Difference between revisions of "Simulation Methods in Physics II SS 2013"

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(Recommended literature)
 
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== Exams ==
 +
The following dates and times have been scheduled for the oral exams.Please send an e-mail ([[Maria Fyta]], [[Jens Smiatek]]) noting your preference. We will send an e-mail back confirming (or not) the date.
 +
 +
Thu. Sep 19: 10:00, 11:00, 13:00, and 14:00
 +
 
== Overview ==
 
== Overview ==
  
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;Course language
 
;Course language
 
:English
 
:English
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 +
:{{Infobox|<b> NO lecture on 11.07.The lecture on 18.07 will start earlier at 11am</b>.}}
  
 
;Lectures
 
;Lectures
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=== Recommended literature ===
 
=== Recommended literature ===
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a,thijssen07,succi01,tuckerman10,steinhauser08,martin04,kaxiras03,leach01</bibentry>
+
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a,thijssen07,succi01a,tuckerman10a,steinhauser08a,martin04a,kaxiras03a,leach01a</bibentry>
  
 
=== Useful online resources ===
 
=== Useful online resources ===
  
* Introduction to electronic structure methods, Roethlisberger, Tavernarelli, EPFL, Lausanne, 2011: [lcbcpc21.epfl.ch/Group_members/ivano/bachelor.pdf].
+
* Roethlisberger, Tavernarelli, EPFL, Lausanne, 2011: [http://lcbcpc21.epfl.ch/Group_members/ivano/bachelor.pdf Introduction to electronic structure methods.]
  
* E-book: D.P. Landau and K. Binder: [http://www.netlibrary.com/urlapi.asp?action=summary&v=1&bookid=139749  A guide to Monte Carlo Simulations in Statistical Physics]
+
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]
  
 
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.
 
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.
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* A good and freely available book about using Linux: [http://writers.fultus.com/garrels/ebooks/Machtelt_Garrels_Introduction_to_Linux_3nd_Ed.pdf Introduction to Linux by M. Garrels]
 
* A good and freely available book about using Linux: [http://writers.fultus.com/garrels/ebooks/Machtelt_Garrels_Introduction_to_Linux_3nd_Ed.pdf Introduction to Linux by M. Garrels]
  
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT] (Often used by myself as a cheat sheet)
+
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]
  
 
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]
 
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]
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* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]
 
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]
 +
 +
* [http://ocw.mit.edu/courses/materials-science-and-engineering/3-021j-introduction-to-modeling-and-simulation-spring-2011/lecture-notes-and-readings/MIT3_021JS11_P1_L8.pdf MIT Opencourseware "Reactive potentials and applications"]
 +
 +
* [http://people.virginia.edu/~lz2n/mse627/notes/Intro.pdf University of Virginia, Introduction to atomistic simulations]
 +
 +
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]
  
 
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.
 
* Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.
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== Lecture  ==
 
== Lecture  ==
 
To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.
 
To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.
 +
 +
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font>
  
 
{| class="wikitable"
 
{| class="wikitable"
 
|-valign="top"
 
|-valign="top"
!Date !! Subject || Ressources
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!Date !! Subject || Resources
  
 
|-
 
|-
| 11.04.2012 || Introduction, elements of quantum mechanics, electronic stucture || [{{Download|simmethodsII_ss13_lecture1.pdf|Lecture Notes}}]
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| 11.04.2013 || Introduction, electronic stucture || [{{Download|simmethodsII_ss13_lecture1.pdf|Lecture Notes}}]
  
 
|-
 
|-
| 18.04.2012 || Hartree-Fock method, Density functional theory (DFT) ||
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| 18.04.2013 || Elements of quantum mechanics, Hartree and Hartree-Fock approximations  || [{{Download|simmethodsII_ss13_lecture2.pdf|Lecture Notes}}]
[Lecture Notes]
+
 
 
|-
 
|-
| 25.04.2012 || Post-Hartree-Fock methods, band structure calculations, pseudopotentials || [Lecture Notes]
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| 25.04.2013 || Density functional theory (DFT), functionals, pseudopotentials, elements of solid state physics || [{{Download|simmethodsII_ss13_lecture3.pdf|Lecture Notes}}]
  
 
|-
 
|-
| 30.04.2012 || CPMD, quantum Monte Carlo, QM/MM, tight-binding || [Lecture Notes]  
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| 30.04.2013 || Time-dependent density functional theory, post-Hartree-Fock methods|| [{{Download|simmethodsII_ss13_lecture4.pdf|Lecture Notes}}]
  
 
|-
 
|-
| 09.05.2012 || ''Holiday (Christi Himmelfahrt)'' ||
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| 09.05.2013 || ''Holiday (Christi Himmelfahrt)'' ||
  
 
|-
 
|-
| 16.05.2012 ||Classical force fields, atomistic simulations, biomolecules, materials<!--Coarse-grained models, simulations of macromolecules and soft matter--> || [Lecture Notes]  
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| 16.05.2013 ||QM forces, energy minimization, CPMD, quantum Monte Carlo, QM/MM, tight-binding<!--simulations of macromolecules and soft matter--> || [{{Download|simmethodsII_ss13_lecture5.pdf|Lecture Notes}}]  
  
 
|-
 
|-
| 23.05.2012 || '' Holiday (Pfingsten) '' ||  
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| 23.05.2013 || '' Holiday (Pfingsten) '' ||  
  
 
|-
 
|-
| 30.05.2012 || '' Holiday (Fronleichnam) '' ||
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| 30.05.2013 || '' Holiday (Fronleichnam) '' ||
  
 
|-
 
|-
| 06.06.2012 || Water models, Solvation models<!--Long range interactions in periodic boundary conditions--> || [Lecture Notes]  
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| 06.06.2013 ||Classical force fields, explicit water models<!--Long range interactions in periodic boundary conditions--> || [{{Download|simmethodsII_ss13_lecture6_watermodels.pdf|Lecture Notes 1}},  {{Download|simmethodsII_ss13_lecture6_MD.pdf|Lecture Notes 2}}]  
  
 
|-
 
|-
| 13.06.2012 || <!--Poisson-Boltzmann theory, charged polymers-->
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| 13.06.2013 || Implicit solvent models  || {{Download|simmethodsII_ss13_lecture7.pdf|Lecture Notes}}
|| [Lecture Notes]
 
  
 
|-
 
|-
| 20.06.2012 || <!--Hydrodynamic methods: Lattice-Boltzmann, Brownian Dynamics, DPD, SRD--> || [Lecture Notes]  
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| 20.06.2013 || MD simulations of biomolecules, force fields || [{{Download|simmethodsII_ss13_lecture8.pdf|Lecture Notes}}]
  
 
|-
 
|-
| 27.06.2012 || <!--Hydrodynamic methods II--> || [Lecture Notes]
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| 27.06.2013 || Hydrodynamic methods: Brownian Dynamics, DPD, Lattice-Boltzmann || [{{Download|simmethodsII_ss13_lecture9.pdf|Lecture Notes}}]
  
 
|-
 
|-
| 04.07.2012 || <!--Advanced MC/MD methods--> || [Lecture Notes]
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| 04.07.2013 || Interatomic potentials <!--Advanced MC/MD methods--> || [{{Download|simmethodsII_ss13_lecture10.pdf|Lecture Notes}}]
  
 
|-
 
|-
| 11.07.2012 || Free energy methods || [Lecture Notes]
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| 11.07.2013 || Cancelled <!--Free energy methods -->|| []
  
 
|-
 
|-
| 18.07.2012 || Multiscale simulations<!--Free energy methods II--> || [Lecture Notes]
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| 18.07.2013 || EAM, coarse-graining and nuggets on multiscale simulations || [{{Download|simmethodsII_ss13_lecture12.pdf|Lecture Notes 1}},  {{Download|simmethodsII_ss13_lecture12_multiscale.pdf|Lecture Notes 2}}]  
 
|}
 
|}
  
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*The tutorials will take place on Tuesdays between 8-10 am in the ICP CIP-Pool.
 
*The tutorials will take place on Tuesdays between 8-10 am in the ICP CIP-Pool.
  
;Scheduling of tutorials
+
*New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 18.04. The following week is dedicated to working on problems related to the last worksheet. Homework in the form of a report should be sent to [[Jens Smiatek]] before the next worksheet will be handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.
:New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 18.04. The following week is dedicated to working on problems related to the last worksheet. Homework in the form of a report should be sent to the tutors before the next worksheet is handed out, until Tuesday 12pm, before the next worksheet will be handed out. The first worksheet is then due on Tue 30.04. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.
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 +
== Work sheets ==
 +
*'''[[Media:worksheet1.zip|Worksheet 1 (zip-File with SIESTA input files and attachments)]]''' ''Quantum mechanical approaches - Hückel approximation and DFT methods''
 +
** [[Media:tutorial1.pdf|Worksheet 1 (the work sheet as a single PDF file)]]
 +
** [http://icmab.cat/leem/siesta/CodeAccess/Code/downloads.html SIESTA Download]
 +
** [http://www.pa.msu.edu/people/tomanek/SIESTA-installation.html SIESTA Installation Guide]
 +
** [http://icmab.cat/leem/siesta/Documentation/Tutorials/Lyon-2007/index.html Hands-on-tutorial for SIESTA, Lyon 2007]
 +
 
 +
*'''[[Media:worksheet2.zip|Worksheet 2 (zip-File with si.fdf)]]''' ''Properties of fermions and Density functional theory''
 +
 
 +
*'''[[Media:ws3.zip|Worksheet 3 (zip-File with water topology and input files for GROMACS)]]''' ''Diffusion processes and atomistic water model properties''
 +
** [[Media:tut3.pdf|Worksheet 3 (the work sheet as a single PDF file)]]
 +
** [http://www.gromacs.org GROMACS Download]
  
;Please send the report to the responsible person indicated with the given tutorial.
+
*'''[[Media:alanine_dipeptide.zip|Worksheet 4 (zip-File with input files)]]''' ''All-atom Molecular Dynamics simulations of the alanine dipeptide''
:In general, it should be the same person who handed out the tutorial. <!--The name and e-mail in the worksheet are those of the worksheet author, not the responsible tutor!-->
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** [[Media:alanine_dipeptide.pdf|Worksheet 4 (the work sheet as a single PDF file)]]
 +
** [http://www.gromacs.org GROMACS Download]
 +
** [http://www.gromacs.org/Documentation/Manual GROMACS Manual]
 +
** [http://manual.gromacs.org/online/speptide.html Example: How to set up a GROMACS simulation]
 +
** [http://www.csc.fi/english/csc/courses/archive/material/gmx-gpu-materials/vmd-gromacs-exercises.pdf How to visualize GROMACS trajectories with VMD]
  
 +
*'''[[Media:ws5.zip|Worksheet 5 (zip-File with script files for ESPResSo)]]''' ''Coarse-grained simulations with ESPResSo''
 +
** [[Media:tut5.pdf|Worksheet 5 (the work sheet as a single PDF file)]]
 +
** [http://espressomd.org/ ESPResSo-Homepage]
 +
** [http://espressomd.org/wordpress/download/ ESPResSo-Download]
 +
** [http://espressomd.org/jenkins/job/ESPResSo/lastSuccessfulBuild/artifact/doc/ug/ug.pdf ESPResSo-Manual]
 
== Examination ==
 
== Examination ==
  

Latest revision as of 23:04, 27 November 2013

Exams

The following dates and times have been scheduled for the oral exams.Please send an e-mail (Maria Fyta, Jens Smiatek) noting your preference. We will send an e-mail back confirming (or not) the date.

Thu. Sep 19: 10:00, 11:00, 13:00, and 14:00

Overview

Type
Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
Lecturer
JP. Dr. Maria Fyta, (Lecture); Dr. Jens Smiatek(Tutorials)
Course language
English
Lectures
Time: Thursdays, 11:30 - 13:00, ICP, Allmandring 3, Seminarroom 1
Tutorials
Time: Tuesdays, 08:00-10:00, ICP, Allmandring 3, CIP-Pool

The tutorials have their own title "Simulationsmethoden in der Praxis", as they can be attended independently of the lecture and are in fact part part of the Physics MSc module "Fortgeschrittene Simulationsmethoden" and not of the module that contains the lecture "Simulation Methods in Physics II".

The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis. The tutorials build on each other, therefore continuous attendance is expected.

Scope

The course intends to give an overview about modern simulation methods used in physics today. The stress of the lecture will be to introduce different approaches to simulate a problem, hence we will not go too to deep into specific details but rather try to cover a broad range of methods. For an idea about the content look at the lecture schedule.

Prerequisites

We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations, as well as knowledge of a programming language. The knowledge of the previous course Simulation Methods I is expected.

Certificate Requirements

1. Attendance of the exercise classes
2. Obtaining 50% of the possible marks in the hand-in exercises

There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II) determined at the end of lecture Simulation Methods II.

The final grade will be determined in the following way: There will be an oral examination performed at (or after) the end of the course Simulation Methods II (SS 2012).

Recommended literature


Useful online resources

  • Linux cheat sheet application_pdf.pnghere (53 KB)Info circle.png.
  • Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.

Lecture

To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.

A script on the course material is now available, thanks to Larissa Dill application_pdf.pngScript (670 KB)Info circle.png.

Date Subject Resources
11.04.2013 Introduction, electronic stucture Lecture Notes (3.19 MB)Info circle.png
18.04.2013 Elements of quantum mechanics, Hartree and Hartree-Fock approximations Lecture Notes (3.22 MB)Info circle.png
25.04.2013 Density functional theory (DFT), functionals, pseudopotentials, elements of solid state physics Lecture Notes (5.51 MB)Info circle.png
30.04.2013 Time-dependent density functional theory, post-Hartree-Fock methods Lecture Notes (5.12 MB)Info circle.png
09.05.2013 Holiday (Christi Himmelfahrt)
16.05.2013 QM forces, energy minimization, CPMD, quantum Monte Carlo, QM/MM, tight-binding Lecture Notes (7.41 MB)Info circle.png
23.05.2013 Holiday (Pfingsten)
30.05.2013 Holiday (Fronleichnam)
06.06.2013 Classical force fields, explicit water models Lecture Notes 1 (3.1 MB)Info circle.png, application_pdf.pngLecture Notes 2 (2.11 MB)Info circle.png
13.06.2013 Implicit solvent models application_pdf.pngLecture Notes (4.71 MB)Info circle.png
20.06.2013 MD simulations of biomolecules, force fields Lecture Notes (5.91 MB)Info circle.png
27.06.2013 Hydrodynamic methods: Brownian Dynamics, DPD, Lattice-Boltzmann Lecture Notes (4.66 MB)Info circle.png
04.07.2013 Interatomic potentials Lecture Notes (4 MB)Info circle.png
11.07.2013 Cancelled []
18.07.2013 EAM, coarse-graining and nuggets on multiscale simulations Lecture Notes 1 (2.04 MB)Info circle.png, application_pdf.pngLecture Notes 2 (5.96 MB)Info circle.png

Tutorials

  • The tutorials will take place on Tuesdays between 8-10 am in the ICP CIP-Pool.
  • New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 18.04. The following week is dedicated to working on problems related to the last worksheet. Homework in the form of a report should be sent to Jens Smiatek before the next worksheet will be handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.

Work sheets

Examination

Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:

BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP
  • Obtain 50% of the possible points in the hands-in excercises of this lecture as well as for the first part of the lecture as a prerequisite for the examination (USL-V)
  • 60 min of oral examination (PL)
    • After the lecture (i.e. Summer 2013)
    • Contents: both lectures and the excercises of "Simulation Methods in Physics I"
International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005)
  • Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination
  • 30 min of oral examination (PL) about the lecture and the excercises
BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????)
  • Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)
  • 40 min of oral examination (PL) about the lecture and the excercises
MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????)
  • The marks for the module are the marks obtained in the excercises (BSL)