Difference between revisions of "Simulation Methods in Physics II SS 2018"

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Further information and materials will be added soon.
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{{Infobox| Possible exam dates: 
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<!--*Fri 28.07.2017 between 11am-1pm,-->
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<!--*Fri 04.08.2017 between 11am-2pm,-->
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<!--*Wed 04.10.2017 1pm-2pm-->
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<!-- *Thu 05.10.2017 between 10am-2pm,-->
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<!-- *Fri 06.10.2017 at 10am or between 12pm-2pm,-->
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<!--*Thu 14.09.2017 between 1pm-3pm,-->
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<!--*from Mon-Tue 09.10-10.10.2017 between 1pm-3pm,-->
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<!--*Wed 11.10.2017 at 2pm.-->
 +
 
 +
For you preferred date and time, send an e-mail to [[Christian Holm]] and [[Maria Fyta]]. }}
 +
 
 +
== Overview ==
 +
 
 +
;Type
 +
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
 +
;Lecturer
 +
:Prof. Dr. [[Christian Holm]], 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, 15:45 – 17:15 (Tutors: Dr. [[Frank Uhlig]], [[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 ===
 +
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry>
 +
 
 +
=== Useful online resources ===
 +
 
 +
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]
 +
 
 +
* 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://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]
 +
 
 +
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]
 +
 
 +
* Density-functional-theory tight-binding (DFTB): Phil. Trans. R. Soc. A, 372(2011), 20120483. [http://rsta.royalsocietypublishing.org/content/372/2011/20120483], Computational Materials Science 47 (2009) 237–253 [http://www.sciencedirect.com/science/article/pii/S0927025609003036]
 +
 
 +
* "Ab Initio Molecular Dynamics: Theory and Implementation" in Modern Methods and Algorithms, NIC Series Vol 1. (2000) [https://juser.fz-juelich.de/record/44687/files/NIC-Band-1.pdf]
 +
 
 +
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]
 +
 
 +
* 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
 +
|-
 +
<!-- |- -->
 +
<!-- | 13.04.2017 || Classical force fields, Atomistic simulations, Biomolecules  || <!--{{  Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}} {{  Download|simmethodsII_ss16_lecture1notes.pdf|Lecture Notes}}--> -->
 +
<!-- |- -->
 +
<!-- | 20.04.2017 ||  Water models  || <!--{{ |Lecture Notes}} --> -->
 +
<!-- |- -->
 +
<!-- | 27.04.2017 ||  Coarse-grained models, simulations of macromolecules and soft matter  ||{{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}  -->
 +
<!-- |- -->
 +
<!-- | 04.05.2017 || Charged macromolecules || {{DownloadExt|/teaching/2015-ss-sim_methods/lecture07_notes.pdf|Slides}} -->
 +
<!-- |- -->
 +
<!-- | 11.05.2017 || Poisson-Boltzmann theory || <!--{{|Lecture Notes}} --> -->
 +
<!-- |- -->
 +
<!-- | 18.05.2017 ||  Hydrodynamic methods  || [[:File:Lecture Notes Hydrodynamics.pdf|Lecture Notes Hydrodynamics]] {{DownloadExt|/teaching/2015-ss-sim_methods/lecture10_notes.pdf|Lecture Notes LB}} [[:File:Lattice-boltzmann intro.pdf|Intro to LB]] -->
 +
<!-- |-
 +
<!-- | 25.05.2017 || '' Holiday (Christi Himmelfahrt) '' ||  ||  -->
 +
<!-- |- -->
 +
<!-- | 01.06.2017 || Free energy methods ||  [[:File:SKMBT_C454e17072118140.pdf|Free energy calculations]]  -->
 +
<!-- |- -->
 +
<!-- | 08.06.2017 || '' Holiday (Pfingsten) ''  ||  -->
 +
<!-- |- -->
 +
<!-- | 15.06.2017 || '' Holiday (Fronleichnam) '' ||  -->
 +
<!-- |- -->
 +
<!-- | 22.06.2017 || Quantum-mechanical methods, introduction || {{Download|simmethodsII_ss17_lecture1.pdf|Slides}} {{  Download|simmethodsII_ss17_lecture1notes.pdf|Lecture Notes}}  -->
 +
<!-- |- -->
 +
<!-- | 29.06.2017 ||Hartree-Fock,  post Hartree Fock || {{Download|simmethodsII_ss17_lecture2.pdf|Lecture Notes}} -->
 +
<!-- |- -->
 +
<!-- | 06.07.2017 || Density functional theory  and functionals || {{Download|simmethodsII_ss17_lecture3.pdf|Lecture Notes}} -->
 +
<!-- |- -->
 +
<!-- | 13.07.2017 ||  Time-dependent DFT, <i>ab initio</i> MD|| {{Download|simmethodsII_ss17_lecture4.pdf|Lecture Notes}} -->
 +
<!-- |- -->
 +
<!-- | 20.07.2017 || state-of-the art, review || <!--{{Download|simmethodsII_ss17_QM_summary.pdf| QM summary}} {{Download|simmethodsII_ss17_multiscale.pdf|Multiscale examples}} {{|Lecture Notes}}--> -->
 +
|}
 +
 
 +
== 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: [[Frank Uhlig]] / [[David Sean]] )
 +
 
 +
=== Worksheets ===
 +
 
 +
<!--
 +
==== Worksheet 6: Advanced MD/MC: The Widom insertion method ====
 +
* Available online: June 27, 2016
 +
* Deadline: '''July 11, 2016'''
 +
* {{Download|SS_2016_SM2_worksheet6.pdf|Worksheet 6}}
 +
* {{Download|SS_2016_SM2_worksheet6_template.tcl|template.tcl|txt}} - ESPResSo sample script
 +
* {{Download|SS_2016_SM2_WS6_solution.pdf|Solution|pdf}} - Sample solution
 +
 
 +
==== Worksheet 2: Diffusion processes and properties of atomistic water models ====
 +
* Deadline: '''May 9, 2016'''
 +
* {{Download|SimmethodsII ss16 worksheet2.pdf|Worksheet 2}}
 +
* {{Download|SS_2015_SM2_worksheet2_templates.tar.gz|templates.tar.gz|tgz}} - Archive containing GROMACS input files
 +
* {{Download|SS_2016_SM2_WS2_solution.pdf|Solution|pdf}} - Sample solution
 +
-->
 +
 
 +
 
 +
<!--
 +
==== Worksheet 1: Properties and Fitting of Atomistic Water models ====
 +
* Deadline: '''May 1, 2017'''
 +
* {{Download|SimmethodsII_ss17_worksheet1.pdf|Worksheet}}
 +
* {{Download|SimmethodsII_ss17_worksheet1_templates.tar.gz|templates.tar.gz|tgz}}
 +
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report
 +
-->
 +
 
 +
<!--
 +
* {{Download|SS_2015_SM2_WS1_solution.tar.gz|solution.tar.gz|tgz}} - Archive containing the sample solution
 +
-->
 +
 
 +
<!--
 +
==== Worksheet 2: Properties of Coarse-grained Polymers ====
 +
* Deadline: '''May 15, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_02''' as subject line.
 +
* {{Download|SimmethodsII_ss17_worksheet2.pdf|Worksheet}}
 +
* {{Download|SimmethodsII_ss17_template.py|template}}
 +
* {{Download|SimmethodsII_ss17_espresso_install.sh|ESPResSo install}}
 +
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report
 +
 
 +
 
 +
==== Worksheet 3: Charge distribution around a charged rod ====
 +
* Deadline: '''May 29, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_03''' as subject line.
 +
* {{Download|SimmethodsII_ss17_worksheet3.pdf|Worksheet 3}}
 +
* {{Download|SimmethodsII_ss17_template3.py|template}} - ESPResSo sample script
 +
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}
 +
 
 +
 
 +
==== Worksheet 4: Flow Between Plates and Free Energy ====
 +
* Deadline: '''June 19, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.
 +
* {{Download|SimmethodsII_ss17_worksheet4.pdf|Worksheet 4}}
 +
* {{Download|SimmethodsII_ss17_template4.py|template}} - ESPResSo sample script
 +
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}
 +
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report
 +
 
 +
==== Worksheet 5: Quantum chemistry and simple models ====
 +
* Deadline: '''July 3, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_05''' as subject line.
 +
* {{Download|SimmethodsII_ss17_worksheet5.pdf|Worksheet 5}}
 +
* {{Download|SimmethodsII_ss17_template5.tar.gz|template}} - CP2K input files
 +
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report
 +
 
 +
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====
 +
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.
 +
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}
 +
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files
 +
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report
 +
 
 +
-->
 +
 
 +
=== General Remarks ===
 +
 
 +
* 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/2017</code>.
 +
* 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.
 +
* 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 ([[Frank Uhlig]] 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.
 +
<!--
 +
== 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 ([[Christian Holm]], [[Maria Fyta]]).
 +
<!--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 11:04, 4 April 2018

Overview

Type
Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)
Lecturer
Prof. Dr. Christian Holm, 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, 15:45 – 17:15 (Tutors: Dr. Frank Uhlig, 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


Useful online resources

  • Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [1]
  • Linux cheat sheet application_pdf.pnghere (53 KB)Info circle.png.
  • 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

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: Frank Uhlig / David Sean )

Worksheets

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/2017.
  • For the reports, we have a nice txt.pngLaTeX template (7 KB)Info circle.png.
  • 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 (Frank Uhlig 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.