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

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:English
 
:English
  
<!--
 
:{{Infobox|<b> The lecture on 18.07 will start earlier at 11am</b>.}}
 
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;Lectures
 
;Lectures
 
:Time:  Thursdays, 11:30 - 13:00,  ICP, Allmandring 3, Seminarroom 1  
 
:Time:  Thursdays, 11:30 - 13:00,  ICP, Allmandring 3, Seminarroom 1  
:{{Infobox|<b> Exception: the lecture on 17.04 will be moved to Tue 15.04 at 9:00-10:30</b>. There will be two lectures in the week 21-25.04 (Tue 22:04 at 9-10:30 and Thu 24.04 at 11:30-13:00) and NO lecture on the 05.06.}}
 
 
;Tutorials
 
;Tutorials
 
:Time: Wednesdays, 8:00-9:30,  ICP, Allmandring 3, CIP-Pool  
 
:Time: Wednesdays, 8:00-9:30,  ICP, Allmandring 3, CIP-Pool  
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The final grade will be determined from the final oral examination.
 
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 ===
 
=== Recommended literature ===
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a ,newman99a,thijssen07,succi01a,tuckerman10a,steinhauser08a,martin04a,kaxiras03a,leach01a</bibentry>
+
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry>
  
 
=== Useful online resources ===
 
=== Useful online resources ===
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|-
 
|-
| 10.04.2014 || Introduction, electronic stucture || [{{Download|simmethodsII_ss14_lecture1.pdf|Lecture Notes}}]
+
| 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}}]
+
| 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.}}]
+
| 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 <!--QM forces, energy minimization, CPMD, quantum Monte Carlo, QM/MM, tight-binding--> ||
+
| 24.04.2014 || Time-dependent density functional theory, post-Hartree-Fock methods ab initio MD  || {{Download|simmethodsII_ss14_lecture4.pdf |Lecture Notes}}
  
 
|-
 
|-
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|-
 
|-
| 08.05.2014 || Water models (explicit, implicit), Born model of solvation  ||
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| 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  ||  
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| 15.05.2014 ||  Coarse-grained models, simulations of macromolecules and soft matter  || {{Download|Lecture_Notes.pdf |Lecture Notes}}
  
 
|-
 
|-
| 22.05.2014 || Long range interactions in periodic boundary conditions  ||  
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| 22.05.2014 || Continuation: CG models || {{Download|L7_addendum_macromolecules.pdf |Lecture Notes}} 
  
 
|-
 
|-
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|-
 
|-
| 12.06.2014 || '' Holiday (Pfingsten) '' Implicit solvent models  ||  
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| 05.06.2014 || Long range interactions in periodic boundary conditions  || {{Download|20140605-SM2.pdf|Lecture Notes}}
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 +
|-
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| 12.06.2014 || '' Holiday (Pfingsten) '' ||  
  
 
|-
 
|-
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|-
 
|-
| 26.06.2014 || Poisson-Boltzmann theory, charged polymers  ||  
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| 26.06.2014 || Poisson-Boltzmann theory, charged polymers  || {{Download|Lecture9_PB_aufschrieb.pdf|Lecture Notes}}
  
 
|-
 
|-
| 03.07.2014 || Hydrodynamic methods:  DPD, Lattice-Boltzmann ||  
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| 03.07.2014 || Free energy methods || {{Download|Lecture_Free_NRG_Methods.pdf|Lecture Notes}}
  
 
|-
 
|-
| 10.07.2014 || Advanced MC/MD methods ||  
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| 10.07.2014 || Advanced MC/MD methods|| {{Download|10.7.2014_advanced2.pdf|Lecture Notes}}
  
 
|-
 
|-
| 17.07.2014 || Free energy methods ||  
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| 17.07.2014 || Hydrodynamic methods:  DPD, Lattice-Boltzmann|| {{Download|17.7.2014_Hydrodynamics.pdf|Lecture Notes}}
  
 
|}
 
|}
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|-  
 
|-  
| Worksheet 3 || 08.04.2014|| 20.05.2014
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| Worksheet 3 || 08.05.2014|| 20.05.2014
  
 
|-  
 
|-  
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|-  
 
|-  
| Worksheet 5 || 05.06.2014|| 24.06.2014
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| Worksheet 5 || 12.06.2014|| 01.07.2014
  
 
|-  
 
|-  
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** [http://icmab.cat/leem/siesta/Documentation/Tutorials/Lyon-2007/index.html Hands-on-tutorial for SIESTA, Lyon 2007]
 
** [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:worksheet2.zip|Worksheet 2 (zip-File with si.fdf)]]''' ''Properties of fermions and Density functional theory''
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** [[Media:Sim_MethodsII_2014_worksheet2.pdf|Worksheet 2 (the work sheet as a single PDF file)]]
 
 
*'''[[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''  
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*'''[[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:alanine_dipeptide.pdf|Worksheet 4 (the work sheet as a single PDF file)]]
+
** [[Media:tut3_SMII_2014.pdf|Worksheet 3 (the work sheet as a single PDF file)]]
 
** [http://www.gromacs.org GROMACS Download]
 
** [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]
 
** [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:tutorial.pdf|Worksheet 4 (pdf-file of the tutorial sheet)]]''' ''Coarse-grained polymers and their properties''  
** [[Media:tut5.pdf|Worksheet 5 (the work sheet as a single PDF file)]]
+
** [[Media:poly.tcl|ESPResSo script-file of the tutorial sheet]]'''
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** [[Media:Hint.tar.gz|Hint for theoretical task]]'''
 
** [http://espressomd.org/ ESPResSo-Homepage]
 
** [http://espressomd.org/ ESPResSo-Homepage]
** [http://espressomd.org/wordpress/download/ ESPResSo-Download]
+
** [http://www.espressomd.org/wordpress/download Espresso Download]
** [http://espressomd.org/jenkins/job/ESPResSo/lastSuccessfulBuild/artifact/doc/ug/ug.pdf ESPResSo-Manual]
+
** [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 ==
 
== Examination ==

Latest revision as of 14:22, 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


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).