Difference between revisions of "Simulation Methods in Physics II SS 2018"
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− | + | {{Infobox| Possible exam dates: | |
− | For you preferred date and time, send an e-mail to | + | |
− | + | Tuesday 24.07.2018 between 10am-2pm, <br> | |
+ | Wednesday 25.07.2018 between 10am-2pm, <br> | ||
+ | Thursday 26.07.2018 between 10am-2pm, <br> | ||
+ | Tuesday 31.07.2018 between 11am-2pm, <br> | ||
+ | Wednesday 01.08.2018 between 10am-2pm, <br> | ||
+ | <!--Thursday 02.08.2018 between 11am-2pm, <br--> | ||
+ | Tuesday 11.09.2018 between 12pm-2pm, <br> | ||
+ | Wednesday 12.09.2018 between 11am-2pm, <br> | ||
+ | <!--Monday 01.10.2018 between 1pm-2pm, <br--> | ||
+ | Tuesday 02.10.2018 between 12pm-2pm, <br> | ||
+ | <!-- Thursday 04.10.2018 between 12pm-2pm, <br> | ||
+ | Monday 22.10.2018 between 12pm-14pm. <br--> | ||
+ | |||
+ | For you preferred date and time, send an e-mail to [[Maria Fyta]]. }} | ||
+ | |||
== Overview == | == Overview == | ||
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;Location and Time | ;Location and Time | ||
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079) | :'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079) | ||
− | :'''Tutorials''': Thu, 15: | + | :'''Tutorials''': Thu, 14:00-15:30 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; ICP, Allmandring 3, CIP-Pool (room 01.033) |
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 containing the lecture "Simulation Methods in Physics II". | 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 containing the lecture "Simulation Methods in Physics II". | ||
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=== Recommended literature === | === Recommended literature === | ||
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry> | <bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry> | ||
− | |||
=== Useful online resources === | === Useful online resources === | ||
− | * Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https:// | + | * Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0] |
− | * E-Book: Kieron Burke et al.,University of California, 2007: [http:// | + | * E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/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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* 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. | ||
+ | |||
== 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.--> | ||
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!Date !! Subject || Resources | !Date !! Subject || Resources | ||
|- | |- | ||
− | | 12.04.2018 || Introduction/organisation, electronic structure | + | | 12.04.2018 || Introduction/organisation, electronic structure || {{Download|simmethodsII_ss18_lecture1.pdf|Slides}}, {{Download|simmethodsII_ss18_lecture1notes.pdf|Lecture Notes}} |
|- | |- | ||
− | | 19.04.2018 || | + | | 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || {{Download|simmethodsII_ss18_lecture2.pdf|Lecture Notes}} |
|- | |- | ||
− | | 26.04.2018 || | + | | 26.04.2018 || Density Functional Theory (DFT) || {{Download|simmethodsII_ss18_lecture3.pdf|Lecture Notes (1)}}, {{Download|simmethodsII_ss18_lecture3b.pdf|Lecture Notes (2)}} |
|- | |- | ||
− | | | + | | 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} |
− | |||
− | |||
|- | |- | ||
− | | 10.05.2018 || Holiday (Christi Himmelfahrt) || | + | | 10.05.2018 || Holiday (Christi Himmelfahrt) || --- |
|- | |- | ||
− | | 17.05.2018 || | + | | 17.05.2018 || Classical force fields and water models || {{Download|simmethodsII_ss18_lecture5slides.pdf|Slides}}, {{Download|simmethodsII_ss18_lecture5.pdf|Lecture Notes}} |
|- | |- | ||
− | | 24.05.2018 || '' Holiday (Pfingsten) '' || | + | | 24.05.2018 || '' Holiday (Pfingsten) '' || --- |
|- | |- | ||
− | | 31.05.2018 || Holiday (Fronleichnam) '' || | + | | 31.05.2018 || Holiday (Fronleichnam) '' || --- |
|- | |- | ||
− | | 07.06.2018 || | + | | 07.06.2018 || Simulations of macromolecules and soft matter || {{Download|simmethodsII_ss18_lecture6.pdf|Lecture Notes}} |
|- | |- | ||
− | | 14.06.2018 || | + | | 14.06.2018 || Poisson-Boltzmann theory, charged polymers || {{Download|Poisson-Boltzmann-DavidNotes.pdf |Poisson-Boltzmann}} {{Download|Flory-DavidNotes.pdf|Polymer scaling}} |
|- | |- | ||
− | | 21.06.2018 || | + | | 21.06.2018 || Hydrodynamic methods I (Brownian and Langevin Dynamics) || {{Download|simmethodsII_ss18_lecture8.pdf|Lecture Notes}} |
|- | |- | ||
− | | 28.06.2018 || | + | | 28.06.2018 || Hydrodynamic methods II (DPD, Lattice-Boltzmann) (contd.) || {{Download|simmethodsII_ss18_lecture9.pdf|Lecture Notes}} |
|- | |- | ||
− | | 05.07.2018 || | + | | 05.07.2018 || Lattice-Boltzmann (contd.)|| {{Download|simmethodsII_ss18_lecture9b.pdf|Lecture Notes (LBM)}} |
|- | |- | ||
− | | 12.07.2018 || Free energy methods || | + | | 12.07.2018 || Free energy methods <!--Energy minimization, Interatomic potentials (pair-potentials, EAM) (solid-state systems)-->|| {{Download|simmethodsII_ss18_lecture10.pdf|Lecture Notes}}, --><!--{{Download|simmethodsII_ss18_lecture12.pdf|Lecture Notes (TB, DFTB)}} --> |
|- | |- | ||
| 19.07.2018 ||Coarse-graining, multiscale simulations || | | 19.07.2018 ||Coarse-graining, multiscale simulations || | ||
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=== Location and Time === | === Location and Time === | ||
− | * The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu, 15:45 – 17:15 (Tutors: [[ | + | * The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] ) |
=== Worksheets === | === Worksheets === | ||
+ | |||
+ | There will be in total 6 worksheets, which will be handed out every two weeks on Wednesdays at 14:00. The deadline for the solutions will be two weeks after on Wednesdays before 13:00. | ||
+ | <b>The first worksheet will be uploaded on Wed. April 18th. The deadline will be Wed. May 2nd. </b> | ||
<!-- | <!-- | ||
− | ==== Worksheet | + | ==== Worksheet 1: Quantum chemistry and simple models ==== |
− | + | * Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line. | |
− | * Deadline: ''' | + | * {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}} |
− | + | * {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files | |
− | + | * {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report | |
− | |||
− | |||
− | |||
− | |||
− | * {{Download| | ||
− | * {{Download| | ||
− | * {{Download| | ||
− | |||
+ | ==== Worksheet 2: Density Functional Theory ==== | ||
+ | * additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout | ||
+ | * Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line. | ||
+ | * {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}} | ||
+ | * {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files | ||
+ | * {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report | ||
− | + | ==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ==== | |
− | ==== Worksheet | + | * Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line. |
− | * Deadline: '''May | + | * {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}} |
− | * {{Download| | + | * {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files |
− | * {{Download| | ||
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report | * {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report | ||
− | |||
− | + | ==== Worksheet 4: Properties of Coarse-grained Polymers ==== | |
− | + | * Deadline: '''June 20, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line. | |
− | + | * {{Download|SimmethodsII_ss18_worksheet4.pdf|Worksheet}} | |
− | + | * {{Download|SimmethodsII_ss18_template.py|template}} | |
− | |||
− | ==== Worksheet | ||
− | * Deadline: ''' | ||
− | * {{Download| | ||
− | * {{Download| | ||
* {{Download|SimmethodsII_ss17_espresso_install.sh|ESPResSo install}} | * {{Download|SimmethodsII_ss17_espresso_install.sh|ESPResSo install}} | ||
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report | * {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report | ||
− | ==== Worksheet | + | ==== Worksheet 5: Charge distribution around a charged rod ==== |
− | * Deadline: ''' | + | * Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line. |
− | * {{Download| | + | * {{Download|SimmethodsII_ss18_worksheet5.pdf| the Worksheet}} |
− | * {{Download| | + | * {{Download|SimmethodsII_ss18_worksheet5NEW.pdf| NEW Worksheet}} |
+ | * {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script | ||
* {{Download|espresso_install_script_rod.sh|ESPResSo install}} | * {{Download|espresso_install_script_rod.sh|ESPResSo install}} | ||
− | + | ==== Worksheet 6: Flow Between Plates and Free Energy ==== | |
− | ==== Worksheet | + | * Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line. |
− | * Deadline: ''' | + | * {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}} |
− | * {{Download| | + | * {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script |
− | * {{Download| | ||
* {{Download|espresso_install_script_LB.sh|ESPResSo install}} | * {{Download|espresso_install_script_LB.sh|ESPResSo install}} | ||
− | |||
− | |||
− | |||
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* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report | * {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report | ||
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* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files | * {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files | ||
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report | * {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report | ||
− | |||
--> | --> | ||
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* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]]. | * For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]]. | ||
− | * All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/ | + | * All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>. |
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}. | * For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}. | ||
* 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. | * 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. | ||
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* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report. | * A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report. | ||
* You have two weeks to prepare the report for each worksheet. | * You have two weeks to prepare the report for each worksheet. | ||
− | * The report has to be sent to your tutor via email ([[ | + | * The report has to be sent to your tutor via email ([[Miriam Kohagen]] or [[David Sean]]). |
* 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. | * 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. | ||
Latest revision as of 15:17, 17 June 2019
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Possible exam dates:
Tuesday 24.07.2018 between 10am-2pm, |
Overview
- Type
- Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
- Lecturer
- JP Dr. Maria Fyta
- Course language
- English
- Location and Time
- Lecture: Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)
- Tutorials: Thu, 14:00-15:30 (Tutors: Dr. Miriam Kohagen, Dr. David Sean; ICP, Allmandring 3, CIP-Pool (room 01.033)
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 containing the lecture "Simulation Methods in Physics II".
These hands-on-tutorials 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. Obtaining 50% of the possible marks in the hand-in exercises.
The final grade will be determined from the final oral examination.
Oral Examination
Please email to Christian Holm or Maria Fyta 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
- Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [1]
- E-Book: Kieron Burke et al.,University of California, 2007: E-Book: The ABC of DFT.
- Linux cheat sheet
here (53 KB)
.
- A good and freely available book about using Linux: Introduction to Linux by M. Garrels
- Density-functional-theory tight-binding (DFTB): Phil. Trans. R. Soc. A, 372(2011), 20120483. [2], Computational Materials Science 47 (2009) 237–253 [3]
- "Ab Initio Molecular Dynamics: Theory and Implementation" in Modern Methods and Algorithms, NIC Series Vol 1. (2000) [4]
- University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [5]
- 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 |
---|---|---|
12.04.2018 | Introduction/organisation, electronic structure | ![]() ![]() ![]() ![]() |
19.04.2018 | Hartree and Hartree-Fock (HF) approximations, post HF | ![]() ![]() |
26.04.2018 | Density Functional Theory (DFT) | ![]() ![]() ![]() ![]() |
03.05.2018 | ab initio MD, QM/MM | ![]() ![]() |
10.05.2018 | Holiday (Christi Himmelfahrt) | --- |
17.05.2018 | Classical force fields and water models | ![]() ![]() ![]() ![]() |
24.05.2018 | Holiday (Pfingsten) | --- |
31.05.2018 | Holiday (Fronleichnam) | --- |
07.06.2018 | Simulations of macromolecules and soft matter | ![]() ![]() |
14.06.2018 | Poisson-Boltzmann theory, charged polymers | ![]() ![]() ![]() ![]() |
21.06.2018 | Hydrodynamic methods I (Brownian and Langevin Dynamics) | ![]() ![]() |
28.06.2018 | Hydrodynamic methods II (DPD, Lattice-Boltzmann) (contd.) | ![]() ![]() |
05.07.2018 | Lattice-Boltzmann (contd.) | ![]() ![]() |
12.07.2018 | Free energy methods | ![]() ![]() |
19.07.2018 | Coarse-graining, multiscale simulations |
Tutorials
Location and Time
- The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu, 15:45 – 17:15 (Tutors: Miriam Kohagen / David Sean )
Worksheets
There will be in total 6 worksheets, which will be handed out every two weeks on Wednesdays at 14:00. The deadline for the solutions will be two weeks after on Wednesdays before 13:00. The first worksheet will be uploaded on Wed. April 18th. The deadline will be Wed. May 2nd.
General Remarks
- For the tutorials, you will get a personal account for the ICP machines.
- All material required for the tutorials can also be found on the ICP computers in the directory
/group/sm/2018
. - For the reports, we have a nice
LaTeX template (7 KB)
.
- You can do the exercises in the CIP-Pool when it is not occupied by another course. The pool is accessible on all days, except weekends and late evenings.
- If you do the exercises in the CIP-Pool, all required software and tools are available.
Hand-in-exercises
- 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.
- A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.
- You have two weeks to prepare the report for each worksheet.
- The report has to be sent to your tutor via email (Miriam Kohagen or David Sean).
- 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.
What happens in a tutorial
- The tutorials take place every week.
- You will receive the new worksheet on the days before the tutorial.
- 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.
- In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.
- You will have to hand in the reports on Monday after the second tutorial.
- In the third tutorial after you received the worksheet, the solutions will be discussed:
- The tutor will ask a team to present their solution.
- The tutor will choose one of the members of the team to present each task.
- This means that each team member should be able to present any task.
- At the end of the term, everybody should have presented at least once.