)<br />
* J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)<br />
* T. Kobayashi <i>et al</i>, "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches", Phys.Chem.Chem.Phys. 19, 18924 (2017)<br />
<br />
=== Part 2: Model Development and Simulations ===<br />
<br />
==== Description ====<br />
<br />
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will develop Generalized Amber Force Fields (GAFF) [http://ambermd.org/antechamber/gaff.html] with the help of the ACPYPE program [http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder] for the osmolytes (urea, hydroxyectoine, ectoine) which will be used for the study of solvent properties like the thermodynamics of hydrogen bonding ans the diffusivity according to J. Phys. Chem. B 118, 771 (2014).<br />
In comparison to pure water, the students will analyze several water parameters and elucidate the differences in presence of osmolytes and their concentration dependent behavior. The Kirkwood-Buff theory will be used to calculate derivatives of the activity coefficients and the derivative of the chemical activity for the osmolytes. <br />
<br />
==== Force Fields for ectoine and hydroxyectoine ====<br />
<br />
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}<br />
* {{Download| hectoinzwittmp2.gro |gro-File for Hydroxyectoine}}<br />
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}<br />
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}<br />
<br />
=== Part 3: Tasks ===<br />
1. Implement the developed force fields for the osmolytes (urea, ectoine and hydroxyectoine) in combination with the SPC/E water model. After energy minimization and warm up, run 20-30 ns simulations with GROMACS for osmolyte concentrations between c = 0 - 6 M.<br />
<br />
2. Study the following properties for the different osmolytes and concentrations:<br />
* diffusion coefficients<br />
* hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs<br />
* water mean relaxation times<br />
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?<br />
<br />
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.<br />
Use this information to compute the<br />
* Kirkwood-Buff integrals<br />
* derivatives of the chemical activity<br />
* derivatives of the activity coefficient<br />
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004). <br />
<br />
==== Literature ====<br />
<br />
* D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media", J. Phys. Chem. B 110, 4393 (2006)<br />
* J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem. 25, 1157 (2004)<br />
<br />
=== Report ===<br />
<br />
Please write a report of about 5 pages containing and discussing your results and hand it in until TBA.<br />
<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 3: [[Christian Holm]], Electrostatics, Lattice Boltzmann, and Electrokinetics==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: TBA in the ICP meeting room. <br />
<br />
Final meeting: TBA in the ICP meeting room. <br />
<br />
=== Description ===<br />
<br />
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people.<br />
It consists of one lecture on electrostatic algorithms, simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation<br />
and hand in one report. The Module 3 consists of three parts:<br />
<br />
=== Contact ===<br />
If you have any questions regarding the organisation or content of this module please do not hesitate to contact [[Christian Holm]].<br />
For questions regarding the practical part of the module and technical help contact [[David Sean]].<br />
<br />
=== Part 1: Electrostatics ===<br />
==== Description ====<br />
This part is about the theory of electrostatic algorithms for molecular dynamics simulations.<br />
It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald<br />
methods. To this end the students should read the referenced literature. [[Christian Holm]] will give an hour long lecture. Afterwards we will discuss the content and try to resolve open questions. The presentation should foster the students understanding of the P3M method as well<br />
as give them an overview of its performance compared to other modern electrostatics methods.<br />
<br />
==== Literature ====<br />
:* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''. <br /> [[Media:longrange.pdf|[PDF]]] (15.4 MB) <br /><br />
<bibentry>deserno98a,arnold13b,arnold05a</bibentry><br />
<br />
=== Part 2: Slit Pore ===<br />
==== Description ====<br />
[[File:Slitpore.png|550px|right|Electroosmotic flow in a slit pore]]<br />
This part is practical. It is concerned with the movement of ions in an charged slit pore.<br />
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]<br />
which is recommended reading. A slit pore consists of two infinite charge walls as shown<br />
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].<br />
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented<br />
by charge Week-Chandler-Anderson spheres. In addition to the charge on the walls, the ions are also subject to an external<br />
electrical field parallel to the walls. Electrostatics should be handled by the P3M algorithm.<br />
A set of realistic parameters and an more in detail description of the system can be found in the<br />
thesis.<br />
You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit<br />
pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high<br />
salt limit (Debye-Hueckel-Limit). Calculate the ion profiles in one or both of these cases and compare the results with<br />
the simulation.<br />
<br />
==== Instructions and Literature ====<br />
General part and parts 4 & 6 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
Georg Rempfer, {{Download|BSc_thesis_rempfer.pdf|"Lattice-Boltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart<br />
<bibentry>grass09c</bibentry><br />
<br />
=== Part 3: Electrophoresis of Polyelectrolytes ===<br />
==== Description ====<br />
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions.<br />
Set up a system consisting of a charge polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled<br />
the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer<br />
for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and<br />
experimental results (see literature).<br />
<br />
==== Instructions and Literatur ====<br />
General part and part 5 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
<bibentry>grass08a, grass09c</bibentry><br />
<br />
=== Report ===<br />
<br />
At the final meeting day of this module, one group will give a presentation about the learned and performed work. In addition, they write a report of about 5 pages containing and discussing the obtained results and hand it in together with the reports of the other modules at the end of the course (see above).<br />
<br />
The final report is due electronically Friday night, TBA<br />
<br />
<br />
<br />
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.--></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:Longrange.pdf&diff=23280File:Longrange.pdf2018-06-22T10:28:18Z<p>Holm: </p>
<hr />
<div></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Advanced_Simulation_Methods_SS_2018&diff=23279Advanced Simulation Methods SS 20182018-06-22T10:27:51Z<p>Holm: /* Literature */</p>
<hr />
<div><br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students should send an email to [[Maria Fyta]] as soon as possible.<br />
<br><br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).</b>}}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture and Tutorials (2 SWS in total)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]], JP. Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]], Dr. [[David Sean]]<br />
;Course language<br />
:English or German<br />
;Location<br />
:ICP, Allmandring 3; Room: ICP Meeting Room<br />
;Time<br />
:(see below)<br />
The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP. Dr. [[Maria Fyta]] and will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules.<br />
The students can work in groups. All groups should write a report on each module, which they should submit to the responsible person for each module by the deadline set for each module.<br />
<!-- [[Maria Fyta]] no later than Friday July 15, 2016. The report does not need to be longer than 20 pages.--><br />
<br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students write an Email to [[Maria Fyta]] until TBA.</b>}}<br />
<br />
== Module 1: [[Maria Fyta]], [[Frank Uhlig]], Inter-atomic interactions modeled with quantum mechanical simulations ==<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<!--ue 05.04.2016 at 14:00 in the ICP meeting room.--><br />
<br />
Tutorials: TBA in the ICP CIP-Pool.<br />
<br />
Talks: TBA am in the ICP meeting room.<br />
<br />
=== Description ===<br />
<br />
This module focuses on the influence of using quantum mechanical simulations. The quantum mechanical schemes which will be applied in this module are based on density functional theory (DFT). This method allows the investigation of the electronic properties of a system. An understanding of the method, an analysis of the results from the simulations is the main goal of this module. The analysis of the simulations should be written up in a report. The talk will be a presentation of a DFT-related journal paper. For this, one of the following papers can be chosen:<br />
<br />
* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J. Klimeš and A. Michaelides, The Journal of Chemical Physics 137, 120901 (2012); doi: 10.1063/1.4754130<br />
* Challenges for Density Functional Theory, A.J. Cohen, P. Mori-Sanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.<br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module please do not hesitate to contact [[Maria Fyta]]. For practical guidance regarding the simulations [[Frank Uhlig]].<br />
<br />
=== Density functional theory and exchange-correlation functionals ===<br />
<br />
==== Description ====<br />
<br />
Many modern catalyses are performed using noble metals. In particular at the<br />
surface of these catalysts, which come in a multitude of shapes and chemical<br />
composition. The overall catalysis is determined by many factors, including the<br />
actual reactivity of chemical species at the surface, adsorption of reactants<br />
and desorption of products, as well as kinetics of the diffusion on the surface.<br />
<br />
In this exercise you will look at the desorption behavior of hydrogen gas from<br />
the surface of noble metals. This process is important in the production of<br />
hydrogen gas for energy storage applications [1]. However, modeling this process<br />
using modern methods of quantum-mechanical density functional theory (DFT) is<br />
very challenging. Only very advanced and quite recent density functionals are<br />
able to describe the long-range dispersion interactions [2]. Hence, effective<br />
methods based on pair potentials have been developed. These methods can achieve<br />
comparable accuracy to more ab initio methods while coming at a signifcantly<br />
lower computational effort [3,4].<br />
<br />
Your task is to develop such a pair-wise dispersion correction for the<br />
interaction of hydrogen gas with a metal surface. The first step is to<br />
understand and document the metallic behavior of your metal substrate, followed<br />
by investigation of the performance of common DFT functionals for the desorption<br />
process, and finally developing a dispersion correction by determining<br />
individual dispersion coefficients for the involved species [5].<br />
<br />
[1] https://dx.doi.org/10.1038/ncomms6848<br />
<br />
[2] https://dx.doi.org/10.1063/1.4754130<br />
<br />
[3] https://dx.doi.org/10.1103/PhysRevLett.102.073005<br />
<br />
[4] https://dx.doi.org/10.1063/1.3382344<br />
<br />
[5] https://dx.doi.org/10.1063/1.2746031<br />
<br />
[6] [[:Media:Asm_2018_info.txt|ASM tutorial info links]]<br />
<br />
==== Literature ====<br />
<br />
* A bird's-eye view of density-functional theory, Klaus Capelle, arXiv:cond-mat/0211443 (2002).<br />
* Self-Consistent Equations Including Exchange and Correlation Effects, W. Kohn and L.J. Sham, , Phys. Rev. (140), A1133 (1965).<br />
* Understanding and Reducing Errors in Density Functional Calculations, Min-Cheol Kim, Eunji Sim, and Kieron Burke, Phys. Rev. Lett. 111, 073003 (2013).<br />
<!--* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J Klimeš, A Michaelides, J. Chem. Phys. 137, 120901 (2012).--><br />
* An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases, V.R. Cooper, T. Thonhauser, and D.C. Langreth, J. Chem. Phys. 128, 204102 (2008).<br />
* On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit, B. Santra, A. Michaelides, and M. Scheffler, J. Chem. Phys. 127, 184104 (2007).<br />
* On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level, I. Dąbkowska, P. Jurečka, and P. Hobza, J. Chem. Phys. 122, 204322 (2005).<br />
<br />
=== Report ===<br />
<br />
Please write a report 5-10 pages containing and discussing your results and hand it in by Friday TBA.<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 2: [[Maria Fyta]], [[Narayanan Krishnamoorthy Anand]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: 18.05.2018 in the ICP meeting room. <br />
<br />
Final meeting: 15.06.2018 in the ICP meeting room.<br />
<br />
Deadline for reports: 15.06.2018<br />
=== Description ===<br />
<br />
This module focuses on atomistic Molecular Dynamics simulations and the study of biological co-solutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological co-solutes, often also called osmolytes are omnipresent in biological cells. A main function of these small-weight organic <br />
molecules is given by the protection of protein structures under harsh environmental conditions (protein stabilizers) or the denaturation of proteins (protein denaturants). The underlying mechanism leading to these effects is still unknown. It has been often discussed that osmolytes have a significant impact on the aqueous solution.<br />
The module consists of model development, simulation, analysis and oral and written presentation part. <br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Narayanan Krishnamoorthy Anand]].<br />
<br />
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the Kirkwood-Buff theory which can be well applied to computer simulations.<br />
The students should study the literature given below and present their findings. The presentation should at a minimum contain an introduction to Kirkwood-Buff theory in the context of the simulations.<br />
<br />
==== Literature ====<br />
<br />
* D. R. Canchi and A. E. Garcia, "Co-solvent effects on protein stability", Ann. Rev. Phys. Chem. 64. 273 (2013)<br />
* J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951) <br />
* V. Pierce, M. Kang, M. Aburi, S. Weerasinghe and P. E. Smith, "Recent applications of Kirkwood–Buff theory to biological systems", Cell Biochem. Biophys. 50, 1 (2008)<br />
* S. Weerasinghe and P. E. Smith, "A Kirkwood–Buff derived force field for sodium chloride in water", The Journal of Chemical Physics 119, 11342 (2003).<br />
* J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)<br />
* J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)<br />
* T. Kobayashi <i>et al</i>, "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches", Phys.Chem.Chem.Phys. 19, 18924 (2017)<br />
<br />
=== Part 2: Model Development and Simulations ===<br />
<br />
==== Description ====<br />
<br />
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will develop Generalized Amber Force Fields (GAFF) [http://ambermd.org/antechamber/gaff.html] with the help of the ACPYPE program [http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder] for the osmolytes (urea, hydroxyectoine, ectoine) which will be used for the study of solvent properties like the thermodynamics of hydrogen bonding ans the diffusivity according to J. Phys. Chem. B 118, 771 (2014).<br />
In comparison to pure water, the students will analyze several water parameters and elucidate the differences in presence of osmolytes and their concentration dependent behavior. The Kirkwood-Buff theory will be used to calculate derivatives of the activity coefficients and the derivative of the chemical activity for the osmolytes. <br />
<br />
==== Force Fields for ectoine and hydroxyectoine ====<br />
<br />
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}<br />
* {{Download| hectoinzwittmp2.gro |gro-File for Hydroxyectoine}}<br />
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}<br />
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}<br />
<br />
=== Part 3: Tasks ===<br />
1. Implement the developed force fields for the osmolytes (urea, ectoine and hydroxyectoine) in combination with the SPC/E water model. After energy minimization and warm up, run 20-30 ns simulations with GROMACS for osmolyte concentrations between c = 0 - 6 M.<br />
<br />
2. Study the following properties for the different osmolytes and concentrations:<br />
* diffusion coefficients<br />
* hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs<br />
* water mean relaxation times<br />
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?<br />
<br />
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.<br />
Use this information to compute the<br />
* Kirkwood-Buff integrals<br />
* derivatives of the chemical activity<br />
* derivatives of the activity coefficient<br />
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004). <br />
<br />
==== Literature ====<br />
<br />
* D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media", J. Phys. Chem. B 110, 4393 (2006)<br />
* J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem. 25, 1157 (2004)<br />
<br />
=== Report ===<br />
<br />
Please write a report of about 5 pages containing and discussing your results and hand it in until TBA.<br />
<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 3: [[Christian Holm]], Electrostatics, Lattice Boltzmann, and Electrokinetics==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: TBA in the ICP meeting room. <br />
<br />
Final meeting: TBA in the ICP meeting room. <br />
<br />
=== Description ===<br />
<br />
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people.<br />
It consists of one lecture on electrostatic algorithms, simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation<br />
and hand in one report. The Module 3 consists of three parts:<br />
<br />
=== Contact ===<br />
If you have any questions regarding the organisation or content of this module please do not hesitate to contact [[Christian Holm]].<br />
For questions regarding the practical part of the module and technical help contact [[David Sean]].<br />
<br />
=== Part 1: Electrostatics ===<br />
==== Description ====<br />
This part is about the theory of electrostatic algorithms for molecular dynamics simulations.<br />
It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald<br />
methods. To this end the students should read the referenced literature. [[Christian Holm]] will give an hour long lecture. Afterwards we will discuss the content and try to resolve open questions. The presentation should foster the students understanding of the P3M method as well<br />
as give them an overview of its performance compared to other modern electrostatics methods.<br />
<br />
==== Literature ====<br />
:* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''. [[Media:longrange.pdf]]<br /><br />
<bibentry>deserno98a,arnold13b,arnold05a</bibentry><br />
<br />
=== Part 2: Slit Pore ===<br />
==== Description ====<br />
[[File:Slitpore.png|550px|right|Electroosmotic flow in a slit pore]]<br />
This part is practical. It is concerned with the movement of ions in an charged slit pore.<br />
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]<br />
which is recommended reading. A slit pore consists of two infinite charge walls as shown<br />
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].<br />
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented<br />
by charge Week-Chandler-Anderson spheres. In addition to the charge on the walls, the ions are also subject to an external<br />
electrical field parallel to the walls. Electrostatics should be handled by the P3M algorithm.<br />
A set of realistic parameters and an more in detail description of the system can be found in the<br />
thesis.<br />
You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit<br />
pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high<br />
salt limit (Debye-Hueckel-Limit). Calculate the ion profiles in one or both of these cases and compare the results with<br />
the simulation.<br />
<br />
==== Instructions and Literature ====<br />
General part and parts 4 & 6 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
Georg Rempfer, {{Download|BSc_thesis_rempfer.pdf|"Lattice-Boltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart<br />
<bibentry>grass09c</bibentry><br />
<br />
=== Part 3: Electrophoresis of Polyelectrolytes ===<br />
==== Description ====<br />
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions.<br />
Set up a system consisting of a charge polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled<br />
the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer<br />
for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and<br />
experimental results (see literature).<br />
<br />
==== Instructions and Literatur ====<br />
General part and part 5 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
<bibentry>grass08a, grass09c</bibentry><br />
<br />
=== Report ===<br />
<br />
At the final meeting day of this module, one group will give a presentation about the learned and performed work. In addition, they write a report of about 5 pages containing and discussing the obtained results and hand it in together with the reports of the other modules at the end of the course (see above).<br />
<br />
The final report is due electronically Friday night, TBA<br />
<br />
<br />
<br />
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.--></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Advanced_Simulation_Methods_SS_2018&diff=23278Advanced Simulation Methods SS 20182018-06-22T10:26:38Z<p>Holm: /* Literature */</p>
<hr />
<div><br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students should send an email to [[Maria Fyta]] as soon as possible.<br />
<br><br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).</b>}}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture and Tutorials (2 SWS in total)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]], JP. Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]], Dr. [[David Sean]]<br />
;Course language<br />
:English or German<br />
;Location<br />
:ICP, Allmandring 3; Room: ICP Meeting Room<br />
;Time<br />
:(see below)<br />
The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP. Dr. [[Maria Fyta]] and will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules.<br />
The students can work in groups. All groups should write a report on each module, which they should submit to the responsible person for each module by the deadline set for each module.<br />
<!-- [[Maria Fyta]] no later than Friday July 15, 2016. The report does not need to be longer than 20 pages.--><br />
<br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students write an Email to [[Maria Fyta]] until TBA.</b>}}<br />
<br />
== Module 1: [[Maria Fyta]], [[Frank Uhlig]], Inter-atomic interactions modeled with quantum mechanical simulations ==<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<!--ue 05.04.2016 at 14:00 in the ICP meeting room.--><br />
<br />
Tutorials: TBA in the ICP CIP-Pool.<br />
<br />
Talks: TBA am in the ICP meeting room.<br />
<br />
=== Description ===<br />
<br />
This module focuses on the influence of using quantum mechanical simulations. The quantum mechanical schemes which will be applied in this module are based on density functional theory (DFT). This method allows the investigation of the electronic properties of a system. An understanding of the method, an analysis of the results from the simulations is the main goal of this module. The analysis of the simulations should be written up in a report. The talk will be a presentation of a DFT-related journal paper. For this, one of the following papers can be chosen:<br />
<br />
* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J. Klimeš and A. Michaelides, The Journal of Chemical Physics 137, 120901 (2012); doi: 10.1063/1.4754130<br />
* Challenges for Density Functional Theory, A.J. Cohen, P. Mori-Sanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.<br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module please do not hesitate to contact [[Maria Fyta]]. For practical guidance regarding the simulations [[Frank Uhlig]].<br />
<br />
=== Density functional theory and exchange-correlation functionals ===<br />
<br />
==== Description ====<br />
<br />
Many modern catalyses are performed using noble metals. In particular at the<br />
surface of these catalysts, which come in a multitude of shapes and chemical<br />
composition. The overall catalysis is determined by many factors, including the<br />
actual reactivity of chemical species at the surface, adsorption of reactants<br />
and desorption of products, as well as kinetics of the diffusion on the surface.<br />
<br />
In this exercise you will look at the desorption behavior of hydrogen gas from<br />
the surface of noble metals. This process is important in the production of<br />
hydrogen gas for energy storage applications [1]. However, modeling this process<br />
using modern methods of quantum-mechanical density functional theory (DFT) is<br />
very challenging. Only very advanced and quite recent density functionals are<br />
able to describe the long-range dispersion interactions [2]. Hence, effective<br />
methods based on pair potentials have been developed. These methods can achieve<br />
comparable accuracy to more ab initio methods while coming at a signifcantly<br />
lower computational effort [3,4].<br />
<br />
Your task is to develop such a pair-wise dispersion correction for the<br />
interaction of hydrogen gas with a metal surface. The first step is to<br />
understand and document the metallic behavior of your metal substrate, followed<br />
by investigation of the performance of common DFT functionals for the desorption<br />
process, and finally developing a dispersion correction by determining<br />
individual dispersion coefficients for the involved species [5].<br />
<br />
[1] https://dx.doi.org/10.1038/ncomms6848<br />
<br />
[2] https://dx.doi.org/10.1063/1.4754130<br />
<br />
[3] https://dx.doi.org/10.1103/PhysRevLett.102.073005<br />
<br />
[4] https://dx.doi.org/10.1063/1.3382344<br />
<br />
[5] https://dx.doi.org/10.1063/1.2746031<br />
<br />
[6] [[:Media:Asm_2018_info.txt|ASM tutorial info links]]<br />
<br />
==== Literature ====<br />
<br />
* A bird's-eye view of density-functional theory, Klaus Capelle, arXiv:cond-mat/0211443 (2002).<br />
* Self-Consistent Equations Including Exchange and Correlation Effects, W. Kohn and L.J. Sham, , Phys. Rev. (140), A1133 (1965).<br />
* Understanding and Reducing Errors in Density Functional Calculations, Min-Cheol Kim, Eunji Sim, and Kieron Burke, Phys. Rev. Lett. 111, 073003 (2013).<br />
<!--* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J Klimeš, A Michaelides, J. Chem. Phys. 137, 120901 (2012).--><br />
* An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases, V.R. Cooper, T. Thonhauser, and D.C. Langreth, J. Chem. Phys. 128, 204102 (2008).<br />
* On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit, B. Santra, A. Michaelides, and M. Scheffler, J. Chem. Phys. 127, 184104 (2007).<br />
* On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level, I. Dąbkowska, P. Jurečka, and P. Hobza, J. Chem. Phys. 122, 204322 (2005).<br />
<br />
=== Report ===<br />
<br />
Please write a report 5-10 pages containing and discussing your results and hand it in by Friday TBA.<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 2: [[Maria Fyta]], [[Narayanan Krishnamoorthy Anand]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: 18.05.2018 in the ICP meeting room. <br />
<br />
Final meeting: 15.06.2018 in the ICP meeting room.<br />
<br />
Deadline for reports: 15.06.2018<br />
=== Description ===<br />
<br />
This module focuses on atomistic Molecular Dynamics simulations and the study of biological co-solutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological co-solutes, often also called osmolytes are omnipresent in biological cells. A main function of these small-weight organic <br />
molecules is given by the protection of protein structures under harsh environmental conditions (protein stabilizers) or the denaturation of proteins (protein denaturants). The underlying mechanism leading to these effects is still unknown. It has been often discussed that osmolytes have a significant impact on the aqueous solution.<br />
The module consists of model development, simulation, analysis and oral and written presentation part. <br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Narayanan Krishnamoorthy Anand]].<br />
<br />
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the Kirkwood-Buff theory which can be well applied to computer simulations.<br />
The students should study the literature given below and present their findings. The presentation should at a minimum contain an introduction to Kirkwood-Buff theory in the context of the simulations.<br />
<br />
==== Literature ====<br />
<br />
* D. R. Canchi and A. E. Garcia, "Co-solvent effects on protein stability", Ann. Rev. Phys. Chem. 64. 273 (2013)<br />
* J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951) <br />
* V. Pierce, M. Kang, M. Aburi, S. Weerasinghe and P. E. Smith, "Recent applications of Kirkwood–Buff theory to biological systems", Cell Biochem. Biophys. 50, 1 (2008)<br />
* S. Weerasinghe and P. E. Smith, "A Kirkwood–Buff derived force field for sodium chloride in water", The Journal of Chemical Physics 119, 11342 (2003).<br />
* J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)<br />
* J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)<br />
* T. Kobayashi <i>et al</i>, "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches", Phys.Chem.Chem.Phys. 19, 18924 (2017)<br />
<br />
=== Part 2: Model Development and Simulations ===<br />
<br />
==== Description ====<br />
<br />
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will develop Generalized Amber Force Fields (GAFF) [http://ambermd.org/antechamber/gaff.html] with the help of the ACPYPE program [http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder] for the osmolytes (urea, hydroxyectoine, ectoine) which will be used for the study of solvent properties like the thermodynamics of hydrogen bonding ans the diffusivity according to J. Phys. Chem. B 118, 771 (2014).<br />
In comparison to pure water, the students will analyze several water parameters and elucidate the differences in presence of osmolytes and their concentration dependent behavior. The Kirkwood-Buff theory will be used to calculate derivatives of the activity coefficients and the derivative of the chemical activity for the osmolytes. <br />
<br />
==== Force Fields for ectoine and hydroxyectoine ====<br />
<br />
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}<br />
* {{Download| hectoinzwittmp2.gro |gro-File for Hydroxyectoine}}<br />
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}<br />
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}<br />
<br />
=== Part 3: Tasks ===<br />
1. Implement the developed force fields for the osmolytes (urea, ectoine and hydroxyectoine) in combination with the SPC/E water model. After energy minimization and warm up, run 20-30 ns simulations with GROMACS for osmolyte concentrations between c = 0 - 6 M.<br />
<br />
2. Study the following properties for the different osmolytes and concentrations:<br />
* diffusion coefficients<br />
* hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs<br />
* water mean relaxation times<br />
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?<br />
<br />
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.<br />
Use this information to compute the<br />
* Kirkwood-Buff integrals<br />
* derivatives of the chemical activity<br />
* derivatives of the activity coefficient<br />
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004). <br />
<br />
==== Literature ====<br />
<br />
* D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media", J. Phys. Chem. B 110, 4393 (2006)<br />
* J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem. 25, 1157 (2004)<br />
<br />
=== Report ===<br />
<br />
Please write a report of about 5 pages containing and discussing your results and hand it in until TBA.<br />
<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 3: [[Christian Holm]], Electrostatics, Lattice Boltzmann, and Electrokinetics==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: TBA in the ICP meeting room. <br />
<br />
Final meeting: TBA in the ICP meeting room. <br />
<br />
=== Description ===<br />
<br />
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people.<br />
It consists of one lecture on electrostatic algorithms, simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation<br />
and hand in one report. The Module 3 consists of three parts:<br />
<br />
=== Contact ===<br />
If you have any questions regarding the organisation or content of this module please do not hesitate to contact [[Christian Holm]].<br />
For questions regarding the practical part of the module and technical help contact [[David Sean]].<br />
<br />
=== Part 1: Electrostatics ===<br />
==== Description ====<br />
This part is about the theory of electrostatic algorithms for molecular dynamics simulations.<br />
It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald<br />
methods. To this end the students should read the referenced literature. [[Christian Holm]] will give an hour long lecture. Afterwards we will discuss the content and try to resolve open questions. The presentation should foster the students understanding of the P3M method as well<br />
as give them an overview of its performance compared to other modern electrostatics methods.<br />
<br />
==== Literature ====<br />
:* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''. [File: longrange.pdf]<br /><br />
<bibentry>deserno98a,arnold13b,arnold05a</bibentry><br />
<br />
=== Part 2: Slit Pore ===<br />
==== Description ====<br />
[[File:Slitpore.png|550px|right|Electroosmotic flow in a slit pore]]<br />
This part is practical. It is concerned with the movement of ions in an charged slit pore.<br />
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]<br />
which is recommended reading. A slit pore consists of two infinite charge walls as shown<br />
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].<br />
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented<br />
by charge Week-Chandler-Anderson spheres. In addition to the charge on the walls, the ions are also subject to an external<br />
electrical field parallel to the walls. Electrostatics should be handled by the P3M algorithm.<br />
A set of realistic parameters and an more in detail description of the system can be found in the<br />
thesis.<br />
You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit<br />
pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high<br />
salt limit (Debye-Hueckel-Limit). Calculate the ion profiles in one or both of these cases and compare the results with<br />
the simulation.<br />
<br />
==== Instructions and Literature ====<br />
General part and parts 4 & 6 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
Georg Rempfer, {{Download|BSc_thesis_rempfer.pdf|"Lattice-Boltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart<br />
<bibentry>grass09c</bibentry><br />
<br />
=== Part 3: Electrophoresis of Polyelectrolytes ===<br />
==== Description ====<br />
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions.<br />
Set up a system consisting of a charge polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled<br />
the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer<br />
for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and<br />
experimental results (see literature).<br />
<br />
==== Instructions and Literatur ====<br />
General part and part 5 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
<bibentry>grass08a, grass09c</bibentry><br />
<br />
=== Report ===<br />
<br />
At the final meeting day of this module, one group will give a presentation about the learned and performed work. In addition, they write a report of about 5 pages containing and discussing the obtained results and hand it in together with the reports of the other modules at the end of the course (see above).<br />
<br />
The final report is due electronically Friday night, TBA<br />
<br />
<br />
<br />
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.--></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Advanced_Simulation_Methods_SS_2018&diff=23277Advanced Simulation Methods SS 20182018-06-22T10:07:04Z<p>Holm: /* Module 3: Christian Holm, Electrostatics, Lattice Boltzmann, and Electrokinetics */</p>
<hr />
<div><br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students should send an email to [[Maria Fyta]] as soon as possible.<br />
<br><br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).</b>}}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture and Tutorials (2 SWS in total)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]], JP. Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]], Dr. [[David Sean]]<br />
;Course language<br />
:English or German<br />
;Location<br />
:ICP, Allmandring 3; Room: ICP Meeting Room<br />
;Time<br />
:(see below)<br />
The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP. Dr. [[Maria Fyta]] and will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules.<br />
The students can work in groups. All groups should write a report on each module, which they should submit to the responsible person for each module by the deadline set for each module.<br />
<!-- [[Maria Fyta]] no later than Friday July 15, 2016. The report does not need to be longer than 20 pages.--><br />
<br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students write an Email to [[Maria Fyta]] until TBA.</b>}}<br />
<br />
== Module 1: [[Maria Fyta]], [[Frank Uhlig]], Inter-atomic interactions modeled with quantum mechanical simulations ==<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<!--ue 05.04.2016 at 14:00 in the ICP meeting room.--><br />
<br />
Tutorials: TBA in the ICP CIP-Pool.<br />
<br />
Talks: TBA am in the ICP meeting room.<br />
<br />
=== Description ===<br />
<br />
This module focuses on the influence of using quantum mechanical simulations. The quantum mechanical schemes which will be applied in this module are based on density functional theory (DFT). This method allows the investigation of the electronic properties of a system. An understanding of the method, an analysis of the results from the simulations is the main goal of this module. The analysis of the simulations should be written up in a report. The talk will be a presentation of a DFT-related journal paper. For this, one of the following papers can be chosen:<br />
<br />
* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J. Klimeš and A. Michaelides, The Journal of Chemical Physics 137, 120901 (2012); doi: 10.1063/1.4754130<br />
* Challenges for Density Functional Theory, A.J. Cohen, P. Mori-Sanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.<br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module please do not hesitate to contact [[Maria Fyta]]. For practical guidance regarding the simulations [[Frank Uhlig]].<br />
<br />
=== Density functional theory and exchange-correlation functionals ===<br />
<br />
==== Description ====<br />
<br />
Many modern catalyses are performed using noble metals. In particular at the<br />
surface of these catalysts, which come in a multitude of shapes and chemical<br />
composition. The overall catalysis is determined by many factors, including the<br />
actual reactivity of chemical species at the surface, adsorption of reactants<br />
and desorption of products, as well as kinetics of the diffusion on the surface.<br />
<br />
In this exercise you will look at the desorption behavior of hydrogen gas from<br />
the surface of noble metals. This process is important in the production of<br />
hydrogen gas for energy storage applications [1]. However, modeling this process<br />
using modern methods of quantum-mechanical density functional theory (DFT) is<br />
very challenging. Only very advanced and quite recent density functionals are<br />
able to describe the long-range dispersion interactions [2]. Hence, effective<br />
methods based on pair potentials have been developed. These methods can achieve<br />
comparable accuracy to more ab initio methods while coming at a signifcantly<br />
lower computational effort [3,4].<br />
<br />
Your task is to develop such a pair-wise dispersion correction for the<br />
interaction of hydrogen gas with a metal surface. The first step is to<br />
understand and document the metallic behavior of your metal substrate, followed<br />
by investigation of the performance of common DFT functionals for the desorption<br />
process, and finally developing a dispersion correction by determining<br />
individual dispersion coefficients for the involved species [5].<br />
<br />
[1] https://dx.doi.org/10.1038/ncomms6848<br />
<br />
[2] https://dx.doi.org/10.1063/1.4754130<br />
<br />
[3] https://dx.doi.org/10.1103/PhysRevLett.102.073005<br />
<br />
[4] https://dx.doi.org/10.1063/1.3382344<br />
<br />
[5] https://dx.doi.org/10.1063/1.2746031<br />
<br />
[6] [[:Media:Asm_2018_info.txt|ASM tutorial info links]]<br />
<br />
==== Literature ====<br />
<br />
* A bird's-eye view of density-functional theory, Klaus Capelle, arXiv:cond-mat/0211443 (2002).<br />
* Self-Consistent Equations Including Exchange and Correlation Effects, W. Kohn and L.J. Sham, , Phys. Rev. (140), A1133 (1965).<br />
* Understanding and Reducing Errors in Density Functional Calculations, Min-Cheol Kim, Eunji Sim, and Kieron Burke, Phys. Rev. Lett. 111, 073003 (2013).<br />
<!--* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J Klimeš, A Michaelides, J. Chem. Phys. 137, 120901 (2012).--><br />
* An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases, V.R. Cooper, T. Thonhauser, and D.C. Langreth, J. Chem. Phys. 128, 204102 (2008).<br />
* On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit, B. Santra, A. Michaelides, and M. Scheffler, J. Chem. Phys. 127, 184104 (2007).<br />
* On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level, I. Dąbkowska, P. Jurečka, and P. Hobza, J. Chem. Phys. 122, 204322 (2005).<br />
<br />
=== Report ===<br />
<br />
Please write a report 5-10 pages containing and discussing your results and hand it in by Friday TBA.<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 2: [[Maria Fyta]], [[Narayanan Krishnamoorthy Anand]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: 18.05.2018 in the ICP meeting room. <br />
<br />
Final meeting: 15.06.2018 in the ICP meeting room.<br />
<br />
Deadline for reports: 15.06.2018<br />
=== Description ===<br />
<br />
This module focuses on atomistic Molecular Dynamics simulations and the study of biological co-solutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological co-solutes, often also called osmolytes are omnipresent in biological cells. A main function of these small-weight organic <br />
molecules is given by the protection of protein structures under harsh environmental conditions (protein stabilizers) or the denaturation of proteins (protein denaturants). The underlying mechanism leading to these effects is still unknown. It has been often discussed that osmolytes have a significant impact on the aqueous solution.<br />
The module consists of model development, simulation, analysis and oral and written presentation part. <br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Narayanan Krishnamoorthy Anand]].<br />
<br />
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the Kirkwood-Buff theory which can be well applied to computer simulations.<br />
The students should study the literature given below and present their findings. The presentation should at a minimum contain an introduction to Kirkwood-Buff theory in the context of the simulations.<br />
<br />
==== Literature ====<br />
<br />
* D. R. Canchi and A. E. Garcia, "Co-solvent effects on protein stability", Ann. Rev. Phys. Chem. 64. 273 (2013)<br />
* J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951) <br />
* V. Pierce, M. Kang, M. Aburi, S. Weerasinghe and P. E. Smith, "Recent applications of Kirkwood–Buff theory to biological systems", Cell Biochem. Biophys. 50, 1 (2008)<br />
* S. Weerasinghe and P. E. Smith, "A Kirkwood–Buff derived force field for sodium chloride in water", The Journal of Chemical Physics 119, 11342 (2003).<br />
* J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)<br />
* J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)<br />
* T. Kobayashi <i>et al</i>, "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches", Phys.Chem.Chem.Phys. 19, 18924 (2017)<br />
<br />
=== Part 2: Model Development and Simulations ===<br />
<br />
==== Description ====<br />
<br />
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will develop Generalized Amber Force Fields (GAFF) [http://ambermd.org/antechamber/gaff.html] with the help of the ACPYPE program [http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder] for the osmolytes (urea, hydroxyectoine, ectoine) which will be used for the study of solvent properties like the thermodynamics of hydrogen bonding ans the diffusivity according to J. Phys. Chem. B 118, 771 (2014).<br />
In comparison to pure water, the students will analyze several water parameters and elucidate the differences in presence of osmolytes and their concentration dependent behavior. The Kirkwood-Buff theory will be used to calculate derivatives of the activity coefficients and the derivative of the chemical activity for the osmolytes. <br />
<br />
==== Force Fields for ectoine and hydroxyectoine ====<br />
<br />
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}<br />
* {{Download| hectoinzwittmp2.gro |gro-File for Hydroxyectoine}}<br />
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}<br />
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}<br />
<br />
=== Part 3: Tasks ===<br />
1. Implement the developed force fields for the osmolytes (urea, ectoine and hydroxyectoine) in combination with the SPC/E water model. After energy minimization and warm up, run 20-30 ns simulations with GROMACS for osmolyte concentrations between c = 0 - 6 M.<br />
<br />
2. Study the following properties for the different osmolytes and concentrations:<br />
* diffusion coefficients<br />
* hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs<br />
* water mean relaxation times<br />
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?<br />
<br />
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.<br />
Use this information to compute the<br />
* Kirkwood-Buff integrals<br />
* derivatives of the chemical activity<br />
* derivatives of the activity coefficient<br />
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004). <br />
<br />
==== Literature ====<br />
<br />
* D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media", J. Phys. Chem. B 110, 4393 (2006)<br />
* J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem. 25, 1157 (2004)<br />
<br />
=== Report ===<br />
<br />
Please write a report of about 5 pages containing and discussing your results and hand it in until TBA.<br />
<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 3: [[Christian Holm]], Electrostatics, Lattice Boltzmann, and Electrokinetics==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: TBA in the ICP meeting room. <br />
<br />
Final meeting: TBA in the ICP meeting room. <br />
<br />
=== Description ===<br />
<br />
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people.<br />
It consists of one lecture on electrostatic algorithms, simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation<br />
and hand in one report. The Module 3 consists of three parts:<br />
<br />
=== Contact ===<br />
If you have any questions regarding the organisation or content of this module please do not hesitate to contact [[Christian Holm]].<br />
For questions regarding the practical part of the module and technical help contact [[David Sean]].<br />
<br />
=== Part 1: Electrostatics ===<br />
==== Description ====<br />
This part is about the theory of electrostatic algorithms for molecular dynamics simulations.<br />
It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald<br />
methods. To this end the students should read the referenced literature. [[Christian Holm]] will give an hour long lecture. Afterwards we will discuss the content and try to resolve open questions. The presentation should foster the students understanding of the P3M method as well<br />
as give them an overview of its performance compared to other modern electrostatics methods.<br />
<br />
==== Literature ====<br />
:* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''.<br /><br />
<bibentry>deserno98a,arnold13b,arnold05a</bibentry><br />
<br />
=== Part 2: Slit Pore ===<br />
==== Description ====<br />
[[File:Slitpore.png|550px|right|Electroosmotic flow in a slit pore]]<br />
This part is practical. It is concerned with the movement of ions in an charged slit pore.<br />
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]<br />
which is recommended reading. A slit pore consists of two infinite charge walls as shown<br />
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].<br />
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented<br />
by charge Week-Chandler-Anderson spheres. In addition to the charge on the walls, the ions are also subject to an external<br />
electrical field parallel to the walls. Electrostatics should be handled by the P3M algorithm.<br />
A set of realistic parameters and an more in detail description of the system can be found in the<br />
thesis.<br />
You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit<br />
pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high<br />
salt limit (Debye-Hueckel-Limit). Calculate the ion profiles in one or both of these cases and compare the results with<br />
the simulation.<br />
<br />
==== Instructions and Literature ====<br />
General part and parts 4 & 6 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
Georg Rempfer, {{Download|BSc_thesis_rempfer.pdf|"Lattice-Boltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart<br />
<bibentry>grass09c</bibentry><br />
<br />
=== Part 3: Electrophoresis of Polyelectrolytes ===<br />
==== Description ====<br />
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions.<br />
Set up a system consisting of a charge polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled<br />
the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer<br />
for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and<br />
experimental results (see literature).<br />
<br />
==== Instructions and Literatur ====<br />
General part and part 5 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
<bibentry>grass08a, grass09c</bibentry><br />
<br />
=== Report ===<br />
<br />
At the final meeting day of this module, one group will give a presentation about the learned and performed work. In addition, they write a report of about 5 pages containing and discussing the obtained results and hand it in together with the reports of the other modules at the end of the course (see above).<br />
<br />
The final report is due electronically Friday night, TBA<br />
<br />
<br />
<br />
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.--></div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2017/2018&diff=23018Simulation Methods in Physics I WS 2017/20182018-02-08T11:13:32Z<p>Holm: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Wed, 15:45-17:15 (Tutor: [[David Sean]]) and Fri, 14:00-15:30 (Tutor: [[Michael Kuron]]); ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|2017-10-19 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2017-10-26 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-02 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-09 ||Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-16 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-23 ||Observables, Brownian motion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-30 || D, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-07 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-14 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-21 || B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|2018-01-11 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-18 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-25 || Critical Exponent ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-01 || Finite Size Scaling ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
|-<br />
|2018-02-08 || Reweighting, Lattice QCD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture15_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[David Sean]])<br />
** Fridays 14:00-15:30 (Tutor: [[Michael Kuron]])<br />
* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators || 2017-11-13 12:00 || {{Download|WS_2017_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics || 2017-11-27 12:00 || {{Download|WS_2017_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables || 2017-12-11 12:00 || {{Download|WS_2017_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion || 2018-01-08 12:00 (both groups submit to Michael) || {{Download|WS_2017_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo || 2018-01-22 12:00 || {{Download|WS_2017_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling || 2018-02-05 12:00 (both groups submit to David) || {{Download|WS_2017_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<br />
|}<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|txt}}.<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics I, II" (240918-005):<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech I" (40520):<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker I" (35840):<br />
:* The marks for the module are the marks obtained in the excercises (BSL)<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [http://www.iris.uni-stuttgart.de/lehre/lehrveranstaltungen-wintersemester-20172018/kompaktkurs-programmieren-in-c.html C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2017/2018&diff=23017Simulation Methods in Physics I WS 2017/20182018-02-08T11:13:03Z<p>Holm: /* Useful online resources */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Wed, 15:45-17:15 (Tutor: [[David Sean]]) and Fri, 14:00-15:30 (Tutor: [[Michael Kuron]]); ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|2017-10-19 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2017-10-26 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-02 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-09 ||Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-16 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-23 ||Observables, Brownian motion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-30 || D, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-07 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-14 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-21 || B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|2018-01-11 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-18 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-25 || Critical Exponent ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-01 || Finite Size Scaling ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
|-<br />
|2018-02-08 || t.b.a. || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture15_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[David Sean]])<br />
** Fridays 14:00-15:30 (Tutor: [[Michael Kuron]])<br />
* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators || 2017-11-13 12:00 || {{Download|WS_2017_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics || 2017-11-27 12:00 || {{Download|WS_2017_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables || 2017-12-11 12:00 || {{Download|WS_2017_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion || 2018-01-08 12:00 (both groups submit to Michael) || {{Download|WS_2017_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo || 2018-01-22 12:00 || {{Download|WS_2017_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling || 2018-02-05 12:00 (both groups submit to David) || {{Download|WS_2017_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<br />
|}<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|txt}}.<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics I, II" (240918-005):<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech I" (40520):<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker I" (35840):<br />
:* The marks for the module are the marks obtained in the excercises (BSL)<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [http://www.iris.uni-stuttgart.de/lehre/lehrveranstaltungen-wintersemester-20172018/kompaktkurs-programmieren-in-c.html C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2017/2018&diff=23016Simulation Methods in Physics I WS 2017/20182018-02-08T11:12:23Z<p>Holm: /* Useful online resources */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Wed, 15:45-17:15 (Tutor: [[David Sean]]) and Fri, 14:00-15:30 (Tutor: [[Michael Kuron]]); ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|2017-10-19 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2017-10-26 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-02 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-09 ||Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-16 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-23 ||Observables, Brownian motion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-30 || D, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-07 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-14 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-21 || B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|2018-01-11 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-18 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-25 || Critical Exponent ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-01 || Finite Size Scaling ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
|-<br />
|2018-02-08 || t.b.a. || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture15_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* Reweighing: W. Janke, [https://link.springer.com/chapter/10.1007/978-94-010-0173-1_7 <i>Histograms and all that</i>], Computer Simulations of Surfaces and Interfaces, pp 137-157, Springer book<br />
<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[David Sean]])<br />
** Fridays 14:00-15:30 (Tutor: [[Michael Kuron]])<br />
* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators || 2017-11-13 12:00 || {{Download|WS_2017_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics || 2017-11-27 12:00 || {{Download|WS_2017_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables || 2017-12-11 12:00 || {{Download|WS_2017_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion || 2018-01-08 12:00 (both groups submit to Michael) || {{Download|WS_2017_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo || 2018-01-22 12:00 || {{Download|WS_2017_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling || 2018-02-05 12:00 (both groups submit to David) || {{Download|WS_2017_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<br />
|}<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|txt}}.<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics I, II" (240918-005):<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech I" (40520):<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker I" (35840):<br />
:* The marks for the module are the marks obtained in the excercises (BSL)<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [http://www.iris.uni-stuttgart.de/lehre/lehrveranstaltungen-wintersemester-20172018/kompaktkurs-programmieren-in-c.html C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2017/2018&diff=22969Simulation Methods in Physics I WS 2017/20182018-01-25T18:20:06Z<p>Holm: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Wed, 15:45-17:15 (Tutor: [[David Sean]]) and Fri, 14:00-15:30 (Tutor: [[Michael Kuron]]); ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|2017-10-19 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2017-10-26 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-02 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-09 ||Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-16 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-23 ||Observables, Brownian motion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-30 || D, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-07 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-14 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-21 || B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|2018-01-11 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-18 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-25 || Critical Exponent ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-01 || Finite Size Scaling , Binder Parameters || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-08 || t.b.a. || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture15_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[David Sean]])<br />
** Fridays 14:00-15:30 (Tutor: [[Michael Kuron]])<br />
* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators || 2017-11-13 12:00 || {{Download|WS_2017_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics || 2017-11-27 12:00 || {{Download|WS_2017_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables || 2017-12-11 12:00 || {{Download|WS_2017_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion || 2018-01-08 12:00 (both groups submit to Michael) || {{Download|WS_2017_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo || 2018-01-22 12:00 || {{Download|WS_2017_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling || 2018-02-05 12:00 (both groups submit to David) || {{Download|WS_2017_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<br />
|}<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|txt}}.<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics I, II" (240918-005):<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech I" (40520):<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker I" (35840):<br />
:* The marks for the module are the marks obtained in the excercises (BSL)<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [http://www.iris.uni-stuttgart.de/lehre/lehrveranstaltungen-wintersemester-20172018/kompaktkurs-programmieren-in-c.html C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2017/2018&diff=22968Simulation Methods in Physics I WS 2017/20182018-01-25T18:19:36Z<p>Holm: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Wed, 15:45-17:15 (Tutor: [[David Sean]]) and Fri, 14:00-15:30 (Tutor: [[Michael Kuron]]); ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|2017-10-19 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2017-10-26 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-02 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-09 ||Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-16 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-23 ||Observables, Brownian motion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-30 || D, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-07 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-14 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-21 || B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|2018-01-11 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-18 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-25 || Critical Exponent ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-01 || Finite Size Scaling , Binder Parameters || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-08 || Error Analysis || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture15_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[David Sean]])<br />
** Fridays 14:00-15:30 (Tutor: [[Michael Kuron]])<br />
* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators || 2017-11-13 12:00 || {{Download|WS_2017_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics || 2017-11-27 12:00 || {{Download|WS_2017_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables || 2017-12-11 12:00 || {{Download|WS_2017_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion || 2018-01-08 12:00 (both groups submit to Michael) || {{Download|WS_2017_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo || 2018-01-22 12:00 || {{Download|WS_2017_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling || 2018-02-05 12:00 (both groups submit to David) || {{Download|WS_2017_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<br />
|}<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|txt}}.<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<br />
Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics I, II" (240918-005):<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech I" (40520):<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker I" (35840):<br />
:* The marks for the module are the marks obtained in the excercises (BSL)<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [http://www.iris.uni-stuttgart.de/lehre/lehrveranstaltungen-wintersemester-20172018/kompaktkurs-programmieren-in-c.html C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2017/2018&diff=22767Simulation Methods in Physics I WS 2017/20182017-11-24T10:43:14Z<p>Holm: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Wed, 15:45-17:15 (Tutor: [[David Sean]]) and Fri, 14:00-15:30 (Tutor: [[Michael Kuron]]); ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating 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 lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|2017-10-19 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2017-10-26 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-02 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-09 ||Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-16 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-23 ||Observables, Brownian motion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-30 || D, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-07 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-14 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-21 || B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|2018-01-11 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-18 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-25 || Finite Size Scaling ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-01 || Binder Parameters || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-08 || Error Analysis || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture15_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3) on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[David Sean]])<br />
** Fridays 14:00-15:30 (Tutor: [[Michael Kuron]])<br />
* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
<!-- * Michael's tutorial on February 9th is moved to February 23rd. --><br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators || 2017-11-13 12:00 || {{Download|WS_2017_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics || 2017-11-27 12:00 || {{Download|WS_2017_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables || 2017-12-11 12:00 || {{Download|WS_2017_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion || 2018-01-08 12:00 || {{Download|WS_2017_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo || 2018-01-22 12:00 || {{Download|WS_2017_SM1_worksheet5.pdf|Worksheet 5}} ||<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling || 2018-02-05 12:00 || {{Download|WS_2017_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
|}<br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|txt}}.<br />
* You can do the exercises in the CIP-Pool when it is not [[CIP Pool Occupancy|occupied by another course]]. The pool is accessible on all days, except weekends and late evenings.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* The worksheets are to be solved in groups of two or three people. We will ''not'' accept hand-in-exercises that only have a single name on it.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download on the days before the tutorial.<br />
* In the first tutorial after you received a worksheet, the solutions of the previous worksheet will be presented (see below) and the new worksheet will be discussed.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<br />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules. You will also need to install a compatible C compiler ([http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] and, if you are running 64-bit Windows, [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers)).<br />
<br />
== Examination ==<br />
<br />
Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics I, II" (240918-005):<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech I" (40520):<br />
:* Obtain 50% of the possible points in the hand-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker I" (35840):<br />
:* The marks for the module are the marks obtained in the excercises (BSL)<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [http://www.iris.uni-stuttgart.de/lehre/lehrveranstaltungen-wintersemester-20172018/kompaktkurs-programmieren-in-c.html C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Takeshi_Kobayashi&diff=22694Takeshi Kobayashi2017-11-08T17:52:38Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|image=<br />
|email=tkobayashi<br />
|name=Kobayashi, Takeshi<br />
|title=<br />
|status=Master student<br />
|room=1.077<br />
|phone=<br />
|category=fyta<br />
topical=sampling<br />
}}</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Jens_Smiatek&diff=22692Jens Smiatek2017-11-08T15:58:34Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|name=Smiatek, Jens<br />
|title=Dr.<br />
|status=Group leader<br />
|category=smiatek<br />
|phone=63757<br />
|room=1.032<br />
|email=smiatek<br />
|image=Smiatek_DNA1.jpg<br />
|researcherid=G-9933-2012<br />
|topical=sampling<br />
|ordering=1<br />
}}<br />
<br />
== Research interests ==<br />
<br />
* Biomolecules and specific DNA structures: i-motif and g-quadruplex<br />
<br />
* Solvent effects<br />
<br />
* Free energy landscapes<br />
<br />
* Solvent-solute interactions<br />
<br />
* Osmolytes and co-solutes<br />
<br />
* Electrohydrodynamics<br />
<br />
* Polyelectrolytes and interactions with ions<br />
<br />
* Microscale flows<br />
<br />
* Method development<br />
<br />
== Curriculum Vitae ==<br />
<br />
A detailed CV can be found [[Media:cv_smiatek_ICP_0217.pdf|here]].<br />
<br />
== Publications ==<br />
My profile at [http://scholar.google.de/citations?user=-RgaRekAAAAJ "Scholar Google"]<br />
:* Markthaler, D.; Zeman, J.; Baz, J.; Smiatek, J.; Hansen, N.<br />
:: '''Validation of Trimethylamine-N-Oxide (TMAO) Force Fields Based on Thermophysical Properties of Aqueous TMAO Solutions.'''<br />
:: ''J. Phys. Chem. B'', [http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b07774 DOI: 10.1021/acs.jpcb.7b07774] (2017)<br />
:* Belyanchikov, M. A.; Zhukov, E. S.; Tertia, S.; Zhugayevych, A.; Dressel, M.; Uhlig, F.; Smiatek, J.; Fyta, M.; Thomas, V. G.; Gorshunov, B. P.<br />
:: '''Vibrational states of nano-confined water molecules in beryl based on first principles calculations and optical experiments.''' <br />
:: ''Phys. Chem. Chem. Phys.'', [http://pubs.rsc.org/en/content/articlelanding/2017/cp/c7cp06472a#!divAbstract| DOI: 10.1039/C7CP06472A] (2017)<br />
<bibentry><br />
uhlig17a,<br />
roy17b,<br />
niskanen17a,<br />
roy17a,<br />
kobayashi17a,<br />
diddens17a,<br />
szuttor17a,<br />
smiatek17b,<br />
landsgesell17b,<br />
landsgesell17a,<br />
michalowsky17a,<br />
smiatek17a,<br />
schroer16a,<br />
krishnamoorthy16a,<br />
lesch16b,<br />
hahn16a,<br />
breitsprecher16a,<br />
sanchez16a,<br />
micciulla16a,<br />
lesch16a,<br />
vogele15b,<br />
hahn15a,<br />
fahrenberger15c,<br />
lesch15b,<br />
fahrenberger15b,<br />
vogele15a,<br />
lesch15a,<br />
wohlfarth15a,<br />
zhou14a,<br />
heuer14a,<br />
krishnamoorthy14a,<br />
micciulla14a,<br />
hickey14a,<br />
smiatek14d,<br />
bohner14a,<br />
smiatek14a,<br />
smiatek14b,<br />
smiatek14c,<br />
smiatek13a,<br />
smiatek13b,<br />
hentschel13a,<br />
smiatek12c,<br />
meinhardt12a,<br />
smiatek12a,<br />
smiatek12b,<br />
smiatek12d,<br />
smiatek11d,<br />
smiatek11c,<br />
smiatek11b,<br />
smiatek11a,<br />
smiatek10a,<br />
smiatek09b,<br />
smiatek09a,<br />
smiatek08a<br />
</bibentry><br />
<br />
''Submitted Manuscripts''<br />
<br />
* Zeman, J.; Uhlig, F.; Smiatek, J.; Holm, C.<br />
*: A coarse-grained polarizable force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate, submitted (2017)<br />
<br />
* Weyman, A.: Bier, M.; Holm, C.; Smiatek, J.<br />
*: Microphase separation and the formation of ion conductivity channels in poly(ionic liquid)s: a coarse-grained molecular dynamics study, submitted (2017)<br />
<br />
* Uhlig, F.; Zeman, J.; Smiatek, J.; Holm, C.<br />
*: First-principles parameterization of polarizable coarse-grained force fields for ionic liquids, submitted (2017)<br />
<br />
* Oprzeska-Zingrebe, E. A.; Smiatek, J.<br />
*: Thermodynamic aspects concerning the preferential binding of urea to single-stranded DNA structures: a molecular dynamics simulation study, submitted (2017)<br />
<br />
* Ribeiro Tzaras, E.; Weik, F.; Holm, C.; Smiatek, J.<br />
*: Polymer translocation through thin nano pores: An unbiased perspective on free energy landscapes and essential dynamics, submitted (2016)<br />
<br />
* Smiatek, J.; Riedl, D.; Heuer, A.<br />
*: Statistical properties of soccer, basketball and handball - A quantitative comparison, submitted (2016)</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Jens_Smiatek&diff=22691Jens Smiatek2017-11-08T15:58:03Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|name=Smiatek, Jens<br />
|title=Dr.<br />
|status=Group leader<br />
|category=smiatek<br />
|phone=63757<br />
|room=1.032<br />
|email=smiatek<br />
|image=Smiatek_DNA1.jpg<br />
|researcherid=G-9933-2012<br />
|topical=sampling<br />
|topical6=ionic_liquids<br />
|ordering=1<br />
}}<br />
<br />
== Research interests ==<br />
<br />
* Biomolecules and specific DNA structures: i-motif and g-quadruplex<br />
<br />
* Solvent effects<br />
<br />
* Free energy landscapes<br />
<br />
* Solvent-solute interactions<br />
<br />
* Osmolytes and co-solutes<br />
<br />
* Electrohydrodynamics<br />
<br />
* Polyelectrolytes and interactions with ions<br />
<br />
* Microscale flows<br />
<br />
* Method development<br />
<br />
== Curriculum Vitae ==<br />
<br />
A detailed CV can be found [[Media:cv_smiatek_ICP_0217.pdf|here]].<br />
<br />
== Publications ==<br />
My profile at [http://scholar.google.de/citations?user=-RgaRekAAAAJ "Scholar Google"]<br />
:* Markthaler, D.; Zeman, J.; Baz, J.; Smiatek, J.; Hansen, N.<br />
:: '''Validation of Trimethylamine-N-Oxide (TMAO) Force Fields Based on Thermophysical Properties of Aqueous TMAO Solutions.'''<br />
:: ''J. Phys. Chem. B'', [http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b07774 DOI: 10.1021/acs.jpcb.7b07774] (2017)<br />
:* Belyanchikov, M. A.; Zhukov, E. S.; Tertia, S.; Zhugayevych, A.; Dressel, M.; Uhlig, F.; Smiatek, J.; Fyta, M.; Thomas, V. G.; Gorshunov, B. P.<br />
:: '''Vibrational states of nano-confined water molecules in beryl based on first principles calculations and optical experiments.''' <br />
:: ''Phys. Chem. Chem. Phys.'', [http://pubs.rsc.org/en/content/articlelanding/2017/cp/c7cp06472a#!divAbstract| DOI: 10.1039/C7CP06472A] (2017)<br />
<bibentry><br />
uhlig17a,<br />
roy17b,<br />
niskanen17a,<br />
roy17a,<br />
kobayashi17a,<br />
diddens17a,<br />
szuttor17a,<br />
smiatek17b,<br />
landsgesell17b,<br />
landsgesell17a,<br />
michalowsky17a,<br />
smiatek17a,<br />
schroer16a,<br />
krishnamoorthy16a,<br />
lesch16b,<br />
hahn16a,<br />
breitsprecher16a,<br />
sanchez16a,<br />
micciulla16a,<br />
lesch16a,<br />
vogele15b,<br />
hahn15a,<br />
fahrenberger15c,<br />
lesch15b,<br />
fahrenberger15b,<br />
vogele15a,<br />
lesch15a,<br />
wohlfarth15a,<br />
zhou14a,<br />
heuer14a,<br />
krishnamoorthy14a,<br />
micciulla14a,<br />
hickey14a,<br />
smiatek14d,<br />
bohner14a,<br />
smiatek14a,<br />
smiatek14b,<br />
smiatek14c,<br />
smiatek13a,<br />
smiatek13b,<br />
hentschel13a,<br />
smiatek12c,<br />
meinhardt12a,<br />
smiatek12a,<br />
smiatek12b,<br />
smiatek12d,<br />
smiatek11d,<br />
smiatek11c,<br />
smiatek11b,<br />
smiatek11a,<br />
smiatek10a,<br />
smiatek09b,<br />
smiatek09a,<br />
smiatek08a<br />
</bibentry><br />
<br />
''Submitted Manuscripts''<br />
<br />
* Zeman, J.; Uhlig, F.; Smiatek, J.; Holm, C.<br />
*: A coarse-grained polarizable force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate, submitted (2017)<br />
<br />
* Weyman, A.: Bier, M.; Holm, C.; Smiatek, J.<br />
*: Microphase separation and the formation of ion conductivity channels in poly(ionic liquid)s: a coarse-grained molecular dynamics study, submitted (2017)<br />
<br />
* Uhlig, F.; Zeman, J.; Smiatek, J.; Holm, C.<br />
*: First-principles parameterization of polarizable coarse-grained force fields for ionic liquids, submitted (2017)<br />
<br />
* Oprzeska-Zingrebe, E. A.; Smiatek, J.<br />
*: Thermodynamic aspects concerning the preferential binding of urea to single-stranded DNA structures: a molecular dynamics simulation study, submitted (2017)<br />
<br />
* Ribeiro Tzaras, E.; Weik, F.; Holm, C.; Smiatek, J.<br />
*: Polymer translocation through thin nano pores: An unbiased perspective on free energy landscapes and essential dynamics, submitted (2016)<br />
<br />
* Smiatek, J.; Riedl, D.; Heuer, A.<br />
*: Statistical properties of soccer, basketball and handball - A quantitative comparison, submitted (2016)</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Slavko_Kondrat&diff=22690Slavko Kondrat2017-11-08T15:34:50Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|name=Kondrat, Slavko<br />
|status=Postdoc<br />
|phone=63613<br />
|room=1.039<br />
|email=skondrat@icp.uni-stuttgart.de<br />
|category=former<br />
|topical=supercapacitors<br />
|topical2=ionic liquids<br />
}}</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Nicolai_Roth&diff=22689Nicolai Roth2017-11-08T15:34:21Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|name=Roth, Nicolai<br />
|status=Master student<br />
|category=former<br />
|phone= 63594<br />
|room=1.041<br />
|email=nroth<br />
}}</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Robin_Bardakcioglu&diff=22688Robin Bardakcioglu2017-11-08T15:32:13Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|name=Bardakcioglu, Robin<br />
|status=Student assistant<br />
|category=former<br />
|phone=63627<br />
|room=1.070<br />
|email=Robin.Bardakcioglu<br />
}}</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Narayanan_Krishnamoorthy_Anand&diff=22687Narayanan Krishnamoorthy Anand2017-11-08T15:30:57Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|name=Narayanan Krishnamoorthy, Anand<br />
|status=PhD student<br />
|phone=67701<br />
|room=1.076<br />
|email=anand<br />
|image=38710.jpg <br />
|category=holm<br />
|topical2=nanopore<br />
|topical=sampling<br />
}}</div>Holmhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Florian_Weik&diff=22686Florian Weik2017-11-08T15:30:27Z<p>Holm: </p>
<hr />
<div>{{Person<br />
|name=Weik, Florian<br />
|status=PhD student<br />
|phone=67703<br />
|room=1.039<br />
|email=fweik<br />
|category=holm<br />
|topical=<br />
|topical2=espresso<br />
|topical3=electrokinetics<br />
|image=Fweik.jpg<br />
}}<br />
<br />
=== PGP Key ===<br />
{{Download|Fweik.asc|0x0562F11D|application_pgp_keys}}</div>Holm