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
 +
 
 +
<!--
 +
:{{Infobox|<b> The lecture on 18.07 will start earlier at 11am</b>.}}
 +
-->
 +
;Lectures
 +
:Time:  Thursdays, 11:30 - 13:00,  ICP, Allmandring 3, Seminarroom 1
 +
:{{Infobox|<b> Exception: the lecture on 17.04 will be moved to another day (more information soon)</b>. There will be two lectures in the week 21-25.04 and NO lecture on the 05.06.}}
 +
;Tutorials
 +
:Time: TBA,  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.
 +
 
 +
=== Recommended literature ===
 +
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a,thijssen07,succi01a,tuckerman10a,steinhauser08a,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_ss13_lecture1.pdf|Lecture Notes}}]-->
 +
 
 +
|-
 +
| 15.04.2014 || Elements of quantum mechanics, Hartree and Hartree-Fock approximations  ||
 +
 
 +
|-
 +
| 22.04.2014 || Density functional theory (DFT), functionals, pseudopotentials ||
 +
 
 +
|-
 +
| 24.04.2014 || Time-dependent density functional theory, post-Hartree-Fock methods <!--QM forces, energy minimization, CPMD, quantum Monte Carlo, QM/MM, tight-binding--> ||
 +
 
 +
|-
 +
| 01.05.2014 || '' Holiday (Labor Day) ''  ||
 +
 
 +
|-
 +
| 08.05.2014 || Water models (explicit, implicit), Born model of solvation  ||
 +
 
 +
|-
 +
| 15.05.2014 ||  Coarse-grained models, simulations of macromolecules and soft matter  ||
 +
 
 +
|-
 +
| 22.05.2014 || Long range interactions in periodic boundary conditions  ||
 +
 
 +
|-
 +
| 29.05.2014 || '' Holiday (Christi Himmelfahrt) ''||
 +
 
 +
|-
 +
| 12.06.2014 || '' Holiday (Pfingsten) '' Implicit solvent models  ||
 +
 
 +
|-
 +
| 19.06.2014 || '' Holiday (Fronleichnam) '' ||
 +
 
 +
|-
 +
| 26.06.2014 || Poisson-Boltzmann theory, charged polymers  ||
 +
 
 +
|-
 +
| 03.07.2014 || Hydrodynamic methods:  DPD, Lattice-Boltzmann ||
 +
 
 +
|-
 +
| 10.07.2014 || Advanced MC/MD methods ||
 +
 
 +
|-
 +
| 17.07.2014 || Free energy methods ||
 +
 
 +
|}
 +
 
 +
== Tutorials ==
 +
 
 +
*The tutorials will take place in the ICP CIP-Pool. Day and time will be announced
 +
 
 +
*New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 17.04. 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.
 +
 
 +
* 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.
 +
 
 +
== Worksheets ==
 +
<!--
 +
 
 +
*'''[[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]
 +
 
 +
*'''[[Media:alanine_dipeptide.zip|Worksheet 4 (zip-File with input files)]]''' ''All-atom Molecular Dynamics simulations of the alanine dipeptide''
 +
** [[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 ==
 +
 
 +
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)
 +
-->

Revision as of 14:39, 31 March 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
Information icon-40x40.png Exception: the lecture on 17.04 will be moved to another day (more information soon). There will be two lectures in the week 21-25.04 and NO lecture on the 05.06.
Tutorials
Time: TBA, 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.

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.
  • 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.
  • Martin O. Steinhauser, Kai Grass, Elmar Strassburger, Alexander Blumen.
    Impact failure of granular materials – Non-equilibrium multiscale simulations and high-speed experiments.
    International Journal of Plasticity XXX:XXX, 2008.
    [PDF] (5.2 MB)
  • 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
15.04.2014 Elements of quantum mechanics, Hartree and Hartree-Fock approximations
22.04.2014 Density functional theory (DFT), functionals, pseudopotentials
24.04.2014 Time-dependent density functional theory, post-Hartree-Fock methods
01.05.2014 Holiday (Labor Day)
08.05.2014 Water models (explicit, implicit), Born model of solvation
15.05.2014 Coarse-grained models, simulations of macromolecules and soft matter
22.05.2014 Long range interactions in periodic boundary conditions
29.05.2014 Holiday (Christi Himmelfahrt)
12.06.2014 Holiday (Pfingsten) Implicit solvent models
19.06.2014 Holiday (Fronleichnam)
26.06.2014 Poisson-Boltzmann theory, charged polymers
03.07.2014 Hydrodynamic methods: DPD, Lattice-Boltzmann
10.07.2014 Advanced MC/MD methods
17.07.2014 Free energy methods

Tutorials

  • The tutorials will take place in the ICP CIP-Pool. Day and time will be announced
  • New worksheets are handed out every two weeks. The first worksheet will be handed out on Thu. 17.04. 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.
  • 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.

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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