https://www.icp.uni-stuttgart.de/~icp/mediawiki/api.php?action=feedcontributions&user=Mfyta&feedformat=atomICPWiki - User contributions [en]2019-08-21T13:23:04ZUser contributionsMediaWiki 1.31.3https://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24429Simulation Methods in Physics II SS 20192019-08-03T07:27:42Z<p>Mfyta: </p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
<!--Wednesday 18.09.2019 between 1pm-2pm, <br--><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 1pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT, <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{Download|simmethodsII_ss19_lecture10.pdf | Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{Download|simmethodsII_ss19_lecture11.pdf | Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle interactions <!-- Coarse-graining, multiscale simulations -->|| {{Download|simmethodsII_ss19_lecture12.pdf| Lecture Notes}}, {{Download|simmethodsII_ss19_lecture12_slides.pdf| slides}}<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
==== Worksheet 6: Computational Fluid Dynamics and Free Energy ====<br />
* Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24424Simulation Methods in Physics II SS 20192019-07-30T11:17:23Z<p>Mfyta: </p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 1pm-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 1pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT, <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{Download|simmethodsII_ss19_lecture10.pdf | Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{Download|simmethodsII_ss19_lecture11.pdf | Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle interactions <!-- Coarse-graining, multiscale simulations -->|| {{Download|simmethodsII_ss19_lecture12.pdf| Lecture Notes}}, {{Download|simmethodsII_ss19_lecture12_slides.pdf| slides}}<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
==== Worksheet 6: Computational Fluid Dynamics and Free Energy ====<br />
* Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24418Simulation Methods in Physics II SS 20192019-07-18T11:10:29Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 12pm-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 1pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT, <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{Download|simmethodsII_ss19_lecture10.pdf | Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{Download|simmethodsII_ss19_lecture11.pdf | Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle interactions <!-- Coarse-graining, multiscale simulations -->|| {{Download|simmethodsII_ss19_lecture12.pdf| Lecture Notes}}, {{Download|simmethodsII_ss19_lecture12_slides.pdf| slides}}<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
==== Worksheet 6: Computational Fluid Dynamics and Free Energy ====<br />
* Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24414Simulation Methods in Physics II SS 20192019-07-16T15:41:41Z<p>Mfyta: </p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 12pm-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 1pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT, <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{Download|simmethodsII_ss19_lecture10.pdf | Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{Download|simmethodsII_ss19_lecture11.pdf | Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle interactions <!-- Coarse-graining, multiscale simulations -->|| <!--{{Download|simmethodsII_ss19_lecture12.pdf| Lecture Notes}}, {{Download|simmethodsII_ss19_lecture12_slides.pdf| slides}}--><br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
==== Worksheet 6: Computational Fluid Dynamics and Free Energy ====<br />
* Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture12.pdf&diff=24413File:SimmethodsII ss19 lecture12.pdf2019-07-16T15:08:03Z<p>Mfyta: Mfyta uploaded a new version of File:SimmethodsII ss19 lecture12.pdf</p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24407Simulation Methods in Physics II SS 20192019-07-15T07:46:32Z<p>Mfyta: </p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 11am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 1pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT, <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{Download|simmethodsII_ss19_lecture10.pdf | Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{Download|simmethodsII_ss19_lecture11.pdf | Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle interactions <!-- Coarse-graining, multiscale simulations -->|| <!--{{Download|simmethodsII_ss19_lecture12.pdf| Lecture Notes}}, {{Download|simmethodsII_ss19_lecture12_slides.pdf| slides}}--><br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
==== Worksheet 6: Computational Fluid Dynamics and Free Energy ====<br />
* Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture12.pdf&diff=24406File:SimmethodsII ss19 lecture12.pdf2019-07-11T12:47:57Z<p>Mfyta: </p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24405Simulation Methods in Physics II SS 20192019-07-11T11:15:22Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 1pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT, <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{Download|simmethodsII_ss19_lecture10.pdf | Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{Download|simmethodsII_ss19_lecture11.pdf | Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle interactions <!-- Coarse-graining, multiscale simulations -->|| <!--{{Download|simmethodsII_ss19_lecture12.pdf| Lecture Notes}}, {{Download|simmethodsII_ss19_lecture12_slides.pdf| slides}}--><br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
==== Worksheet 6: Computational Fluid Dynamics and Free Energy ====<br />
* Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24404Simulation Methods in Physics II SS 20192019-07-11T11:15:03Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 1pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT, <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{Download|simmethodsII_ss19_lecture10.pdf | Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{Download|simmethodsII_ss19_lecture11.pdf | Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle Interactions <!-- Coarse-graining, multiscale simulations -->|| <!--{{Download|simmethodsII_ss19_lecture12.pdf| Lecture Notes}}, {{Download|simmethodsII_ss19_lecture12_slides.pdf| slides}}--><br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
==== Worksheet 6: Computational Fluid Dynamics and Free Energy ====<br />
* Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24401Simulation Methods in Physics II SS 20192019-07-11T08:22:45Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 1pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT, <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{Download|simmethodsII_ss19_lecture10.pdf | Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{<!--Download|simmethodsII_ss19_lecture11.pdf-->| Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle Interactions <!-- Coarse-graining, multiscale simulations -->|| <!--{{Download|simmethodsII_ss19_lecture12.pdf| Lecture Notes}}, {{Download|simmethodsII_ss19_lecture12_slides.pdf| slides}}--><br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
==== Worksheet 6: Computational Fluid Dynamics and Free Energy ====<br />
* Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture12_slides.pdf&diff=24400File:SimmethodsII ss19 lecture12 slides.pdf2019-07-11T08:21:29Z<p>Mfyta: </p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24399Simulation Methods in Physics II SS 20192019-07-11T06:51:15Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 1pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT, <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{Download|simmethodsII_ss19_lecture10.pdf | Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{<!--Download|simmethodsII_ss19_lecture11.pdf-->| Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle Interactions <!-- Coarse-graining, multiscale simulations -->|| {{<!--Download|simmethodsII_ss19_lecture12.pdf-->| Lecture Notes}} <br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
==== Worksheet 6: Computational Fluid Dynamics and Free Energy ====<br />
* Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24398Simulation Methods in Physics II SS 20192019-07-11T06:50:55Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 1pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT, <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{Download|simmethodsII_ss19_lecture10.pdf | Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{<!--Download|simmethodsII_ss19_lecture11.pdf-->| Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle Interactions <!-- Coarse-graining, multiscale simulations -->|| {{<!--Download|simmethodsII_ss19_lecture12.pdf-->| Lecture Notes}} <br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
==== Worksheet 6: Computational Fluid Dynamics and Free Energy ====<br />
* Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24389Simulation Methods in Physics II SS 20192019-07-04T21:43:43Z<p>Mfyta: </p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 1pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{Download|simmethodsII_ss19_lecture10.pdf | Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{<!--Download|simmethodsII_ss19_lecture11.pdf-->| Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle Interactions <!-- Coarse-graining, multiscale simulations -->|| {{<!--Download|simmethodsII_ss19_lecture12.pdf-->| Lecture Notes}} <br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
==== Worksheet 6: Computational Fluid Dynamics and Free Energy ====<br />
* Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24388Simulation Methods in Physics II SS 20192019-07-04T11:21:04Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{Download|simmethodsII_ss19_lecture10.pdf | Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{<!--Download|simmethodsII_ss19_lecture11.pdf-->| Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle Interactions <!-- Coarse-graining, multiscale simulations -->|| {{<!--Download|simmethodsII_ss19_lecture12.pdf-->| Lecture Notes}} <br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
==== Worksheet 6: Computational Fluid Dynamics and Free Energy ====<br />
* Deadline: '''July 17, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24366Simulation Methods in Physics II SS 20192019-06-28T21:52:27Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods <!--(Brownian, Langevin, DPD) Lattice-Boltzmann--> || {{<!--Download|simmethodsII_ss19_lecture10.pdf-->| Lecture Notes}} <br />
|- <br />
| 11.07.2019 || Free energy methods || {{<!--Download|simmethodsII_ss19_lecture11.pdf-->| Lecture Notes}} <br />
|- <br />
| 18.07.2019 || Particle Interactions <!-- Coarse-graining, multiscale simulations -->|| {{<!--Download|simmethodsII_ss19_lecture12.pdf-->| Lecture Notes}} <br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
<!--<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture10.pdf&diff=24365File:SimmethodsII ss19 lecture10.pdf2019-06-28T21:50:32Z<p>Mfyta: </p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture11.pdf&diff=24364File:SimmethodsII ss19 lecture11.pdf2019-06-28T21:49:42Z<p>Mfyta: </p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture8.pdf&diff=24363File:SimmethodsII ss19 lecture8.pdf2019-06-27T11:09:57Z<p>Mfyta: Mfyta uploaded a new version of File:SimmethodsII ss19 lecture8.pdf</p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24362Simulation Methods in Physics II SS 20192019-06-27T11:08:17Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
<!--<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Main_Page&diff=24361Main Page2019-06-27T07:07:33Z<p>Mfyta: /* Contact */</p>
<hr />
<div><div style="font-size: large; font-weight: bold; margin-bottom: 1em;">Welcome to the home page of the </div><br />
<p><br />
[[Image:ICPLogo_V2.png|left|bottom|500px|link=|alt=ICP]] <span class="plainlinks">[[Image:unistuttgart_logo_englisch.png|center|550px|link=http://www.uni-stuttgart.de|alt=Universitaet Stuttgart]]</span><br />
</p><br />
<br />
<p style="padding: 20px 20px 0 20px;">We use high-performance computing on supercomputers and parallel clusters to solve complex problems in physics that would otherwise be impossible to solve via analytical methods. Our main [[research]] areas are presently to understand the physics of '''soft matter systems''' in general, with a particular emphasis on charged systems like polyelectrolytes, charged colloids, ferrofluids and ionic liquids. In addition we are interested in various biophysical problems. The simulations are performed on parallel computers with help of the simulation package '''{{ES}}''', and we continue to develop algorithms for long range interactions.</p> <br />
<p style="padding: 0 20px 0 20px;">Another <br />
[http://www.icp.uni-stuttgart.de/~hilfer focus of our research] <br />
are transport and relaxation in disordered systems such as<br />
[http://www.icp.uni-stuttgart.de/~hilfer/publikationen/diffusion.php anomalous diffusion],<br />
[http://www.icp.uni-stuttgart.de/~hilfer/publikationen/glasses.php glasses] or<br />
[http://www.icp.uni-stuttgart.de/~hilfer/publikationen/porous.php geometry, flow and transport phenomena in porous media].<br />
Our methods are not only '''computer simulations''', but we apply also <br />
[http://www.icp.uni-stuttgart.de/~hilfer/publikationen/fractional.php fractional calculus],<br />
[http://www.icp.uni-stuttgart.de/~hilfer numerical methods], <br />
[http://www.icp.uni-stuttgart.de/~hilfer stochastic processes], density functional methods, and other approaches<br />
of [http://www.icp.uni-stuttgart.de/~hilfer/publikationen/statphys.php statistical physics]. <br />
</p><br />
<br />
== News ==<br />
<br />
== Contact ==<br />
<br />
{| style="width:100%;align=center;"<br />
!width="40%"| <br />
!width="40%"|<br />
|-<br />
|<div style="border:thin solid black; background-color:#B1CED7; padding:10px; margin-left:auto; margin-right:auto; width:20em;">[[Christian Holm|Prof. Dr. Christian Holm (Director)]]<br /><br />
[http://www.icp.uni-stuttgart.de/~hilfer Rudolf Hilfer] <br />
<br />
[[Maria Fyta|JP Dr. Maria Fyta]]<br /><br />Office:[[Henriette Patzelt]]<br />[http://www.icp.uni-stuttgart.de/nmt.php?page=sekretariat e-Mail]<br /><br />
Phone: 49-(0)711/685-63593<br />Fax: 49-(0)711/685-63658 </div><br />
|<div style="border:thin solid black; background-color:#B1CED7; padding:10px; margin-left:auto; margin-right:auto; width:20em;">Institute for Computational Physics<br/>Universität Stuttgart<br/>Allmandring 3<br/>70569 Stuttgart<br/>Germany<br/><br/>[[How to find us]]?</div><br />
|}<br />
{| style="width:100%;align=center;"<br />
|<div style="border:thin solid black; background-color:#B1CED7; padding:10px; margin-left:auto; margin-right:auto; width:89.2%;">Professor Holm's Office Hours: Monday, 13:15 - 14:00<br/>Professor Hilfer Sprechstunde: Mittwoch 11:30 - 12:15<br/>JP Fyta's Office Hours: Tuesday and Friday, 10:00 - 11:00</div><br />
|}<br />
<br />
== The Group ==<br />
[[Image:2012_group_picture.jpg|thumb|center|500px|ICP group, November 2012]]<br />
[[Image:2010_group_picture.jpg|thumb|center|250px|ICP group, October 2010]]</div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24360Simulation Methods in Physics II SS 20192019-06-25T08:49:11Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || polymer dynamics, Flory theory, Poisson-Boltzmann theory || <!--{{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} --> <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
<!--<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24359Simulation Methods in Physics II SS 20192019-06-25T08:48:52Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || polymer dynamics, Flory theory, Poisson-Boltzmann theory || {{Download|simmethodsII_ss19_lecture9.pdf| Lecture Notes}} --> <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
<!--<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture9.pdf&diff=24358File:SimmethodsII ss19 lecture9.pdf2019-06-25T08:47:13Z<p>Mfyta: </p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24357Simulation Methods in Physics II SS 20192019-06-25T07:18:46Z<p>Mfyta: /* Worksheet 5: Charge distribution and Poisson Boltzmann theory */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymers & solvents, Poisson-Boltzmann theory, charged polymers || <!--{{Download|simmethodsII_ss19_lecture9a.pdf| Polymer models (contnd)}}, {{Download|simmethodsII_ss19_lecture9b.pdf| Poisson-Boltzmann}} --> <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
* {{Download|deserno_cell_PBE_2001.pdf| M. Deserno and C. Holm, 2001 }} - Paper for the cell model and the charged rod.<br />
<br />
<!--<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:Deserno_cell_PBE_2001.pdf&diff=24356File:Deserno cell PBE 2001.pdf2019-06-25T07:16:16Z<p>Mfyta: </p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24355Simulation Methods in Physics II SS 20192019-06-24T08:01:59Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymers & solvents, Poisson-Boltzmann theory, charged polymers || <!--{{Download|simmethodsII_ss19_lecture9a.pdf| Polymer models (contnd)}}, {{Download|simmethodsII_ss19_lecture9b.pdf| Poisson-Boltzmann}} --> <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture9a.pdf&diff=24354File:SimmethodsII ss19 lecture9a.pdf2019-06-24T08:00:51Z<p>Mfyta: </p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24353Simulation Methods in Physics II SS 20192019-06-24T07:19:29Z<p>Mfyta: /* Worksheets */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymers & solvents, Poisson-Boltzmann theory, charged polymers || <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24352Simulation Methods in Physics II SS 20192019-06-24T07:19:11Z<p>Mfyta: </p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
<!--Wednesday 09.10.2019 between 12pm-2pm, <br--><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymers & solvents, Poisson-Boltzmann theory, charged polymers || <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24351Simulation Methods in Physics II SS 20192019-06-24T07:12:16Z<p>Mfyta: </p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
<!--Tuesday 17.09.2019 between 1pm-2pm, <br--><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
Wednesday 09.10.2019 between 12pm-2pm, <br><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymers & solvents, Poisson-Boltzmann theory, charged polymers || <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
==== Worksheet 5: Charge distribution and Poisson Boltzmann theory ====<br />
* Deadline: '''July 3, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet5.pdf|Worksheet 5}}<br />
* {{Download|SimmethodsII_ss19_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24331Simulation Methods in Physics II SS 20192019-06-14T21:39:03Z<p>Mfyta: </p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 11am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-11am, <br><br />
Tuesday 17.09.2019 between 1pm-2pm, <br><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
Wednesday 09.10.2019 between 12pm-2pm, <br><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymers & solvents, Poisson-Boltzmann theory, charged polymers || <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 5: Charge distribution around a charged rod ====<br />
* Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet5.pdf| the Worksheet}}<br />
* {{Download|SimmethodsII_ss18_worksheet5NEW.pdf| NEW Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24324Simulation Methods in Physics II SS 20192019-06-14T10:31:58Z<p>Mfyta: </p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 10am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-2pm, <br><br />
Tuesday 17.09.2019 between 12pm-2pm, <br><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
Wednesday 09.10.2019 between 11am-2pm, <br><br />
<!--Thursday 10.10.2019 between 10am-2pm, <br--><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymers & solvents, Poisson-Boltzmann theory, charged polymers || <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 5: Charge distribution around a charged rod ====<br />
* Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet5.pdf| the Worksheet}}<br />
* {{Download|SimmethodsII_ss18_worksheet5NEW.pdf| NEW Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24318Simulation Methods in Physics II SS 20192019-06-06T11:38:01Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 10am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-2pm, <br><br />
Tuesday 17.09.2019 between 12pm-2pm, <br><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
Wednesday 09.10.2019 between 11am-2pm, <br><br />
Thursday 10.10.2019 between 10am-2pm, <br><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Polymers & solvents, Poisson-Boltzmann theory, charged polymers || <br />
|- <br />
| 04.07.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 5: Charge distribution around a charged rod ====<br />
* Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet5.pdf| the Worksheet}}<br />
* {{Download|SimmethodsII_ss18_worksheet5NEW.pdf| NEW Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture8.pdf&diff=24317File:SimmethodsII ss19 lecture8.pdf2019-06-06T11:36:52Z<p>Mfyta: Mfyta uploaded a new version of File:SimmethodsII ss19 lecture8.pdf</p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture8.pdf&diff=24316File:SimmethodsII ss19 lecture8.pdf2019-06-06T09:26:12Z<p>Mfyta: Mfyta uploaded a new version of File:SimmethodsII ss19 lecture8.pdf</p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24315Simulation Methods in Physics II SS 20192019-06-06T08:46:46Z<p>Mfyta: </p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 10am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-2pm, <br><br />
Tuesday 17.09.2019 between 12pm-2pm, <br><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
Wednesday 09.10.2019 between 11am-2pm, <br><br />
Thursday 10.10.2019 between 10am-2pm, <br><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || <!-- {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} --><br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) || <br />
|- <br />
| 04.07.2019 || Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 5: Charge distribution around a charged rod ====<br />
* Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet5.pdf| the Worksheet}}<br />
* {{Download|SimmethodsII_ss18_worksheet5NEW.pdf| NEW Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24307Simulation Methods in Physics II SS 20192019-06-05T11:01:33Z<p>Mfyta: /* Lecture */</p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 10am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-2pm, <br><br />
Tuesday 17.09.2019 between 10am-2pm, <br><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
Wednesday 09.10.2019 between 10am-2pm, <br><br />
Thursday 10.10.2019 between 10am-2pm, <br><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields Poisson-Boltzmann theory, charged polymers--> Polymer Models || <!-- {{Download|simmethodsII_ss19_lecture8.pdf| Lecture Notes}} --><br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) || <br />
|- <br />
| 04.07.2019 || Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 5: Charge distribution around a charged rod ====<br />
* Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet5.pdf| the Worksheet}}<br />
* {{Download|SimmethodsII_ss18_worksheet5NEW.pdf| NEW Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture8.pdf&diff=24306File:SimmethodsII ss19 lecture8.pdf2019-06-05T11:00:15Z<p>Mfyta: </p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24304Simulation Methods in Physics II SS 20192019-06-04T11:35:26Z<p>Mfyta: </p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 10am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-2pm, <br><br />
Tuesday 17.09.2019 between 10am-2pm, <br><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
Wednesday 09.10.2019 between 10am-2pm, <br><br />
Thursday 10.10.2019 between 10am-2pm, <br><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields--> Poisson-Boltzmann theory, charged polymers || <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) || <br />
|- <br />
| 04.07.2019 || Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 5: Charge distribution around a charged rod ====<br />
* Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet5.pdf| the Worksheet}}<br />
* {{Download|SimmethodsII_ss18_worksheet5NEW.pdf| NEW Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24299Simulation Methods in Physics II SS 20192019-06-04T10:21:06Z<p>Mfyta: </p>
<hr />
<div>{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 10am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-2pm, <br><br />
Tuesday 17.09.2019 between 10am-2pm, <br><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
Wednesday 09.10.2019 between 10am-2pm, <br><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields--> Poisson-Boltzmann theory, charged polymers || <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) || <br />
|- <br />
| 04.07.2019 || Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 5: Charge distribution around a charged rod ====<br />
* Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet5.pdf| the Worksheet}}<br />
* {{Download|SimmethodsII_ss18_worksheet5NEW.pdf| NEW Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24298Simulation Methods in Physics II SS 20192019-06-04T10:20:58Z<p>Mfyta: </p>
<hr />
<div><{{Infobox| Possible exam dates: <br />
<br />
Monday 22.07.2019 between 10am-2pm, <br><br />
Tuesday 23.07.2019 between 10am-2pm, <br><br />
Tuesday 30.07.2019 between 10am-2pm, <br><br />
Wednesday 31.07.2019 between 10am-2pm, <br><br />
Tuesday 17.09.2019 between 10am-2pm, <br><br />
Wednesday 18.09.2019 between 10am-2pm, <br><br />
Wednesday 09.10.2019 between 10am-2pm, <br><br />
Tuesday 15.10.2019 between 12pm-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields--> Poisson-Boltzmann theory, charged polymers || <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) || <br />
|- <br />
| 04.07.2019 || Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 5: Charge distribution around a charged rod ====<br />
* Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet5.pdf| the Worksheet}}<br />
* {{Download|SimmethodsII_ss18_worksheet5NEW.pdf| NEW Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24296Simulation Methods in Physics II SS 20192019-06-03T06:41:49Z<p>Mfyta: /* Worksheet 4: Properties of Coarse-grained Polymers */</p>
<hr />
<div><!--{{Infobox| Possible exam dates: <br />
<br />
Tuesday 24.07.2018 between 10am-2pm, <br><br />
Wednesday 25.07.2018 between 10am-2pm, <br><br />
Thursday 26.07.2018 between 10am-2pm, <br><br />
Tuesday 31.07.2018 between 11am-2pm, <br><br />
Wednesday 01.08.2018 between 10am-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
--><br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields--> Poisson-Boltzmann theory, charged polymers || <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) || <br />
|- <br />
| 04.07.2019 || Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 19, 2019, 12:00 noon''' by email to [[Kartik Jain]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss19_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss19_template.py|template}}<br />
* {{Download|SimmethodsII_ss19_espresso_install.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 5: Charge distribution around a charged rod ====<br />
* Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet5.pdf| the Worksheet}}<br />
* {{Download|SimmethodsII_ss18_worksheet5NEW.pdf| NEW Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulationstechnik_f%C3%BCr_Master-Studierende_B_SS_2019&diff=24268Simulationstechnik für Master-Studierende B SS 20192019-05-23T11:36:51Z<p>Mfyta: /* Übung */</p>
<hr />
<div><!--:{{Infobox|<b> Die Vorlesung vom 18.05.2017 findet am Montag den 15.05.2017 um 11:30-13:00 im SimTech-Gebäude (Raum-0.009) und nicht im ICP statt.</b>}}--><br />
<br />
== Übersicht ==<br />
<br />
;Typ<br />
:Vorlesung <!--(3 SWS) und Übungen (2 SWS)--><br />
;Dozent<br />
:JP. Dr. [[Maria Fyta]]<br />
:Tutoren<br />
: [[Maofeng Dou]], [[Takeshi Kobayashi]]<br />
;Sprache<br />
:Deutsch<br />
;Zeit und Ort<br />
:'''Vorlesung'''<br />
: Di. 08:00-09:30 und Mi. 09:00-09:30 von 08.05.2019-29.05.2019 im SimTech-Gebäude.<br />
<br />
==Vorlesung==<br />
<br />
Ein Überblick der Simulationsmethoden in der Physik mit einem Schwerpunkt auf die sehr kleine quantenmechanische Skala liegen im Schwerpunkt dieses Moduls.<br />
<br />
<br />
Die Folien zur Vorlesung gibt es hier:<br />
<!--<br />
* {{Download|simulationstechnik_ss17_lect1.pdf | Einführung - Quantenmechanische Beschreibung}}<br />
<br />
* {{Download|simulationstechnik_ss17_QM_1.pdf| quantenmechanische Ansätze - Teil 1 }}<br />
<br />
* {{Download|simulationstechnik_ss17_QM_2.pdf| quantenmechanische Ansätze - Teil 2 }}<br />
<br />
* {{Download|simulationstechnik_ss17_QM_3.pdf| quantenmechanische Ansätze - Teil 3 }}<br />
<br />
* {{Download|simulationstechnik_ss17_potentials.pdf| Paar Potentiale }}<br />
<br />
* {{Download|simulationstechnik_ss17_meso.pdf| mesoskopische Ansätze - Gitter Boltzmann }}<br />
<br />
* {{Download|simulationstechnik_ss17_multiscale_cg.pdf| multiskalige & vergröberte Ansätze }}<br />
--><br />
<br />
== Übung ==<br />
<br />
Es finden 2 Tutorien am 15.05.2019 und 29.05.2019 jeweils um 08:00-09:30 im CIP-Pool vom ICP, Allmandring 3, statt.</div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture7b.pdf&diff=24267File:SimmethodsII ss19 lecture7b.pdf2019-05-23T11:36:07Z<p>Mfyta: Mfyta uploaded a new version of File:SimmethodsII ss19 lecture7b.pdf</p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24266Simulation Methods in Physics II SS 20192019-05-23T11:33:32Z<p>Mfyta: /* Lecture */</p>
<hr />
<div><!--{{Infobox| Possible exam dates: <br />
<br />
Tuesday 24.07.2018 between 10am-2pm, <br><br />
Wednesday 25.07.2018 between 10am-2pm, <br><br />
Thursday 26.07.2018 between 10am-2pm, <br><br />
Tuesday 31.07.2018 between 11am-2pm, <br><br />
Wednesday 01.08.2018 between 10am-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
--><br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical water models || {{Download|simmethodsII_ss19_lecture7a.pdf| QMMM}}, {{Download|simmethodsII_ss19_lecture7slides.pdf| explicit models}}, {{Download|simmethodsII_ss19_lecture7b.pdf| implicit models}}<br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,Classical force fields--> Poisson-Boltzmann theory, charged polymers || <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) || <br />
|- <br />
| 04.07.2019 || Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<!--<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 20, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template.py|template}}<br />
* {{Download|SimmethodsII_ss17_espresso_install.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 5: Charge distribution around a charged rod ====<br />
* Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet5.pdf| the Worksheet}}<br />
* {{Download|SimmethodsII_ss18_worksheet5NEW.pdf| NEW Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture7slides.pdf&diff=24265File:SimmethodsII ss19 lecture7slides.pdf2019-05-23T11:32:13Z<p>Mfyta: </p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture7b.pdf&diff=24264File:SimmethodsII ss19 lecture7b.pdf2019-05-23T11:32:00Z<p>Mfyta: </p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss19_lecture7a.pdf&diff=24263File:SimmethodsII ss19 lecture7a.pdf2019-05-23T11:31:35Z<p>Mfyta: </p>
<hr />
<div></div>Mfytahttps://www.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2019&diff=24246Simulation Methods in Physics II SS 20192019-05-17T10:39:39Z<p>Mfyta: /* Lecture */</p>
<hr />
<div><!--{{Infobox| Possible exam dates: <br />
<br />
Tuesday 24.07.2018 between 10am-2pm, <br><br />
Wednesday 25.07.2018 between 10am-2pm, <br><br />
Thursday 26.07.2018 between 10am-2pm, <br><br />
Tuesday 31.07.2018 between 11am-2pm, <br><br />
Wednesday 01.08.2018 between 10am-2pm, <br><br />
<br />
For you preferred date and time, send an e-mail to [[Maria Fyta]]. }}<br />
--><br />
== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials "Simulationsmethoden in der Praxis" (2 SWS)<br />
;Lecturer<br />
:JP Dr. [[Maria Fyta]]<br />
;Course language<br />
:English<br />
<br />
;Location and Time<br />
:'''Lecture''': Thu, 11:30 - 13:00; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available); Tutors: Dr. [[Maofeng Dou]], Dr. [[Kartik Jain]]; ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
<br />
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".<br />
<br />
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.<br />
The tutorials build on each other, therefore continuous attendance is expected.<br />
<br />
=== Scope ===<br />
The course intends to give an overview about modern simulation methods<br />
used in physics today. The stress of the lecture will be to introduce different<br />
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.<br />
<br />
=== Prerequisites ===<br />
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.<br />
<br />
=== Certificate Requirements ===<br />
:1. Obtaining 50% of the possible marks in the hand-in exercises.<br />
<br />
The final grade will be determined from the final oral examination.<br />
<br />
=== Oral Examination ===<br />
<br />
'''Please email to [[Christian Holm]] or [[Maria Fyta]] in order to arrange a date for the oral examination.'''<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,rubinstein03a,newman99a,thijssen07,succi01a,tuckerman10a,martin04a,kaxiras03a,leach01a</bibentry><br />
=== Useful online resources ===<br />
<br />
* Roethlisberger, Tavernelli, EPFL, Lausanne, 2015: [https://archive.org/details/Ursula_Rothlisberger_and_Ivano_Tavernelli__Introduction_to_Electronic_Structure_Methods/page/n0]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://dft.uci.edu/doc/g1.pdf E-Book: The ABC of DFT.]<br />
<br />
* Linux cheat sheet {{Download|Sim_Meth_I_T0_cheat_sheet_10_11.pdf|here}}.<br />
<br />
* 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]<br />
<br />
<!--* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html Not so frequently asked questions about GNUPLOT]--><br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<br />
<br />
* [http://tldp.org/LDP/abs/html/ A more detailed introduction to bash scripting]<br />
<br />
* [http://www6.cityu.edu.hk/ma/ws2011/notes_e.pdf Principles of Multiscale Modeling, Weinan E (2011)]<br />
<br />
* 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]<br />
<br />
* "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]<br />
<br />
* University Intranet: Quantentheorie der Molekuele (DE), Springer Spektrum 2015, [https://link.springer.com/book/10.1007/978-3-658-09410-2]<br />
<br />
* 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.<br />
<br />
== Lecture ==<br />
<br />
The lecture notes will be uploaded in due time after each lecture. In order to access these from outside the University or VPN (ask your tutor about this).<br />
<!--<br />
<font size="4">'''A script on the course material is now available, thanks to Larissa Dill {{Download|simmeth2_vorlesungsmitschrieb.pdf|Script}}.'''</font> --><br />
<br />
{| class="wikitable"<br />
|-valign="top"<br />
!Date !! Subject || Resources<br />
|- <br />
| 11.04.2019 || Introduction/organization, electronic structure || {{Download|simmethodsII_ss19_lecture1.pdf| Lecture Notes}}<br />
|- <br />
| 16.04.2019 || QM methods ingredients, Hartree approximations || {{Download|simmethodsII_ss19_QMingred.pdf| QM ingredients}}, {{Download|simmethodsII_ss19_lecture1notes.pdf| Lecture Notes}}<!-- , {{Download|simmethodsII_ss19_lecture2a.pdf| Hartree}} --><br />
|- <br />
| 18.04.2019 || Hartree-Fock (HF) and post HF methods || {{Download|simmethodsII_ss19_lecture3.pdf| Lecture Notes}}<br />
|- <br />
| 02.05.2019 || Moller-Plesset theory, Density Functional Theory (DFT) || {{Download|simmethodsII_ss19_lecture4.pdf| Perturbation Theory-MPn}}, {{Download|simmethodsII_ss19_lecture4b.pdf| DFT}}<br />
|- <br />
| 09.05.2019 || DFT (continued) || {{Download|simmethodsII_ss19_lecture5.pdf| Lecture Notes}}<br />
|- <br />
| 16.05.2019 || TDDFT <i>ab initio</i> MD ||{{Download|simmethodsII_ss19_lecture6a.pdf| TDDFT}}, {{Download|simmethodsII_ss19_lecture6b.pdf| ab initio MD}}<br />
|- <br />
| 23.05.2019 || QM/MM, Classical force fields and water models || <br />
|- <br />
| 30.05.2019 || '' Holiday (Christi Himmelfahrt)'' || ---<br />
|- <br />
| 06.06.2019 || <!--Simulations of macromolecules and soft matter,--> Poisson-Boltzmann theory, charged polymers || <br />
|- <br />
| 13.06.2019 || '' Holiday (Pfingsten) '' || ---<br />
|-<br />
| 20.06.2018 || '' Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 27.06.2019 || Hydrodynamic methods (Brownian, Langevin, DPD) || <br />
|- <br />
| 04.07.2019 || Lattice-Boltzmann ||<br />
|- <br />
| 11.07.2019 || Free energy methods || <br />
|- <br />
| 18.07.2019 ||Coarse-graining, multiscale simulations ||<br />
|}<br />
<br />
== Tutorials ==<br />
<br />
=== Location and Time ===<br />
* The tutorials take place in the CIP-Pool on the first floor of the ICP (Room 01.033, Allmandring 3), Thu 14:00 - 15:30; Thu 09:45-11:15 (extra tutoring time when the tutors will be partly available) (Tutors: [[Maofeng Dou]] / [[Kartik Jain]] )<br />
<br />
=== Worksheets ===<br />
<br />
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. <br />
<b>The first worksheet will be uploaded on Wed. April 17th. The deadline will be Wed. May 1st. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 1, 2019, 13:00''' by email to [[Maofeng Dou]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2019_WS1-orca.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2019_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* Deadline: '''May 15, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_02''' as subject line.<br />
* {{Download|SMII_2019_w2.pdf|Worksheet 2}}<br />
* {{Download|template_sm2_2019_w2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 3: QM/MM of water molecule on Au surface and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 29, 2019, 13:00 noon''' by email to [[Maofeng Dou]] use '''SM2_03''' as subject line.<br />
* {{Download|SMII_2019_w3.pdf|Worksheet 3}}<br />
* {{Download|template_SMII_SS2019_W3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<!--<br />
==== Worksheet 4: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''June 20, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template.py|template}}<br />
* {{Download|SimmethodsII_ss17_espresso_install.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<br />
==== Worksheet 5: Charge distribution around a charged rod ====<br />
* Deadline: '''July 4, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_05''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet5.pdf| the Worksheet}}<br />
* {{Download|SimmethodsII_ss18_worksheet5NEW.pdf| NEW Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
==== Worksheet 6: Flow Between Plates and Free Energy ====<br />
* Deadline: '''July 18, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss18_worksheet6.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template6.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_LB.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
--><br />
<br />
=== General Remarks ===<br />
<br />
* For the tutorials, you will get a [[ICP Unix Accounts for Students|personal account for the ICP machines]].<br />
* All material required for the tutorials can also be found on the ICP computers in the directory <code>/group/sm/2018</code>.<br />
* For the reports, we have a nice {{Download|latex-template.tex|LaTeX template|txt}}.<br />
* 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.<br />
* If you do the exercises in the CIP-Pool, all required software and tools are available.<br />
<br />
=== Hand-in-exercises ===<br />
<br />
* 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.<br />
* A written report (between 5 and 10 pages) has to be handed in for each worksheet. We recommend using LaTeX to prepare the report.<br />
* You have two weeks to prepare the report for each worksheet.<br />
* The report has to be sent to your tutor via email ([[Maofeng Dou]] or [[Kartik Jain]]).<br />
* 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.<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* You will receive the new worksheet on the days before the tutorial.<br />
* 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.<br />
* In the second tutorial after you received the worksheet, there is time to work on the exercises and to ask questions for the tutor.<br />
* You will have to hand in the reports on Monday after the second tutorial.<br />
* In the third tutorial after you received the worksheet, the solutions will be discussed:<br />
** The tutor will ask a team to present their solution.<br />
** The tutor will choose one of the members of the team to present each task.<br />
** ''This means that each team member should be able to present any task.''<br />
** At the end of the term, everybody should have presented at least once.<br />
<!--<br />
== Examination ==<br />
<br />
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,<br />
<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik": 60 min exam (contents from both parts SMI + SMII will be examined)<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005): 30 min exam (content only from SMII will be examined).<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II": 40 min (content from SMII will be examined).<br />
<br />
For additional information/modules, please contact us ([[Christian Holm]], [[Maria Fyta]]).<br />
<!--Depending on the module that this lecture is part of, there are differences on how to get the credits for the module:<br />
; BSc/MSc Physik, Modul "Simulationsmethoden in der Physik" (36010) and Erasmus Mundus International Master FUSION-EP:<br />
:* 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)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture (i.e. Summer 2013)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics II" (240918-005):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination<br />
:* 30 min of oral examination (PL) about the lecture and the excercises<br />
; BSc/MSc SimTech, Modul "Simulationsmethoden in der Physik für SimTech II" (?????):<br />
:* Obtain 50% of the possible points in the hands-in excercises of this lecture as a prerequisite for the examination (USL-V)<br />
:* 40 min of oral examination (PL) about the lecture and the excercises<br />
; MSc Chemie, Modul "Simulationsmethoden in der Physik für Chemiker II" (?????):<br />
:* The marks for the module are the marks obtained in the excercises (BSL) <br />
--></div>Mfyta