Difference between revisions of "Simulation Methods in Physics II SS 2014"

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== Overview ==
 +
 
 +
;Type
 +
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
 +
:
 +
;Lecturer
 +
:JP. Dr. [[Maria Fyta]], (Lecture), Prof. Dr. [[Christian Holm]]; Dr. [[Jens Smiatek]]; Mr. [[Bibek Adhikari]]; Mr. [[Narayanan Krishnamoorthy Anand]] (Tutorials)
 +
;Course language
 +
:English
 +
 
 +
;Lectures
 +
:Time:  Thursdays, 11:30 - 13:00,  ICP, Allmandring 3, Seminarroom 1
 +
;Tutorials
 +
:Time: Wednesdays, 8:00-9:30,  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 each worksheet
 +
 
 +
The final grade will be determined from the final oral examination.
 +
 
 +
=== Oral Examination ===
 +
 
 +
'''Please email to [[Christian Holm]] in order to arrange a date in September or october for the oral examination.'''
 +
 
 +
 
 +
 
 +
=== Recommended literature ===
 +
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry>
 +
 
 +
=== Useful online resources ===
 +
 
 +
* Roethlisberger, Tavernarelli, EPFL, Lausanne, 2011: [http://lcbcpc21.epfl.ch/Group_members/ivano/bachelor.pdf Introduction to electronic structure methods.]
 +
 
 +
* 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}}.
 +
 
 +
* 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]
 +
 
 +
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]
 +
 
 +
* [http://www.filibeto.org/sun/lib/development/shell/intr_to_bash_scr.html Short introduction to shell scripting (bash)]
 +
 
 +
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]
 +
 
 +
* [http://ocw.mit.edu/courses/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.
 +
 
 +
== Lecture  ==
 +
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.-->
 +
 
 +
<!--
 +
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font>
 +
-->
 +
{| class="wikitable"
 +
|-valign="top"
 +
!Date !! Subject || Resources
 +
 
 +
|-
 +
| 10.04.2014 || Introduction, electronic stucture || {{Download|simmethodsII_ss14_lecture1.pdf|Lecture Notes}}
 +
 
 +
|-
 +
| 15.04.2014 || Elements of quantum mechanics, Hartree and Hartree-Fock approximations  || {{Download|simmethodsII_ss14_lecture2.pdf|Lecture Notes}}
 +
 
 +
|-
 +
| 22.04.2014 || Density functional theory (DFT), functionals, pseudopotentials, elements on solid state physics ||  {{Download|simmethodsII_ss14_lecture3.pdf |Lecture Notes}} {{Download|simmethodsII_ss14_lecture3_solidstate.pdf |Solid State Phys.}}
 +
 
 +
|-
 +
| 24.04.2014 || Time-dependent density functional theory, post-Hartree-Fock methods ab initio MD  || {{Download|simmethodsII_ss14_lecture4.pdf |Lecture Notes}}
 +
 
 +
|-
 +
| 01.05.2014 || '' Holiday (Labor Day) ''  ||
 +
 
 +
|-
 +
| 08.05.2014 || Water models (explicit, implicit), Born model of solvation  || {{Download|Lecture5_SMII_SS2014.pdf |Lecture Notes}}
 +
 
 +
|-
 +
| 15.05.2014 ||  Coarse-grained models, simulations of macromolecules and soft matter  || {{Download|Lecture_Notes.pdf |Lecture Notes}}
 +
 
 +
|-
 +
| 22.05.2014 || Continuation: CG models || {{Download|L7_addendum_macromolecules.pdf |Lecture Notes}} 
 +
 
 +
|-
 +
| 29.05.2014 || '' Holiday (Christi Himmelfahrt) ''||
 +
 
 +
|-
 +
| 05.06.2014 || Long range interactions in periodic boundary conditions  || {{Download|20140605-SM2.pdf|Lecture Notes}}
 +
 
 +
|-
 +
| 12.06.2014 || '' Holiday (Pfingsten) '' ||
 +
 
 +
|-
 +
| 19.06.2014 || '' Holiday (Fronleichnam) '' ||
 +
 
 +
|-
 +
| 26.06.2014 || Poisson-Boltzmann theory, charged polymers  ||  {{Download|Lecture9_PB_aufschrieb.pdf|Lecture Notes}}
 +
 
 +
|-
 +
| 03.07.2014 || Free energy methods || {{Download|Lecture_Free_NRG_Methods.pdf|Lecture Notes}}
 +
 
 +
|-
 +
| 10.07.2014 || Advanced MC/MD methods||  {{Download|10.7.2014_advanced2.pdf|Lecture Notes}}
 +
 
 +
|-
 +
| 17.07.2014 || Hydrodynamic methods:  DPD, Lattice-Boltzmann||  {{Download|17.7.2014_Hydrodynamics.pdf|Lecture Notes}}
 +
 
 +
|}
 +
 
 +
== Tutorials ==
 +
 
 +
*The tutorials will take place in the ICP CIP-Pool every Wednesday at 8:00-9:30.
 +
 
 +
*New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 10.04. The following week is dedicated to working on problems related to the last worksheet. Homework in the form of a report should be sent to the responsible tutor ([[Bibek Adhikari]] or [[Narayanan Krishnamoorthy Anand]]) before the next worksheet will be handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.
 +
 
 +
*The worksheets should be handed in every second Tuesday until 10 am (see dates below).
 +
 
 +
* Assessment of the tutorials
 +
Each task within the tutorial is assigned a given number of points. Each student should have 50 % of the points from each tutorial as a prerequisite for the oral examination.
 +
 
 +
* Dates:
 +
 
 +
{| class="wikitable"
 +
|-valign="top"
 +
!Worksheet !!  Handed out|| To be handed in
 +
 
 +
|-
 +
| Worksheet 1 || 10.04.2014|| 22.04.2014
 +
 
 +
|-
 +
| Worksheet 2 || 24.04.2014|| 06.05.2014
 +
 
 +
|-
 +
| Worksheet 3 || 08.05.2014|| 20.05.2014
 +
 
 +
|-
 +
| Worksheet 4 || 22.05.2014|| 03.06.2014
 +
 
 +
|-
 +
| Worksheet 5 || 12.06.2014|| 01.07.2014
 +
 
 +
|-
 +
| Worksheet 6 || 03.07.2014|| 15.07.2014
 +
 
 +
|}
 +
 
 +
== Worksheets ==
 +
 
 +
*'''[[Media:Sim_MethodsII_2014_ws1.zip|Worksheet 1 (zip-File with SIESTA input files and attachments)]]''' ''Quantum mechanical approaches - Hückel approximation and DFT methods''
 +
** [[Media:Sim_MethodsII_2014_worksheet1.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:Sim_MethodsII_worksheet2.zip|Worksheet 2 (zip-File with si.fdf)]]''' ''Properties of fermions and Density functional theory''
 +
** [[Media:Sim_MethodsII_2014_worksheet2.pdf|Worksheet 2 (the work sheet as a single PDF file)]]
 +
 
 +
*'''[[Media:ws3_SMII_2014.zip|Worksheet 3 (zip-File with water topology and input files for GROMACS)]]''' ''Diffusion processes and properties of atomistic water models''
 +
** [[Media:tut3_SMII_2014.pdf|Worksheet 3 (the work sheet as a single PDF file)]]
 +
** [http://www.gromacs.org GROMACS Download]
 +
** [http://www.csc.fi/english/csc/courses/archive/material/gmx-gpu-materials/vmd-gromacs-exercises.pdf How to visualize GROMACS trajectories with VMD]
 +
 
 +
*'''[[Media:tutorial.pdf|Worksheet 4 (pdf-file of the tutorial sheet)]]''' ''Coarse-grained polymers and their properties''
 +
** [[Media:poly.tcl|ESPResSo script-file of the tutorial sheet]]'''
 +
** [[Media:Hint.tar.gz|Hint for theoretical task]]'''
 +
** [http://espressomd.org/ ESPResSo-Homepage]
 +
** [http://www.espressomd.org/wordpress/download  Espresso Download]
 +
** [http://espressomd.org/jenkins/job/master-doc/lastSuccessfulBuild/artifact/doc/ug/ug.pdf Espresso Manual]
 +
 
 +
*'''[[Media:ws5_SMII_2014.tar.gz|Worksheet 5 (Tar.gz-file of the tutorial sheet with source code)]]''' ''Long range interactions: Direct sum and Ewald summation''
 +
** [[Media:tut5_SMII_2014.pdf|Worksheet 5 (the work sheet as a single PDF file)]]
 +
** [[Media:Literature_Sim_MethodsII.zip|Useful literature]]'''
 +
 
 +
*'''[[Media:Ws6_SMII_2014_version1.tar.gz|Revised Worksheet 6 (Tar.gz-file with the tutorial sheet, source code and literature)]]''' ''Charge distribution around a charged rod''
 +
** [[Media:tut6_ver1.pdf|Revised Worksheet 6 (the work sheet as a single PDF file)]]
 +
** [[Media:tutorial6.tcl|tutorial6.tcl (Tcl-Script for ESPResSo)]]'''
 +
 
 +
== Examination ==
 +
 
 +
There is an oral examination at the end of the semester. All students having obtained 50% of the points from each tutorial are eligible to take the exam. The duration of the exam depends on the module this lecture is part of. Briefly,
 +
 
 +
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)
 +
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).
 +
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).
 +
 
 +
For additional information/modules, please contact us ([[Maria Fyta]], [[Jens Smiatek]]).
 +
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:
 +
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master 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)
 +
-->

Latest revision as of 15:22, 3 September 2014

Overview

Type
Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
Lecturer
JP. Dr. Maria Fyta, (Lecture), Prof. Dr. Christian Holm; Dr. Jens Smiatek; Mr. Bibek Adhikari; Mr. Narayanan Krishnamoorthy Anand (Tutorials)
Course language
English
Lectures
Time: Thursdays, 11:30 - 13:00, ICP, Allmandring 3, Seminarroom 1
Tutorials
Time: Wednesdays, 8:00-9:30, 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 each worksheet

The final grade will be determined from the final oral examination.

Oral Examination

Please email to Christian Holm in order to arrange a date in September or october for the oral examination.


Recommended literature

  • Daan Frenkel, Berend Smit.
    Understanding Molecular Simulation: From Algorithms to Applications.
    Part of Computational Science, volume 1. Edition 2.
    Academic Press, San Diego, 2002. ISBN: 978-0-12-267351-1.
    [DOI]
  • Mike P. Allen, Dominik J. Tildesley.
    Computer Simulation of Liquids.
    Part of Oxford Science Publications. Edition 1.
    Clarendon Press, Oxford, 1987.
  • D. C. Rapaport.
    The Art of Molecular Dynamics Simulation.
    Edition 2.
    Cambridge University Press, 2004. ISBN: 9780511816581.
    [DOI]
  • D. P. Landau, K. Binder.
    A guide to Monte Carlo Simulations in Statistical Physics.
    Edition second edition.
    Cambridge, 2005.
  • Michael Rubinstein, Ralph H. Colby.
    Polymer Physics.
    Oxford University Press, Oxford, UK, 2003.
  • M. E. J. Newman, G. T. Barkema.
    Monte Carlo Methods in Statistical Physics.
    Edition 2002 edition.
    Oxford University Press, 1999.
  • Sauro Succi.
    The lattice Boltzmann equation for fluid dynamics and beyond.
    Oxford University Press, New York, USA, 2001. ISBN: 9780198503989.
    [PDF] (13 MB)
  • M. E. Tuckermann.
    Statistical Mechanics: Theory and Molecular Simulation.
    Oxfor University Press Oxford Graduate Texts, Oxford, 2010.
  • F. Martin, H. Zipse.
    Charge Distribution in the Water Molecule - A Comparison of Methods.
    Journal of Computational Chemistry 26(1):97–105, 2004.
  • E. Kaxiras.
    Atomic and electronic structure of solids.
    apud Cambridge, Cambridge, 2003.
  • Andrew Leach.
    Molecular Modelling: Principles and Applications.
    apud Pearson Education Ltd., 2001. ISBN: 978-0582382107.


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

Date Subject Resources
10.04.2014 Introduction, electronic stucture application_pdf.pngLecture Notes (3.23 MB)Info circle.png
15.04.2014 Elements of quantum mechanics, Hartree and Hartree-Fock approximations application_pdf.pngLecture Notes (7.83 MB)Info circle.png
22.04.2014 Density functional theory (DFT), functionals, pseudopotentials, elements on solid state physics application_pdf.pngLecture Notes (7.34 MB)Info circle.png application_pdf.pngSolid State Phys. (7.75 MB)Info circle.png
24.04.2014 Time-dependent density functional theory, post-Hartree-Fock methods ab initio MD application_pdf.pngLecture Notes (7.9 MB)Info circle.png
01.05.2014 Holiday (Labor Day)
08.05.2014 Water models (explicit, implicit), Born model of solvation application_pdf.pngLecture Notes (3.81 MB)Info circle.png
15.05.2014 Coarse-grained models, simulations of macromolecules and soft matter application_pdf.pngLecture Notes (4.27 MB)Info circle.png
22.05.2014 Continuation: CG models application_pdf.pngLecture Notes (3.78 MB)Info circle.png
29.05.2014 Holiday (Christi Himmelfahrt)
05.06.2014 Long range interactions in periodic boundary conditions application_pdf.pngLecture Notes (2.32 MB)Info circle.png
12.06.2014 Holiday (Pfingsten)
19.06.2014 Holiday (Fronleichnam)
26.06.2014 Poisson-Boltzmann theory, charged polymers application_pdf.pngLecture Notes (8.55 MB)Info circle.png
03.07.2014 Free energy methods application_pdf.pngLecture Notes (3.44 MB)Info circle.png
10.07.2014 Advanced MC/MD methods application_pdf.pngLecture Notes (3.61 MB)Info circle.png
17.07.2014 Hydrodynamic methods: DPD, Lattice-Boltzmann application_pdf.pngLecture Notes (3.84 MB)Info circle.png

Tutorials

  • The tutorials will take place in the ICP CIP-Pool every Wednesday at 8:00-9:30.
  • New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 10.04. The following week is dedicated to working on problems related to the last worksheet. Homework in the form of a report should be sent to the responsible tutor (Bibek Adhikari or Narayanan Krishnamoorthy Anand) before the next worksheet will be handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.
  • The worksheets should be handed in every second Tuesday until 10 am (see dates below).
  • Assessment of the tutorials

Each task within the tutorial is assigned a given number of points. Each student should have 50 % of the points from each tutorial as a prerequisite for the oral examination.

  • Dates:
Worksheet Handed out To be handed in
Worksheet 1 10.04.2014 22.04.2014
Worksheet 2 24.04.2014 06.05.2014
Worksheet 3 08.05.2014 20.05.2014
Worksheet 4 22.05.2014 03.06.2014
Worksheet 5 12.06.2014 01.07.2014
Worksheet 6 03.07.2014 15.07.2014

Worksheets

Examination

There is an oral examination at the end of the semester. All students having obtained 50% of the points from each tutorial are eligible to take the exam. The duration of the exam depends on the module this lecture is part of. Briefly,

BSc/MSc Physik, Modul "Simulationsmethoden in der Physik"
60 min exam (contents from both parts SMI + SMII will be examined)
International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005)
30 min exam (content only from SMII will be examined).
BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II"
40 min (content from SMII will be examined).

For additional information/modules, please contact us (Maria Fyta, Jens Smiatek).

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