https://www2.icp.uni-stuttgart.de/~icp/mediawiki/api.php?action=feedcontributions&user=Dsean&feedformat=atomICPWiki - User contributions [en]2021-12-05T01:03:48ZUser contributionsMediaWiki 1.35.4https://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:Adv_sm_mod3_elpho.pdf&diff=23362File:Adv sm mod3 elpho.pdf2018-07-12T13:35:13Z<p>Dsean: Dsean uploaded a new version of File:Adv sm mod3 elpho.pdf</p>
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<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:Adv_sm_mod3_EOF.pdf&diff=23361File:Adv sm mod3 EOF.pdf2018-07-12T13:34:52Z<p>Dsean: Dsean uploaded a new version of File:Adv sm mod3 EOF.pdf</p>
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<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:Adv_sm_mod3_elpho.pdf&diff=23348File:Adv sm mod3 elpho.pdf2018-07-09T11:11:51Z<p>Dsean: </p>
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<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Advanced_Simulation_Methods_SS_2018&diff=23347Advanced Simulation Methods SS 20182018-07-09T11:11:03Z<p>Dsean: /* Worksheet */</p>
<hr />
<div><br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students should send an email to [[Maria Fyta]] as soon as possible.<br />
<br><br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).</b>}}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture and Tutorials (2 SWS in total)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]], JP. Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]], Dr. [[David Sean]]<br />
;Course language<br />
:English or German<br />
;Location<br />
:ICP, Allmandring 3; Room: ICP Meeting Room<br />
;Time<br />
:(see below)<br />
The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP. Dr. [[Maria Fyta]] and will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules.<br />
The students can work in groups. All groups should write a report on each module, which they should submit to the responsible person for each module by the deadline set for each module.<br />
<!-- [[Maria Fyta]] no later than Friday July 15, 2016. The report does not need to be longer than 20 pages.--><br />
<br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students write an Email to [[Maria Fyta]] until TBA.</b>}}<br />
<br />
== Module 1: [[Maria Fyta]], [[Frank Uhlig]], Inter-atomic interactions modeled with quantum mechanical simulations ==<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<!--ue 05.04.2016 at 14:00 in the ICP meeting room.--><br />
<br />
Tutorials: TBA in the ICP CIP-Pool.<br />
<br />
Talks: TBA am in the ICP meeting room.<br />
<br />
=== Description ===<br />
<br />
This module focuses on the influence of using quantum mechanical simulations. The quantum mechanical schemes which will be applied in this module are based on density functional theory (DFT). This method allows the investigation of the electronic properties of a system. An understanding of the method, an analysis of the results from the simulations is the main goal of this module. The analysis of the simulations should be written up in a report. The talk will be a presentation of a DFT-related journal paper. For this, one of the following papers can be chosen:<br />
<br />
* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J. Klimeš and A. Michaelides, The Journal of Chemical Physics 137, 120901 (2012); doi: 10.1063/1.4754130<br />
* Challenges for Density Functional Theory, A.J. Cohen, P. Mori-Sanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.<br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module please do not hesitate to contact [[Maria Fyta]]. For practical guidance regarding the simulations [[Frank Uhlig]].<br />
<br />
=== Density functional theory and exchange-correlation functionals ===<br />
<br />
==== Description ====<br />
<br />
Many modern catalyses are performed using noble metals. In particular at the<br />
surface of these catalysts, which come in a multitude of shapes and chemical<br />
composition. The overall catalysis is determined by many factors, including the<br />
actual reactivity of chemical species at the surface, adsorption of reactants<br />
and desorption of products, as well as kinetics of the diffusion on the surface.<br />
<br />
In this exercise you will look at the desorption behavior of hydrogen gas from<br />
the surface of noble metals. This process is important in the production of<br />
hydrogen gas for energy storage applications [1]. However, modeling this process<br />
using modern methods of quantum-mechanical density functional theory (DFT) is<br />
very challenging. Only very advanced and quite recent density functionals are<br />
able to describe the long-range dispersion interactions [2]. Hence, effective<br />
methods based on pair potentials have been developed. These methods can achieve<br />
comparable accuracy to more ab initio methods while coming at a signifcantly<br />
lower computational effort [3,4].<br />
<br />
Your task is to develop such a pair-wise dispersion correction for the<br />
interaction of hydrogen gas with a metal surface. The first step is to<br />
understand and document the metallic behavior of your metal substrate, followed<br />
by investigation of the performance of common DFT functionals for the desorption<br />
process, and finally developing a dispersion correction by determining<br />
individual dispersion coefficients for the involved species [5].<br />
<br />
[1] https://dx.doi.org/10.1038/ncomms6848<br />
<br />
[2] https://dx.doi.org/10.1063/1.4754130<br />
<br />
[3] https://dx.doi.org/10.1103/PhysRevLett.102.073005<br />
<br />
[4] https://dx.doi.org/10.1063/1.3382344<br />
<br />
[5] https://dx.doi.org/10.1063/1.2746031<br />
<br />
[6] [[:Media:Asm_2018_info.txt|ASM tutorial info links]]<br />
<br />
==== Literature ====<br />
<br />
* A bird's-eye view of density-functional theory, Klaus Capelle, arXiv:cond-mat/0211443 (2002).<br />
* Self-Consistent Equations Including Exchange and Correlation Effects, W. Kohn and L.J. Sham, , Phys. Rev. (140), A1133 (1965).<br />
* Understanding and Reducing Errors in Density Functional Calculations, Min-Cheol Kim, Eunji Sim, and Kieron Burke, Phys. Rev. Lett. 111, 073003 (2013).<br />
<!--* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J Klimeš, A Michaelides, J. Chem. Phys. 137, 120901 (2012).--><br />
* An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases, V.R. Cooper, T. Thonhauser, and D.C. Langreth, J. Chem. Phys. 128, 204102 (2008).<br />
* On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit, B. Santra, A. Michaelides, and M. Scheffler, J. Chem. Phys. 127, 184104 (2007).<br />
* On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level, I. Dąbkowska, P. Jurečka, and P. Hobza, J. Chem. Phys. 122, 204322 (2005).<br />
<br />
=== Report ===<br />
<br />
Please write a report 5-10 pages containing and discussing your results and hand it in by Friday TBA.<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 2: [[Maria Fyta]], [[Narayanan Krishnamoorthy Anand]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: 18.05.2018 in the ICP meeting room. <br />
<br />
Final meeting: 15.06.2018 in the ICP meeting room.<br />
<br />
Deadline for reports: 15.06.2018<br />
=== Description ===<br />
<br />
This module focuses on atomistic Molecular Dynamics simulations and the study of biological co-solutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological co-solutes, often also called osmolytes are omnipresent in biological cells. A main function of these small-weight organic <br />
molecules is given by the protection of protein structures under harsh environmental conditions (protein stabilizers) or the denaturation of proteins (protein denaturants). The underlying mechanism leading to these effects is still unknown. It has been often discussed that osmolytes have a significant impact on the aqueous solution.<br />
The module consists of model development, simulation, analysis and oral and written presentation part. <br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Narayanan Krishnamoorthy Anand]].<br />
<br />
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the Kirkwood-Buff theory which can be well applied to computer simulations.<br />
The students should study the literature given below and present their findings. The presentation should at a minimum contain an introduction to Kirkwood-Buff theory in the context of the simulations.<br />
<br />
==== Literature ====<br />
<br />
* D. R. Canchi and A. E. Garcia, "Co-solvent effects on protein stability", Ann. Rev. Phys. Chem. 64. 273 (2013)<br />
* J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951) <br />
* V. Pierce, M. Kang, M. Aburi, S. Weerasinghe and P. E. Smith, "Recent applications of Kirkwood–Buff theory to biological systems", Cell Biochem. Biophys. 50, 1 (2008)<br />
* S. Weerasinghe and P. E. Smith, "A Kirkwood–Buff derived force field for sodium chloride in water", The Journal of Chemical Physics 119, 11342 (2003).<br />
* J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)<br />
* J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)<br />
* T. Kobayashi <i>et al</i>, "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches", Phys.Chem.Chem.Phys. 19, 18924 (2017)<br />
<br />
=== Part 2: Model Development and Simulations ===<br />
<br />
==== Description ====<br />
<br />
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will develop Generalized Amber Force Fields (GAFF) [http://ambermd.org/antechamber/gaff.html] with the help of the ACPYPE program [http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder] for the osmolytes (urea, hydroxyectoine, ectoine) which will be used for the study of solvent properties like the thermodynamics of hydrogen bonding ans the diffusivity according to J. Phys. Chem. B 118, 771 (2014).<br />
In comparison to pure water, the students will analyze several water parameters and elucidate the differences in presence of osmolytes and their concentration dependent behavior. The Kirkwood-Buff theory will be used to calculate derivatives of the activity coefficients and the derivative of the chemical activity for the osmolytes. <br />
<br />
==== Force Fields for ectoine and hydroxyectoine ====<br />
<br />
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}<br />
* {{Download| hectoinzwittmp2.gro |gro-File for Hydroxyectoine}}<br />
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}<br />
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}<br />
<br />
=== Part 3: Tasks ===<br />
1. Implement the developed force fields for the osmolytes (urea, ectoine and hydroxyectoine) in combination with the SPC/E water model. After energy minimization and warm up, run 20-30 ns simulations with GROMACS for osmolyte concentrations between c = 0 - 6 M.<br />
<br />
2. Study the following properties for the different osmolytes and concentrations:<br />
* diffusion coefficients<br />
* hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs<br />
* water mean relaxation times<br />
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?<br />
<br />
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.<br />
Use this information to compute the<br />
* Kirkwood-Buff integrals<br />
* derivatives of the chemical activity<br />
* derivatives of the activity coefficient<br />
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004). <br />
<br />
==== Literature ====<br />
<br />
* D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media", J. Phys. Chem. B 110, 4393 (2006)<br />
* J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem. 25, 1157 (2004)<br />
<br />
=== Report ===<br />
<br />
Please write a report of about 5 pages containing and discussing your results and hand it in until TBA.<br />
<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 3: [[Christian Holm]], Electrostatics, Lattice Boltzmann, and Electrokinetics==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: TBA in the ICP meeting room. <br />
<br />
Final meeting: TBA in the ICP meeting room. <br />
<br />
=== Description ===<br />
<br />
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people.<br />
It consists of one lecture on electrostatic algorithms, simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation<br />
and hand in one report. The Module 3 consists of three parts:<br />
<br />
=== Contact ===<br />
If you have any questions regarding the organisation or content of this module please do not hesitate to contact [[Christian Holm]].<br />
For questions regarding the practical part of the module and technical help contact [[David Sean]].<br />
<br />
=== Part 1: Electrostatics ===<br />
==== Description ====<br />
This part is about the theory of electrostatic algorithms for molecular dynamics simulations.<br />
It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald<br />
methods. To this end the students should read the referenced literature. [[Christian Holm]] will give an hour long lecture. Afterwards we will discuss the content and try to resolve open questions. The presentation should foster the students understanding of the P3M method as well<br />
as give them an overview of its performance compared to other modern electrostatics methods.<br />
<br />
==== Literature ====<br />
:* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''. <br /> [[Media:longrange.pdf|[PDF]]] (15.4 MB) <br /><br />
<bibentry>deserno98a,arnold13b,arnold05a</bibentry><br />
<br />
=== Part 2: Electro-Osmotic Flow ===<br />
==== Description ====<br />
[[File:Slitpore.png|550px|right|Electroosmotic flow in a slit pore]]<br />
This part is practical. It is concerned with the movement of ions in an charged slit pore.<br />
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]<br />
which is recommended reading. A slit pore consists of two infinite charge walls as shown<br />
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].<br />
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented<br />
by charge Week-Chandler-Anderson spheres.<br />
In addition to the charge on the walls, the ions are also subject to an external electrical field parallel to the walls.<br />
Electrostatics should be handled by the P3M algorithm with ELC.<br />
A set of realistic parameters and an more in detail description of the system can be found in the<br />
thesis.<br />
You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit<br />
pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high<br />
salt limit (Debye-Hueckel-Limit).<br />
Calculate the ion profiles in one or both of these cases and compare the results with the simulation.<br />
<br />
===== Worksheet =====<br />
<br />
{{Download|adv_sm_mod3_EOF.pdf|Detailed worksheet}}<br />
<br />
==== Literature ====<br />
<br />
Some ESPResSo tutorials can be helpful.<br />
* General part and parts 4 & 6 of [https://github.com/espressomd/espresso/blob/python/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann.pdf the Lattice-Boltzmann tutorial] <br />
* Part 7 of the [https://github.com/espressomd/espresso/blob/python/doc/tutorials/02-charged_system/02-charged_system.pdf charged systems tutorial] to see how to setup proper electrostatics in quasi-2D geometry.<br />
<br />
* Georg Rempfer, {{Download|BSc_thesis_rempfer.pdf|"Lattice-Boltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart<br />
<br />
=== Part 3: Electrophoresis of Polyelectrolytes ===<br />
==== Description ====<br />
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions.<br />
Set up a system consisting of a charged polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled with <br />
the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer<br />
for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and<br />
experimental results (see literature).<br />
<br />
<br />
==== Worksheet ====<br />
{{Download|adv_sm_mod3_elpho.pdf|Detailed worksheet}}<br />
<br />
==== Instructions and Literature ====<br />
General part and part 5 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
<bibentry>grass08a, grass09c</bibentry><br />
<br />
=== Report ===<br />
<br />
At the final meeting day of this module, one group will give a presentation about the learned and performed work. In addition, they write a report of about 5 pages containing and discussing the obtained results and hand it in together with the reports of the other modules at the end of the course (see above).<br />
<br />
The final report is due electronically Friday night, TBA<br />
<br />
<br />
<br />
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.--></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Advanced_Simulation_Methods_SS_2018&diff=23346Advanced Simulation Methods SS 20182018-07-09T11:10:38Z<p>Dsean: /* Part 3: Electrophoresis of Polyelectrolytes */</p>
<hr />
<div><br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students should send an email to [[Maria Fyta]] as soon as possible.<br />
<br><br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).</b>}}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture and Tutorials (2 SWS in total)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]], JP. Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]], Dr. [[David Sean]]<br />
;Course language<br />
:English or German<br />
;Location<br />
:ICP, Allmandring 3; Room: ICP Meeting Room<br />
;Time<br />
:(see below)<br />
The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP. Dr. [[Maria Fyta]] and will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules.<br />
The students can work in groups. All groups should write a report on each module, which they should submit to the responsible person for each module by the deadline set for each module.<br />
<!-- [[Maria Fyta]] no later than Friday July 15, 2016. The report does not need to be longer than 20 pages.--><br />
<br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students write an Email to [[Maria Fyta]] until TBA.</b>}}<br />
<br />
== Module 1: [[Maria Fyta]], [[Frank Uhlig]], Inter-atomic interactions modeled with quantum mechanical simulations ==<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<!--ue 05.04.2016 at 14:00 in the ICP meeting room.--><br />
<br />
Tutorials: TBA in the ICP CIP-Pool.<br />
<br />
Talks: TBA am in the ICP meeting room.<br />
<br />
=== Description ===<br />
<br />
This module focuses on the influence of using quantum mechanical simulations. The quantum mechanical schemes which will be applied in this module are based on density functional theory (DFT). This method allows the investigation of the electronic properties of a system. An understanding of the method, an analysis of the results from the simulations is the main goal of this module. The analysis of the simulations should be written up in a report. The talk will be a presentation of a DFT-related journal paper. For this, one of the following papers can be chosen:<br />
<br />
* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J. Klimeš and A. Michaelides, The Journal of Chemical Physics 137, 120901 (2012); doi: 10.1063/1.4754130<br />
* Challenges for Density Functional Theory, A.J. Cohen, P. Mori-Sanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.<br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module please do not hesitate to contact [[Maria Fyta]]. For practical guidance regarding the simulations [[Frank Uhlig]].<br />
<br />
=== Density functional theory and exchange-correlation functionals ===<br />
<br />
==== Description ====<br />
<br />
Many modern catalyses are performed using noble metals. In particular at the<br />
surface of these catalysts, which come in a multitude of shapes and chemical<br />
composition. The overall catalysis is determined by many factors, including the<br />
actual reactivity of chemical species at the surface, adsorption of reactants<br />
and desorption of products, as well as kinetics of the diffusion on the surface.<br />
<br />
In this exercise you will look at the desorption behavior of hydrogen gas from<br />
the surface of noble metals. This process is important in the production of<br />
hydrogen gas for energy storage applications [1]. However, modeling this process<br />
using modern methods of quantum-mechanical density functional theory (DFT) is<br />
very challenging. Only very advanced and quite recent density functionals are<br />
able to describe the long-range dispersion interactions [2]. Hence, effective<br />
methods based on pair potentials have been developed. These methods can achieve<br />
comparable accuracy to more ab initio methods while coming at a signifcantly<br />
lower computational effort [3,4].<br />
<br />
Your task is to develop such a pair-wise dispersion correction for the<br />
interaction of hydrogen gas with a metal surface. The first step is to<br />
understand and document the metallic behavior of your metal substrate, followed<br />
by investigation of the performance of common DFT functionals for the desorption<br />
process, and finally developing a dispersion correction by determining<br />
individual dispersion coefficients for the involved species [5].<br />
<br />
[1] https://dx.doi.org/10.1038/ncomms6848<br />
<br />
[2] https://dx.doi.org/10.1063/1.4754130<br />
<br />
[3] https://dx.doi.org/10.1103/PhysRevLett.102.073005<br />
<br />
[4] https://dx.doi.org/10.1063/1.3382344<br />
<br />
[5] https://dx.doi.org/10.1063/1.2746031<br />
<br />
[6] [[:Media:Asm_2018_info.txt|ASM tutorial info links]]<br />
<br />
==== Literature ====<br />
<br />
* A bird's-eye view of density-functional theory, Klaus Capelle, arXiv:cond-mat/0211443 (2002).<br />
* Self-Consistent Equations Including Exchange and Correlation Effects, W. Kohn and L.J. Sham, , Phys. Rev. (140), A1133 (1965).<br />
* Understanding and Reducing Errors in Density Functional Calculations, Min-Cheol Kim, Eunji Sim, and Kieron Burke, Phys. Rev. Lett. 111, 073003 (2013).<br />
<!--* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J Klimeš, A Michaelides, J. Chem. Phys. 137, 120901 (2012).--><br />
* An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases, V.R. Cooper, T. Thonhauser, and D.C. Langreth, J. Chem. Phys. 128, 204102 (2008).<br />
* On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit, B. Santra, A. Michaelides, and M. Scheffler, J. Chem. Phys. 127, 184104 (2007).<br />
* On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level, I. Dąbkowska, P. Jurečka, and P. Hobza, J. Chem. Phys. 122, 204322 (2005).<br />
<br />
=== Report ===<br />
<br />
Please write a report 5-10 pages containing and discussing your results and hand it in by Friday TBA.<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 2: [[Maria Fyta]], [[Narayanan Krishnamoorthy Anand]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: 18.05.2018 in the ICP meeting room. <br />
<br />
Final meeting: 15.06.2018 in the ICP meeting room.<br />
<br />
Deadline for reports: 15.06.2018<br />
=== Description ===<br />
<br />
This module focuses on atomistic Molecular Dynamics simulations and the study of biological co-solutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological co-solutes, often also called osmolytes are omnipresent in biological cells. A main function of these small-weight organic <br />
molecules is given by the protection of protein structures under harsh environmental conditions (protein stabilizers) or the denaturation of proteins (protein denaturants). The underlying mechanism leading to these effects is still unknown. It has been often discussed that osmolytes have a significant impact on the aqueous solution.<br />
The module consists of model development, simulation, analysis and oral and written presentation part. <br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Narayanan Krishnamoorthy Anand]].<br />
<br />
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the Kirkwood-Buff theory which can be well applied to computer simulations.<br />
The students should study the literature given below and present their findings. The presentation should at a minimum contain an introduction to Kirkwood-Buff theory in the context of the simulations.<br />
<br />
==== Literature ====<br />
<br />
* D. R. Canchi and A. E. Garcia, "Co-solvent effects on protein stability", Ann. Rev. Phys. Chem. 64. 273 (2013)<br />
* J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951) <br />
* V. Pierce, M. Kang, M. Aburi, S. Weerasinghe and P. E. Smith, "Recent applications of Kirkwood–Buff theory to biological systems", Cell Biochem. Biophys. 50, 1 (2008)<br />
* S. Weerasinghe and P. E. Smith, "A Kirkwood–Buff derived force field for sodium chloride in water", The Journal of Chemical Physics 119, 11342 (2003).<br />
* J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)<br />
* J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)<br />
* T. Kobayashi <i>et al</i>, "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches", Phys.Chem.Chem.Phys. 19, 18924 (2017)<br />
<br />
=== Part 2: Model Development and Simulations ===<br />
<br />
==== Description ====<br />
<br />
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will develop Generalized Amber Force Fields (GAFF) [http://ambermd.org/antechamber/gaff.html] with the help of the ACPYPE program [http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder] for the osmolytes (urea, hydroxyectoine, ectoine) which will be used for the study of solvent properties like the thermodynamics of hydrogen bonding ans the diffusivity according to J. Phys. Chem. B 118, 771 (2014).<br />
In comparison to pure water, the students will analyze several water parameters and elucidate the differences in presence of osmolytes and their concentration dependent behavior. The Kirkwood-Buff theory will be used to calculate derivatives of the activity coefficients and the derivative of the chemical activity for the osmolytes. <br />
<br />
==== Force Fields for ectoine and hydroxyectoine ====<br />
<br />
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}<br />
* {{Download| hectoinzwittmp2.gro |gro-File for Hydroxyectoine}}<br />
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}<br />
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}<br />
<br />
=== Part 3: Tasks ===<br />
1. Implement the developed force fields for the osmolytes (urea, ectoine and hydroxyectoine) in combination with the SPC/E water model. After energy minimization and warm up, run 20-30 ns simulations with GROMACS for osmolyte concentrations between c = 0 - 6 M.<br />
<br />
2. Study the following properties for the different osmolytes and concentrations:<br />
* diffusion coefficients<br />
* hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs<br />
* water mean relaxation times<br />
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?<br />
<br />
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.<br />
Use this information to compute the<br />
* Kirkwood-Buff integrals<br />
* derivatives of the chemical activity<br />
* derivatives of the activity coefficient<br />
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004). <br />
<br />
==== Literature ====<br />
<br />
* D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media", J. Phys. Chem. B 110, 4393 (2006)<br />
* J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem. 25, 1157 (2004)<br />
<br />
=== Report ===<br />
<br />
Please write a report of about 5 pages containing and discussing your results and hand it in until TBA.<br />
<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 3: [[Christian Holm]], Electrostatics, Lattice Boltzmann, and Electrokinetics==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: TBA in the ICP meeting room. <br />
<br />
Final meeting: TBA in the ICP meeting room. <br />
<br />
=== Description ===<br />
<br />
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people.<br />
It consists of one lecture on electrostatic algorithms, simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation<br />
and hand in one report. The Module 3 consists of three parts:<br />
<br />
=== Contact ===<br />
If you have any questions regarding the organisation or content of this module please do not hesitate to contact [[Christian Holm]].<br />
For questions regarding the practical part of the module and technical help contact [[David Sean]].<br />
<br />
=== Part 1: Electrostatics ===<br />
==== Description ====<br />
This part is about the theory of electrostatic algorithms for molecular dynamics simulations.<br />
It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald<br />
methods. To this end the students should read the referenced literature. [[Christian Holm]] will give an hour long lecture. Afterwards we will discuss the content and try to resolve open questions. The presentation should foster the students understanding of the P3M method as well<br />
as give them an overview of its performance compared to other modern electrostatics methods.<br />
<br />
==== Literature ====<br />
:* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''. <br /> [[Media:longrange.pdf|[PDF]]] (15.4 MB) <br /><br />
<bibentry>deserno98a,arnold13b,arnold05a</bibentry><br />
<br />
=== Part 2: Electro-Osmotic Flow ===<br />
==== Description ====<br />
[[File:Slitpore.png|550px|right|Electroosmotic flow in a slit pore]]<br />
This part is practical. It is concerned with the movement of ions in an charged slit pore.<br />
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]<br />
which is recommended reading. A slit pore consists of two infinite charge walls as shown<br />
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].<br />
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented<br />
by charge Week-Chandler-Anderson spheres.<br />
In addition to the charge on the walls, the ions are also subject to an external electrical field parallel to the walls.<br />
Electrostatics should be handled by the P3M algorithm with ELC.<br />
A set of realistic parameters and an more in detail description of the system can be found in the<br />
thesis.<br />
You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit<br />
pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high<br />
salt limit (Debye-Hueckel-Limit).<br />
Calculate the ion profiles in one or both of these cases and compare the results with the simulation.<br />
<br />
===== Worksheet =====<br />
<br />
{{Download|adv_sm_mod3_EOF.pdf|Detailed worksheet}}<br />
<br />
==== Literature ====<br />
<br />
Some ESPResSo tutorials can be helpful.<br />
* General part and parts 4 & 6 of [https://github.com/espressomd/espresso/blob/python/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann.pdf the Lattice-Boltzmann tutorial] <br />
* Part 7 of the [https://github.com/espressomd/espresso/blob/python/doc/tutorials/02-charged_system/02-charged_system.pdf charged systems tutorial] to see how to setup proper electrostatics in quasi-2D geometry.<br />
<br />
* Georg Rempfer, {{Download|BSc_thesis_rempfer.pdf|"Lattice-Boltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart<br />
<br />
=== Part 3: Electrophoresis of Polyelectrolytes ===<br />
==== Description ====<br />
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions.<br />
Set up a system consisting of a charged polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled with <br />
the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer<br />
for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and<br />
experimental results (see literature).<br />
<br />
<br />
==== Worksheet ====<br />
<br />
==== Instructions and Literature ====<br />
General part and part 5 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
<bibentry>grass08a, grass09c</bibentry><br />
<br />
=== Report ===<br />
<br />
At the final meeting day of this module, one group will give a presentation about the learned and performed work. In addition, they write a report of about 5 pages containing and discussing the obtained results and hand it in together with the reports of the other modules at the end of the course (see above).<br />
<br />
The final report is due electronically Friday night, TBA<br />
<br />
<br />
<br />
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.--></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2018&diff=23338Simulation Methods in Physics II SS 20182018-07-05T12:46:39Z<p>Dsean: /* General Remarks */</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 />
Thursday 02.08.2018 between 11am-2pm, <br><br />
Tuesday 11.09.2018 between 12pm-2pm, <br><br />
Wednesday 12.09.2018 between 10am-2pm, <br><br />
Thursday 13.09.2018 between 1pm-2pm, <br><br />
Monday 01.10.2018 between 12pm-2pm, <br><br />
Tuesday 02.10.2018 between 10am-2pm, <br><br />
Thursday 04.10.2018 between 11am-2pm, <br><br />
<!-- Monday 22.10.2018 between 12pm-14pm, <br--><br />
Tuesday 23.10.2018 between 11am-2pm.<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 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; 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 in September or October 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://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]<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 />
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.--><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 />
| 12.04.2018 || Introduction/organisation, electronic structure || {{Download|simmethodsII_ss18_lecture1.pdf|Slides}}, {{Download|simmethodsII_ss18_lecture1notes.pdf|Lecture Notes}}<br />
|- <br />
| 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || {{Download|simmethodsII_ss18_lecture2.pdf|Lecture Notes}}<br />
|- <br />
| 26.04.2018 || Density Functional Theory (DFT) || {{Download|simmethodsII_ss18_lecture3.pdf|Lecture Notes (1)}}, {{Download|simmethodsII_ss18_lecture3b.pdf|Lecture Notes (2)}}<br />
|- <br />
| 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} <br />
|- <br />
| 10.05.2018 || Holiday (Christi Himmelfahrt) || ---<br />
|-<br />
| 17.05.2018 || Classical force fields and water models || {{Download|simmethodsII_ss18_lecture5slides.pdf|Slides}} <br />
|- <br />
| 24.05.2018 || '' Holiday (Pfingsten) '' || ---<br />
|- <br />
| 31.05.2018 || Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 07.06.2018 || Simulations of macromolecules and soft matter || <br />
|- <br />
| 14.06.2018 || Poisson-Boltzmann theory, charged polymers || {{Download|Poisson-Boltzmann-DavidNotes.pdf |Poisson-Boltzmann}} {{Download|Flory-DavidNotes.pdf|Polymer scaling}}<br />
|-<br />
| 21.06.2018 || Hydrodynamic methods I (Brownian and Langevin Dynamics) || {{Download|simmethodsII_ss18_lecture8.pdf|Lecture Notes}} <br />
|- <br />
| 28.06.2018 || Hydrodynamic methods II (DPD, Lattice-Boltzmann) (contd.) || {{Download|simmethodsII_ss18_lecture9.pdf|Lecture Notes}} <br />
|- <br />
| 05.07.2018 || Lattice-Boltzmann (contd.)|| {{Download|simmethodsII_ss18_lecture9b.pdf|Lecture Notes (LBM)}} <br />
|- <br />
| 12.07.2018 || Free energy methods Energy minimization, Interatomic potentials (pair-potentials, EAM) (solid-state systems)|| <!--{{Download|simmethodsII_ss18_lecture10.pdf|Lecture Notes (Free Energy)}} --><br />
|- <br />
| 19.07.2018 ||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, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] )<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 18th. The deadline will be Wed. May 2nd. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout<br />
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}}<br />
* {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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 />
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====<br />
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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 ([[Miriam Kohagen]] or [[David Sean]]).<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>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss18_worksheet5NEW.pdf&diff=23337File:SimmethodsII ss18 worksheet5NEW.pdf2018-07-05T12:42:40Z<p>Dsean: Dsean uploaded a new version of File:SimmethodsII ss18 worksheet5NEW.pdf</p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss18_worksheet6.pdf&diff=23316File:SimmethodsII ss18 worksheet6.pdf2018-07-02T17:54:06Z<p>Dsean: Dsean uploaded a new version of File:SimmethodsII ss18 worksheet6.pdf</p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss18_template6.py&diff=23315File:SimmethodsII ss18 template6.py2018-07-02T17:52:01Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss18_worksheet6.pdf&diff=23314File:SimmethodsII ss18 worksheet6.pdf2018-07-02T17:51:40Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2018&diff=23313Simulation Methods in Physics II SS 20182018-07-02T17:51:07Z<p>Dsean: /* Worksheets */</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 />
Thursday 02.08.2018 between 11am-2pm, <br><br />
Tuesday 11.09.2018 between 12pm-2pm, <br><br />
Wednesday 12.09.2018 between 10am-2pm, <br><br />
Thursday 13.09.2018 between 1pm-2pm, <br><br />
Monday 01.10.2018 between 12pm-2pm, <br><br />
Tuesday 02.10.2018 between 10am-2pm, <br><br />
Thursday 04.10.2018 between 11am-2pm, <br><br />
<!-- Monday 22.10.2018 between 12pm-14pm, <br--><br />
Tuesday 23.10.2018 between 11am-2pm.<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 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; 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 in September or October 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://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]<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 />
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.--><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 />
| 12.04.2018 || Introduction/organisation, electronic structure || {{Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}}<br />
|- <br />
| 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || <!--{{ |Lecture Notes}} --><br />
|- <br />
| 26.04.2018 || Density Functional Theory (DFT) || <!--{{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}--><br />
|- <br />
| 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} <br />
|- <br />
| 10.05.2018 || Holiday (Christi Himmelfahrt) || ---<br />
|-<br />
| 17.05.2018 || Classical force fields and water models || <br />
|- <br />
| 24.05.2018 || '' Holiday (Pfingsten) '' || ---<br />
|- <br />
| 31.05.2018 || Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 07.06.2018 || Simulations of macromolecules and soft matter || <br />
|- <br />
| 14.06.2018 || Poisson-Boltzmann theory, charged polymers || {{Download|Poisson-Boltzmann-DavidNotes.pdf |Poisson-Boltzmann}} {{Download|Flory-DavidNotes.pdf|Polymer scaling}}<br />
|-<br />
| 21.06.2018 || Hydrodynamic methods I (Brownian and Langevin Dynamics) ||<br />
|- <br />
| 28.06.2018 || Hydrodynamic methods II (DPD, Lattice-Boltzmann) (contd.) || {{Download|simmethodsII_ss18_lecture9.pdf|Lecture Notes}} <br />
|- <br />
| 05.07.2018 || Lattice-Boltzmann (contd). Free energy methods ||<br />
|- <br />
| 12.07.2018 || Energy minimization, Interatomic potentials (pair-potentials, EAM) (solid-state systems)||<br />
|- <br />
| 19.07.2018 ||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, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] )<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 18th. The deadline will be Wed. May 2nd. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout<br />
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}}<br />
* {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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 />
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====<br />
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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/2017</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 ([[Miriam Kohagen]] or [[David Sean]]).<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>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss18_worksheet5NEW.pdf&diff=23307File:SimmethodsII ss18 worksheet5NEW.pdf2018-06-28T13:45:43Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2018&diff=23306Simulation Methods in Physics II SS 20182018-06-28T13:45:33Z<p>Dsean: /* Worksheet 5: Charge distribution around a charged rod */</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 />
Thursday 02.08.2018 between 11am-2pm, <br><br />
Tuesday 11.09.2018 between 12pm-2pm, <br><br />
Wednesday 12.09.2018 between 10am-2pm, <br><br />
Thursday 13.09.2018 between 1pm-2pm, <br><br />
Monday 01.10.2018 between 12pm-2pm, <br><br />
Tuesday 02.10.2018 between 10am-2pm, <br><br />
Thursday 04.10.2018 between 11am-2pm, <br><br />
<!-- Monday 22.10.2018 between 12pm-14pm, <br--><br />
Tuesday 23.10.2018 between 11am-2pm.<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 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; 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 in September or October 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://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]<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 />
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.--><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 />
| 12.04.2018 || Introduction/organisation, electronic structure || {{Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}}<br />
|- <br />
| 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || <!--{{ |Lecture Notes}} --><br />
|- <br />
| 26.04.2018 || Density Functional Theory (DFT) || <!--{{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}--><br />
|- <br />
| 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} <br />
|- <br />
| 10.05.2018 || Holiday (Christi Himmelfahrt) || ---<br />
|-<br />
| 17.05.2018 || Classical force fields and water models || <br />
|- <br />
| 24.05.2018 || '' Holiday (Pfingsten) '' || ---<br />
|- <br />
| 31.05.2018 || Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 07.06.2018 || Simulations of macromolecules and soft matter || <br />
|- <br />
| 14.06.2018 || Poisson-Boltzmann theory, charged polymers || {{Download|Poisson-Boltzmann-DavidNotes.pdf |Poisson-Boltzmann}} {{Download|Flory-DavidNotes.pdf|Polymer scaling}}<br />
|-<br />
| 21.06.2018 || Hydrodynamic methods I (Brownian and Langevin Dynamics) ||<br />
|- <br />
| 28.06.2018 || Hydrodynamic methods II (DPD, Lattice-Boltzmann) (contd.) || {{Download|simmethodsII_ss18_lecture9.pdf|Lecture Notes}} <br />
|- <br />
| 05.07.2018 || Lattice-Boltzmann (contd). Free energy methods ||<br />
|- <br />
| 12.07.2018 || Energy minimization, Interatomic potentials (pair-potentials, EAM) (solid-state systems)||<br />
|- <br />
| 19.07.2018 ||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, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] )<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 18th. The deadline will be Wed. May 2nd. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout<br />
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}}<br />
* {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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 />
<!--<br />
==== Worksheet 4: Flow Between Plates and Free Energy ====<br />
* Deadline: '''June 19, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss17_template4.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 />
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====<br />
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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/2017</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 ([[Miriam Kohagen]] or [[David Sean]]).<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>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss18_worksheet5.pdf&diff=23305File:SimmethodsII ss18 worksheet5.pdf2018-06-28T13:44:16Z<p>Dsean: Dsean uploaded a new version of File:SimmethodsII ss18 worksheet5.pdf</p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss18_worksheet5.pdf&diff=23304File:SimmethodsII ss18 worksheet5.pdf2018-06-28T13:36:36Z<p>Dsean: Dsean uploaded a new version of File:SimmethodsII ss18 worksheet5.pdf</p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss18_worksheet5.pdf&diff=23303File:SimmethodsII ss18 worksheet5.pdf2018-06-28T13:31:46Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2018&diff=23301Simulation Methods in Physics II SS 20182018-06-28T13:29:40Z<p>Dsean: /* Worksheet 5: Charge distribution around a charged rod */</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 />
Thursday 02.08.2018 between 11am-2pm, <br><br />
Tuesday 11.09.2018 between 12pm-2pm, <br><br />
Wednesday 12.09.2018 between 10am-2pm, <br><br />
Thursday 13.09.2018 between 1pm-2pm, <br><br />
Monday 01.10.2018 between 12pm-2pm, <br><br />
Tuesday 02.10.2018 between 10am-2pm, <br><br />
Thursday 04.10.2018 between 11am-2pm, <br><br />
<!-- Monday 22.10.2018 between 12pm-14pm, <br--><br />
Tuesday 23.10.2018 between 11am-2pm.<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 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; 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 in September or October 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://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]<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 />
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.--><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 />
| 12.04.2018 || Introduction/organisation, electronic structure || {{Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}}<br />
|- <br />
| 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || <!--{{ |Lecture Notes}} --><br />
|- <br />
| 26.04.2018 || Density Functional Theory (DFT) || <!--{{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}--><br />
|- <br />
| 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} <br />
|- <br />
| 10.05.2018 || Holiday (Christi Himmelfahrt) || ---<br />
|-<br />
| 17.05.2018 || Classical force fields and water models || <br />
|- <br />
| 24.05.2018 || '' Holiday (Pfingsten) '' || ---<br />
|- <br />
| 31.05.2018 || Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 07.06.2018 || Simulations of macromolecules and soft matter || <br />
|- <br />
| 14.06.2018 || Poisson-Boltzmann theory, charged polymers || {{Download|Poisson-Boltzmann-DavidNotes.pdf |Poisson-Boltzmann}} {{Download|Flory-DavidNotes.pdf|Polymer scaling}}<br />
|-<br />
| 21.06.2018 || Hydrodynamic methods I (Brownian and Langevin Dynamics) ||<br />
|- <br />
| 28.06.2018 || Hydrodynamic methods II (DPD, Lattice-Boltzmann) (contd.) || {{Download|simmethodsII_ss18_lecture9.pdf|Lecture Notes}} <br />
|- <br />
| 05.07.2018 || Lattice-Boltzmann (contd). Free energy methods ||<br />
|- <br />
| 12.07.2018 || Energy minimization, Interatomic potentials (pair-potentials, EAM) (solid-state systems)||<br />
|- <br />
| 19.07.2018 ||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, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] )<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 18th. The deadline will be Wed. May 2nd. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout<br />
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}}<br />
* {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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| NEW Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 4: Flow Between Plates and Free Energy ====<br />
* Deadline: '''June 19, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss17_template4.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 />
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====<br />
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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/2017</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 ([[Miriam Kohagen]] or [[David Sean]]).<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>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2018&diff=23300Simulation Methods in Physics II SS 20182018-06-28T13:29:06Z<p>Dsean: /* Worksheet 5: Charge distribution around a charged rod */</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 />
Thursday 02.08.2018 between 11am-2pm, <br><br />
Tuesday 11.09.2018 between 12pm-2pm, <br><br />
Wednesday 12.09.2018 between 10am-2pm, <br><br />
Thursday 13.09.2018 between 1pm-2pm, <br><br />
Monday 01.10.2018 between 12pm-2pm, <br><br />
Tuesday 02.10.2018 between 10am-2pm, <br><br />
Thursday 04.10.2018 between 11am-2pm, <br><br />
<!-- Monday 22.10.2018 between 12pm-14pm, <br--><br />
Tuesday 23.10.2018 between 11am-2pm.<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 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; 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 in September or October 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://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]<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 />
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.--><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 />
| 12.04.2018 || Introduction/organisation, electronic structure || {{Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}}<br />
|- <br />
| 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || <!--{{ |Lecture Notes}} --><br />
|- <br />
| 26.04.2018 || Density Functional Theory (DFT) || <!--{{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}--><br />
|- <br />
| 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} <br />
|- <br />
| 10.05.2018 || Holiday (Christi Himmelfahrt) || ---<br />
|-<br />
| 17.05.2018 || Classical force fields and water models || <br />
|- <br />
| 24.05.2018 || '' Holiday (Pfingsten) '' || ---<br />
|- <br />
| 31.05.2018 || Holiday (Fronleichnam) '' || ---<br />
|- <br />
| 07.06.2018 || Simulations of macromolecules and soft matter || <br />
|- <br />
| 14.06.2018 || Poisson-Boltzmann theory, charged polymers || {{Download|Poisson-Boltzmann-DavidNotes.pdf |Poisson-Boltzmann}} {{Download|Flory-DavidNotes.pdf|Polymer scaling}}<br />
|-<br />
| 21.06.2018 || Hydrodynamic methods I (Brownian and Langevin Dynamics) ||<br />
|- <br />
| 28.06.2018 || Hydrodynamic methods II (DPD, Lattice-Boltzmann) (contd.) || {{Download|simmethodsII_ss18_lecture9.pdf|Lecture Notes}} <br />
|- <br />
| 05.07.2018 || Lattice-Boltzmann (contd). Free energy methods ||<br />
|- <br />
| 12.07.2018 || Energy minimization, Interatomic potentials (pair-potentials, EAM) (solid-state systems)||<br />
|- <br />
| 19.07.2018 ||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, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] )<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 18th. The deadline will be Wed. May 2nd. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout<br />
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}}<br />
* {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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 the NEW ONE|SimmethodsII_ss18_worksheet5.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 4: Flow Between Plates and Free Energy ====<br />
* Deadline: '''June 19, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss17_template4.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 />
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====<br />
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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/2017</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 ([[Miriam Kohagen]] or [[David Sean]]).<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>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:Adv_sm_mod3_EOF.pdf&diff=23290File:Adv sm mod3 EOF.pdf2018-06-26T15:42:43Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Advanced_Simulation_Methods_SS_2018&diff=23289Advanced Simulation Methods SS 20182018-06-26T15:42:16Z<p>Dsean: /* Part 2: Electro-Osmotic Flow */</p>
<hr />
<div><br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students should send an email to [[Maria Fyta]] as soon as possible.<br />
<br><br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).</b>}}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture and Tutorials (2 SWS in total)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]], JP. Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]], Dr. [[David Sean]]<br />
;Course language<br />
:English or German<br />
;Location<br />
:ICP, Allmandring 3; Room: ICP Meeting Room<br />
;Time<br />
:(see below)<br />
The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP. Dr. [[Maria Fyta]] and will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules.<br />
The students can work in groups. All groups should write a report on each module, which they should submit to the responsible person for each module by the deadline set for each module.<br />
<!-- [[Maria Fyta]] no later than Friday July 15, 2016. The report does not need to be longer than 20 pages.--><br />
<br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students write an Email to [[Maria Fyta]] until TBA.</b>}}<br />
<br />
== Module 1: [[Maria Fyta]], [[Frank Uhlig]], Inter-atomic interactions modeled with quantum mechanical simulations ==<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<!--ue 05.04.2016 at 14:00 in the ICP meeting room.--><br />
<br />
Tutorials: TBA in the ICP CIP-Pool.<br />
<br />
Talks: TBA am in the ICP meeting room.<br />
<br />
=== Description ===<br />
<br />
This module focuses on the influence of using quantum mechanical simulations. The quantum mechanical schemes which will be applied in this module are based on density functional theory (DFT). This method allows the investigation of the electronic properties of a system. An understanding of the method, an analysis of the results from the simulations is the main goal of this module. The analysis of the simulations should be written up in a report. The talk will be a presentation of a DFT-related journal paper. For this, one of the following papers can be chosen:<br />
<br />
* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J. Klimeš and A. Michaelides, The Journal of Chemical Physics 137, 120901 (2012); doi: 10.1063/1.4754130<br />
* Challenges for Density Functional Theory, A.J. Cohen, P. Mori-Sanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.<br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module please do not hesitate to contact [[Maria Fyta]]. For practical guidance regarding the simulations [[Frank Uhlig]].<br />
<br />
=== Density functional theory and exchange-correlation functionals ===<br />
<br />
==== Description ====<br />
<br />
Many modern catalyses are performed using noble metals. In particular at the<br />
surface of these catalysts, which come in a multitude of shapes and chemical<br />
composition. The overall catalysis is determined by many factors, including the<br />
actual reactivity of chemical species at the surface, adsorption of reactants<br />
and desorption of products, as well as kinetics of the diffusion on the surface.<br />
<br />
In this exercise you will look at the desorption behavior of hydrogen gas from<br />
the surface of noble metals. This process is important in the production of<br />
hydrogen gas for energy storage applications [1]. However, modeling this process<br />
using modern methods of quantum-mechanical density functional theory (DFT) is<br />
very challenging. Only very advanced and quite recent density functionals are<br />
able to describe the long-range dispersion interactions [2]. Hence, effective<br />
methods based on pair potentials have been developed. These methods can achieve<br />
comparable accuracy to more ab initio methods while coming at a signifcantly<br />
lower computational effort [3,4].<br />
<br />
Your task is to develop such a pair-wise dispersion correction for the<br />
interaction of hydrogen gas with a metal surface. The first step is to<br />
understand and document the metallic behavior of your metal substrate, followed<br />
by investigation of the performance of common DFT functionals for the desorption<br />
process, and finally developing a dispersion correction by determining<br />
individual dispersion coefficients for the involved species [5].<br />
<br />
[1] https://dx.doi.org/10.1038/ncomms6848<br />
<br />
[2] https://dx.doi.org/10.1063/1.4754130<br />
<br />
[3] https://dx.doi.org/10.1103/PhysRevLett.102.073005<br />
<br />
[4] https://dx.doi.org/10.1063/1.3382344<br />
<br />
[5] https://dx.doi.org/10.1063/1.2746031<br />
<br />
[6] [[:Media:Asm_2018_info.txt|ASM tutorial info links]]<br />
<br />
==== Literature ====<br />
<br />
* A bird's-eye view of density-functional theory, Klaus Capelle, arXiv:cond-mat/0211443 (2002).<br />
* Self-Consistent Equations Including Exchange and Correlation Effects, W. Kohn and L.J. Sham, , Phys. Rev. (140), A1133 (1965).<br />
* Understanding and Reducing Errors in Density Functional Calculations, Min-Cheol Kim, Eunji Sim, and Kieron Burke, Phys. Rev. Lett. 111, 073003 (2013).<br />
<!--* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J Klimeš, A Michaelides, J. Chem. Phys. 137, 120901 (2012).--><br />
* An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases, V.R. Cooper, T. Thonhauser, and D.C. Langreth, J. Chem. Phys. 128, 204102 (2008).<br />
* On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit, B. Santra, A. Michaelides, and M. Scheffler, J. Chem. Phys. 127, 184104 (2007).<br />
* On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level, I. Dąbkowska, P. Jurečka, and P. Hobza, J. Chem. Phys. 122, 204322 (2005).<br />
<br />
=== Report ===<br />
<br />
Please write a report 5-10 pages containing and discussing your results and hand it in by Friday TBA.<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 2: [[Maria Fyta]], [[Narayanan Krishnamoorthy Anand]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: 18.05.2018 in the ICP meeting room. <br />
<br />
Final meeting: 15.06.2018 in the ICP meeting room.<br />
<br />
Deadline for reports: 15.06.2018<br />
=== Description ===<br />
<br />
This module focuses on atomistic Molecular Dynamics simulations and the study of biological co-solutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological co-solutes, often also called osmolytes are omnipresent in biological cells. A main function of these small-weight organic <br />
molecules is given by the protection of protein structures under harsh environmental conditions (protein stabilizers) or the denaturation of proteins (protein denaturants). The underlying mechanism leading to these effects is still unknown. It has been often discussed that osmolytes have a significant impact on the aqueous solution.<br />
The module consists of model development, simulation, analysis and oral and written presentation part. <br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Narayanan Krishnamoorthy Anand]].<br />
<br />
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the Kirkwood-Buff theory which can be well applied to computer simulations.<br />
The students should study the literature given below and present their findings. The presentation should at a minimum contain an introduction to Kirkwood-Buff theory in the context of the simulations.<br />
<br />
==== Literature ====<br />
<br />
* D. R. Canchi and A. E. Garcia, "Co-solvent effects on protein stability", Ann. Rev. Phys. Chem. 64. 273 (2013)<br />
* J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951) <br />
* V. Pierce, M. Kang, M. Aburi, S. Weerasinghe and P. E. Smith, "Recent applications of Kirkwood–Buff theory to biological systems", Cell Biochem. Biophys. 50, 1 (2008)<br />
* S. Weerasinghe and P. E. Smith, "A Kirkwood–Buff derived force field for sodium chloride in water", The Journal of Chemical Physics 119, 11342 (2003).<br />
* J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)<br />
* J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)<br />
* T. Kobayashi <i>et al</i>, "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches", Phys.Chem.Chem.Phys. 19, 18924 (2017)<br />
<br />
=== Part 2: Model Development and Simulations ===<br />
<br />
==== Description ====<br />
<br />
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will develop Generalized Amber Force Fields (GAFF) [http://ambermd.org/antechamber/gaff.html] with the help of the ACPYPE program [http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder] for the osmolytes (urea, hydroxyectoine, ectoine) which will be used for the study of solvent properties like the thermodynamics of hydrogen bonding ans the diffusivity according to J. Phys. Chem. B 118, 771 (2014).<br />
In comparison to pure water, the students will analyze several water parameters and elucidate the differences in presence of osmolytes and their concentration dependent behavior. The Kirkwood-Buff theory will be used to calculate derivatives of the activity coefficients and the derivative of the chemical activity for the osmolytes. <br />
<br />
==== Force Fields for ectoine and hydroxyectoine ====<br />
<br />
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}<br />
* {{Download| hectoinzwittmp2.gro |gro-File for Hydroxyectoine}}<br />
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}<br />
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}<br />
<br />
=== Part 3: Tasks ===<br />
1. Implement the developed force fields for the osmolytes (urea, ectoine and hydroxyectoine) in combination with the SPC/E water model. After energy minimization and warm up, run 20-30 ns simulations with GROMACS for osmolyte concentrations between c = 0 - 6 M.<br />
<br />
2. Study the following properties for the different osmolytes and concentrations:<br />
* diffusion coefficients<br />
* hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs<br />
* water mean relaxation times<br />
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?<br />
<br />
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.<br />
Use this information to compute the<br />
* Kirkwood-Buff integrals<br />
* derivatives of the chemical activity<br />
* derivatives of the activity coefficient<br />
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004). <br />
<br />
==== Literature ====<br />
<br />
* D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media", J. Phys. Chem. B 110, 4393 (2006)<br />
* J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem. 25, 1157 (2004)<br />
<br />
=== Report ===<br />
<br />
Please write a report of about 5 pages containing and discussing your results and hand it in until TBA.<br />
<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 3: [[Christian Holm]], Electrostatics, Lattice Boltzmann, and Electrokinetics==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: TBA in the ICP meeting room. <br />
<br />
Final meeting: TBA in the ICP meeting room. <br />
<br />
=== Description ===<br />
<br />
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people.<br />
It consists of one lecture on electrostatic algorithms, simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation<br />
and hand in one report. The Module 3 consists of three parts:<br />
<br />
=== Contact ===<br />
If you have any questions regarding the organisation or content of this module please do not hesitate to contact [[Christian Holm]].<br />
For questions regarding the practical part of the module and technical help contact [[David Sean]].<br />
<br />
=== Part 1: Electrostatics ===<br />
==== Description ====<br />
This part is about the theory of electrostatic algorithms for molecular dynamics simulations.<br />
It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald<br />
methods. To this end the students should read the referenced literature. [[Christian Holm]] will give an hour long lecture. Afterwards we will discuss the content and try to resolve open questions. The presentation should foster the students understanding of the P3M method as well<br />
as give them an overview of its performance compared to other modern electrostatics methods.<br />
<br />
==== Literature ====<br />
:* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''. <br /> [[Media:longrange.pdf|[PDF]]] (15.4 MB) <br /><br />
<bibentry>deserno98a,arnold13b,arnold05a</bibentry><br />
<br />
=== Part 2: Electro-Osmotic Flow ===<br />
==== Description ====<br />
[[File:Slitpore.png|550px|right|Electroosmotic flow in a slit pore]]<br />
This part is practical. It is concerned with the movement of ions in an charged slit pore.<br />
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]<br />
which is recommended reading. A slit pore consists of two infinite charge walls as shown<br />
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].<br />
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented<br />
by charge Week-Chandler-Anderson spheres.<br />
In addition to the charge on the walls, the ions are also subject to an external electrical field parallel to the walls.<br />
Electrostatics should be handled by the P3M algorithm with ELC.<br />
A set of realistic parameters and an more in detail description of the system can be found in the<br />
thesis.<br />
You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit<br />
pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high<br />
salt limit (Debye-Hueckel-Limit).<br />
Calculate the ion profiles in one or both of these cases and compare the results with the simulation.<br />
<br />
===== Worksheet =====<br />
<br />
{{Download|adv_sm_mod3_EOF.pdf|Detailed worksheet}}<br />
<br />
==== Literature ====<br />
<br />
Some ESPResSo tutorials can be helpful.<br />
* General part and parts 4 & 6 of [https://github.com/espressomd/espresso/blob/python/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann.pdf the Lattice-Boltzmann tutorial] <br />
* Part 7 of the [https://github.com/espressomd/espresso/blob/python/doc/tutorials/02-charged_system/02-charged_system.pdf charged systems tutorial] to see how to setup proper electrostatics in quasi-2D geometry.<br />
<br />
* Georg Rempfer, {{Download|BSc_thesis_rempfer.pdf|"Lattice-Boltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart<br />
<br />
=== Part 3: Electrophoresis of Polyelectrolytes ===<br />
==== Description ====<br />
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions.<br />
Set up a system consisting of a charged polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled with <br />
the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer<br />
for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and<br />
experimental results (see literature).<br />
<br />
==== Instructions and Literature ====<br />
General part and part 5 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
<bibentry>grass08a, grass09c</bibentry><br />
<br />
=== Report ===<br />
<br />
At the final meeting day of this module, one group will give a presentation about the learned and performed work. In addition, they write a report of about 5 pages containing and discussing the obtained results and hand it in together with the reports of the other modules at the end of the course (see above).<br />
<br />
The final report is due electronically Friday night, TBA<br />
<br />
<br />
<br />
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.--></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Advanced_Simulation_Methods_SS_2018&diff=23284Advanced Simulation Methods SS 20182018-06-23T17:54:29Z<p>Dsean: /* Part 3: Electrophoresis of Polyelectrolytes */</p>
<hr />
<div><br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students should send an email to [[Maria Fyta]] as soon as possible.<br />
<br><br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).</b>}}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture and Tutorials (2 SWS in total)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]], JP. Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]], Dr. [[David Sean]]<br />
;Course language<br />
:English or German<br />
;Location<br />
:ICP, Allmandring 3; Room: ICP Meeting Room<br />
;Time<br />
:(see below)<br />
The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP. Dr. [[Maria Fyta]] and will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules.<br />
The students can work in groups. All groups should write a report on each module, which they should submit to the responsible person for each module by the deadline set for each module.<br />
<!-- [[Maria Fyta]] no later than Friday July 15, 2016. The report does not need to be longer than 20 pages.--><br />
<br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students write an Email to [[Maria Fyta]] until TBA.</b>}}<br />
<br />
== Module 1: [[Maria Fyta]], [[Frank Uhlig]], Inter-atomic interactions modeled with quantum mechanical simulations ==<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<!--ue 05.04.2016 at 14:00 in the ICP meeting room.--><br />
<br />
Tutorials: TBA in the ICP CIP-Pool.<br />
<br />
Talks: TBA am in the ICP meeting room.<br />
<br />
=== Description ===<br />
<br />
This module focuses on the influence of using quantum mechanical simulations. The quantum mechanical schemes which will be applied in this module are based on density functional theory (DFT). This method allows the investigation of the electronic properties of a system. An understanding of the method, an analysis of the results from the simulations is the main goal of this module. The analysis of the simulations should be written up in a report. The talk will be a presentation of a DFT-related journal paper. For this, one of the following papers can be chosen:<br />
<br />
* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J. Klimeš and A. Michaelides, The Journal of Chemical Physics 137, 120901 (2012); doi: 10.1063/1.4754130<br />
* Challenges for Density Functional Theory, A.J. Cohen, P. Mori-Sanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.<br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module please do not hesitate to contact [[Maria Fyta]]. For practical guidance regarding the simulations [[Frank Uhlig]].<br />
<br />
=== Density functional theory and exchange-correlation functionals ===<br />
<br />
==== Description ====<br />
<br />
Many modern catalyses are performed using noble metals. In particular at the<br />
surface of these catalysts, which come in a multitude of shapes and chemical<br />
composition. The overall catalysis is determined by many factors, including the<br />
actual reactivity of chemical species at the surface, adsorption of reactants<br />
and desorption of products, as well as kinetics of the diffusion on the surface.<br />
<br />
In this exercise you will look at the desorption behavior of hydrogen gas from<br />
the surface of noble metals. This process is important in the production of<br />
hydrogen gas for energy storage applications [1]. However, modeling this process<br />
using modern methods of quantum-mechanical density functional theory (DFT) is<br />
very challenging. Only very advanced and quite recent density functionals are<br />
able to describe the long-range dispersion interactions [2]. Hence, effective<br />
methods based on pair potentials have been developed. These methods can achieve<br />
comparable accuracy to more ab initio methods while coming at a signifcantly<br />
lower computational effort [3,4].<br />
<br />
Your task is to develop such a pair-wise dispersion correction for the<br />
interaction of hydrogen gas with a metal surface. The first step is to<br />
understand and document the metallic behavior of your metal substrate, followed<br />
by investigation of the performance of common DFT functionals for the desorption<br />
process, and finally developing a dispersion correction by determining<br />
individual dispersion coefficients for the involved species [5].<br />
<br />
[1] https://dx.doi.org/10.1038/ncomms6848<br />
<br />
[2] https://dx.doi.org/10.1063/1.4754130<br />
<br />
[3] https://dx.doi.org/10.1103/PhysRevLett.102.073005<br />
<br />
[4] https://dx.doi.org/10.1063/1.3382344<br />
<br />
[5] https://dx.doi.org/10.1063/1.2746031<br />
<br />
[6] [[:Media:Asm_2018_info.txt|ASM tutorial info links]]<br />
<br />
==== Literature ====<br />
<br />
* A bird's-eye view of density-functional theory, Klaus Capelle, arXiv:cond-mat/0211443 (2002).<br />
* Self-Consistent Equations Including Exchange and Correlation Effects, W. Kohn and L.J. Sham, , Phys. Rev. (140), A1133 (1965).<br />
* Understanding and Reducing Errors in Density Functional Calculations, Min-Cheol Kim, Eunji Sim, and Kieron Burke, Phys. Rev. Lett. 111, 073003 (2013).<br />
<!--* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J Klimeš, A Michaelides, J. Chem. Phys. 137, 120901 (2012).--><br />
* An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases, V.R. Cooper, T. Thonhauser, and D.C. Langreth, J. Chem. Phys. 128, 204102 (2008).<br />
* On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit, B. Santra, A. Michaelides, and M. Scheffler, J. Chem. Phys. 127, 184104 (2007).<br />
* On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level, I. Dąbkowska, P. Jurečka, and P. Hobza, J. Chem. Phys. 122, 204322 (2005).<br />
<br />
=== Report ===<br />
<br />
Please write a report 5-10 pages containing and discussing your results and hand it in by Friday TBA.<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 2: [[Maria Fyta]], [[Narayanan Krishnamoorthy Anand]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: 18.05.2018 in the ICP meeting room. <br />
<br />
Final meeting: 15.06.2018 in the ICP meeting room.<br />
<br />
Deadline for reports: 15.06.2018<br />
=== Description ===<br />
<br />
This module focuses on atomistic Molecular Dynamics simulations and the study of biological co-solutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological co-solutes, often also called osmolytes are omnipresent in biological cells. A main function of these small-weight organic <br />
molecules is given by the protection of protein structures under harsh environmental conditions (protein stabilizers) or the denaturation of proteins (protein denaturants). The underlying mechanism leading to these effects is still unknown. It has been often discussed that osmolytes have a significant impact on the aqueous solution.<br />
The module consists of model development, simulation, analysis and oral and written presentation part. <br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Narayanan Krishnamoorthy Anand]].<br />
<br />
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the Kirkwood-Buff theory which can be well applied to computer simulations.<br />
The students should study the literature given below and present their findings. The presentation should at a minimum contain an introduction to Kirkwood-Buff theory in the context of the simulations.<br />
<br />
==== Literature ====<br />
<br />
* D. R. Canchi and A. E. Garcia, "Co-solvent effects on protein stability", Ann. Rev. Phys. Chem. 64. 273 (2013)<br />
* J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951) <br />
* V. Pierce, M. Kang, M. Aburi, S. Weerasinghe and P. E. Smith, "Recent applications of Kirkwood–Buff theory to biological systems", Cell Biochem. Biophys. 50, 1 (2008)<br />
* S. Weerasinghe and P. E. Smith, "A Kirkwood–Buff derived force field for sodium chloride in water", The Journal of Chemical Physics 119, 11342 (2003).<br />
* J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)<br />
* J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)<br />
* T. Kobayashi <i>et al</i>, "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches", Phys.Chem.Chem.Phys. 19, 18924 (2017)<br />
<br />
=== Part 2: Model Development and Simulations ===<br />
<br />
==== Description ====<br />
<br />
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will develop Generalized Amber Force Fields (GAFF) [http://ambermd.org/antechamber/gaff.html] with the help of the ACPYPE program [http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder] for the osmolytes (urea, hydroxyectoine, ectoine) which will be used for the study of solvent properties like the thermodynamics of hydrogen bonding ans the diffusivity according to J. Phys. Chem. B 118, 771 (2014).<br />
In comparison to pure water, the students will analyze several water parameters and elucidate the differences in presence of osmolytes and their concentration dependent behavior. The Kirkwood-Buff theory will be used to calculate derivatives of the activity coefficients and the derivative of the chemical activity for the osmolytes. <br />
<br />
==== Force Fields for ectoine and hydroxyectoine ====<br />
<br />
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}<br />
* {{Download| hectoinzwittmp2.gro |gro-File for Hydroxyectoine}}<br />
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}<br />
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}<br />
<br />
=== Part 3: Tasks ===<br />
1. Implement the developed force fields for the osmolytes (urea, ectoine and hydroxyectoine) in combination with the SPC/E water model. After energy minimization and warm up, run 20-30 ns simulations with GROMACS for osmolyte concentrations between c = 0 - 6 M.<br />
<br />
2. Study the following properties for the different osmolytes and concentrations:<br />
* diffusion coefficients<br />
* hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs<br />
* water mean relaxation times<br />
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?<br />
<br />
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.<br />
Use this information to compute the<br />
* Kirkwood-Buff integrals<br />
* derivatives of the chemical activity<br />
* derivatives of the activity coefficient<br />
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004). <br />
<br />
==== Literature ====<br />
<br />
* D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media", J. Phys. Chem. B 110, 4393 (2006)<br />
* J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem. 25, 1157 (2004)<br />
<br />
=== Report ===<br />
<br />
Please write a report of about 5 pages containing and discussing your results and hand it in until TBA.<br />
<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 3: [[Christian Holm]], Electrostatics, Lattice Boltzmann, and Electrokinetics==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: TBA in the ICP meeting room. <br />
<br />
Final meeting: TBA in the ICP meeting room. <br />
<br />
=== Description ===<br />
<br />
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people.<br />
It consists of one lecture on electrostatic algorithms, simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation<br />
and hand in one report. The Module 3 consists of three parts:<br />
<br />
=== Contact ===<br />
If you have any questions regarding the organisation or content of this module please do not hesitate to contact [[Christian Holm]].<br />
For questions regarding the practical part of the module and technical help contact [[David Sean]].<br />
<br />
=== Part 1: Electrostatics ===<br />
==== Description ====<br />
This part is about the theory of electrostatic algorithms for molecular dynamics simulations.<br />
It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald<br />
methods. To this end the students should read the referenced literature. [[Christian Holm]] will give an hour long lecture. Afterwards we will discuss the content and try to resolve open questions. The presentation should foster the students understanding of the P3M method as well<br />
as give them an overview of its performance compared to other modern electrostatics methods.<br />
<br />
==== Literature ====<br />
:* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''. <br /> [[Media:longrange.pdf|[PDF]]] (15.4 MB) <br /><br />
<bibentry>deserno98a,arnold13b,arnold05a</bibentry><br />
<br />
=== Part 2: Electro-Osmotic Flow ===<br />
==== Description ====<br />
[[File:Slitpore.png|550px|right|Electroosmotic flow in a slit pore]]<br />
This part is practical. It is concerned with the movement of ions in an charged slit pore.<br />
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]<br />
which is recommended reading. A slit pore consists of two infinite charge walls as shown<br />
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].<br />
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented<br />
by charge Week-Chandler-Anderson spheres.<br />
In addition to the charge on the walls, the ions are also subject to an external electrical field parallel to the walls.<br />
Electrostatics should be handled by the P3M algorithm with ELC.<br />
A set of realistic parameters and an more in detail description of the system can be found in the<br />
thesis.<br />
You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit<br />
pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high<br />
salt limit (Debye-Hueckel-Limit).<br />
Calculate the ion profiles in one or both of these cases and compare the results with the simulation.<br />
<br />
==== Instructions and Literature ====<br />
Some ESPResSo tutorials can be helpful.<br />
* General part and parts 4 & 6 of [https://github.com/espressomd/espresso/blob/python/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann.pdf the Lattice-Boltzmann tutorial] <br />
* Part 7 of the [https://github.com/espressomd/espresso/blob/python/doc/tutorials/02-charged_system/02-charged_system.pdf charged systems tutorial] to see how to setup proper electrostatics in quasi-2D geometry.<br />
<br />
* Georg Rempfer, {{Download|BSc_thesis_rempfer.pdf|"Lattice-Boltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart<br />
<br />
=== Part 3: Electrophoresis of Polyelectrolytes ===<br />
==== Description ====<br />
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions.<br />
Set up a system consisting of a charged polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled with <br />
the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer<br />
for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and<br />
experimental results (see literature).<br />
<br />
==== Instructions and Literature ====<br />
General part and part 5 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
<bibentry>grass08a, grass09c</bibentry><br />
<br />
=== Report ===<br />
<br />
At the final meeting day of this module, one group will give a presentation about the learned and performed work. In addition, they write a report of about 5 pages containing and discussing the obtained results and hand it in together with the reports of the other modules at the end of the course (see above).<br />
<br />
The final report is due electronically Friday night, TBA<br />
<br />
<br />
<br />
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.--></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Advanced_Simulation_Methods_SS_2018&diff=23283Advanced Simulation Methods SS 20182018-06-23T17:52:43Z<p>Dsean: /* Part 2: Slit Pore */</p>
<hr />
<div><br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students should send an email to [[Maria Fyta]] as soon as possible.<br />
<br><br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).</b>}}<br />
<br />
== Overview ==<br />
<br />
;Type<br />
:Lecture and Tutorials (2 SWS in total)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]], JP. Dr. [[Maria Fyta]], Dr. [[Frank Uhlig]], Dr. [[David Sean]]<br />
;Course language<br />
:English or German<br />
;Location<br />
:ICP, Allmandring 3; Room: ICP Meeting Room<br />
;Time<br />
:(see below)<br />
The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]], Dr. [[Jens Smiatek]], JP. Dr. [[Maria Fyta]] and will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules.<br />
The students can work in groups. All groups should write a report on each module, which they should submit to the responsible person for each module by the deadline set for each module.<br />
<!-- [[Maria Fyta]] no later than Friday July 15, 2016. The report does not need to be longer than 20 pages.--><br />
<br />
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students write an Email to [[Maria Fyta]] until TBA.</b>}}<br />
<br />
== Module 1: [[Maria Fyta]], [[Frank Uhlig]], Inter-atomic interactions modeled with quantum mechanical simulations ==<br />
<br />
=== Dates ===<br />
<br />
First meeting: Friday, April 13 at 11:30 in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).<!--ue 05.04.2016 at 14:00 in the ICP meeting room.--><br />
<br />
Tutorials: TBA in the ICP CIP-Pool.<br />
<br />
Talks: TBA am in the ICP meeting room.<br />
<br />
=== Description ===<br />
<br />
This module focuses on the influence of using quantum mechanical simulations. The quantum mechanical schemes which will be applied in this module are based on density functional theory (DFT). This method allows the investigation of the electronic properties of a system. An understanding of the method, an analysis of the results from the simulations is the main goal of this module. The analysis of the simulations should be written up in a report. The talk will be a presentation of a DFT-related journal paper. For this, one of the following papers can be chosen:<br />
<br />
* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J. Klimeš and A. Michaelides, The Journal of Chemical Physics 137, 120901 (2012); doi: 10.1063/1.4754130<br />
* Challenges for Density Functional Theory, A.J. Cohen, P. Mori-Sanchez, and W. Yang, Chemical Reviews 112, 289 (2012); dx.doi.org/10.1021/cr200107z.<br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module please do not hesitate to contact [[Maria Fyta]]. For practical guidance regarding the simulations [[Frank Uhlig]].<br />
<br />
=== Density functional theory and exchange-correlation functionals ===<br />
<br />
==== Description ====<br />
<br />
Many modern catalyses are performed using noble metals. In particular at the<br />
surface of these catalysts, which come in a multitude of shapes and chemical<br />
composition. The overall catalysis is determined by many factors, including the<br />
actual reactivity of chemical species at the surface, adsorption of reactants<br />
and desorption of products, as well as kinetics of the diffusion on the surface.<br />
<br />
In this exercise you will look at the desorption behavior of hydrogen gas from<br />
the surface of noble metals. This process is important in the production of<br />
hydrogen gas for energy storage applications [1]. However, modeling this process<br />
using modern methods of quantum-mechanical density functional theory (DFT) is<br />
very challenging. Only very advanced and quite recent density functionals are<br />
able to describe the long-range dispersion interactions [2]. Hence, effective<br />
methods based on pair potentials have been developed. These methods can achieve<br />
comparable accuracy to more ab initio methods while coming at a signifcantly<br />
lower computational effort [3,4].<br />
<br />
Your task is to develop such a pair-wise dispersion correction for the<br />
interaction of hydrogen gas with a metal surface. The first step is to<br />
understand and document the metallic behavior of your metal substrate, followed<br />
by investigation of the performance of common DFT functionals for the desorption<br />
process, and finally developing a dispersion correction by determining<br />
individual dispersion coefficients for the involved species [5].<br />
<br />
[1] https://dx.doi.org/10.1038/ncomms6848<br />
<br />
[2] https://dx.doi.org/10.1063/1.4754130<br />
<br />
[3] https://dx.doi.org/10.1103/PhysRevLett.102.073005<br />
<br />
[4] https://dx.doi.org/10.1063/1.3382344<br />
<br />
[5] https://dx.doi.org/10.1063/1.2746031<br />
<br />
[6] [[:Media:Asm_2018_info.txt|ASM tutorial info links]]<br />
<br />
==== Literature ====<br />
<br />
* A bird's-eye view of density-functional theory, Klaus Capelle, arXiv:cond-mat/0211443 (2002).<br />
* Self-Consistent Equations Including Exchange and Correlation Effects, W. Kohn and L.J. Sham, , Phys. Rev. (140), A1133 (1965).<br />
* Understanding and Reducing Errors in Density Functional Calculations, Min-Cheol Kim, Eunji Sim, and Kieron Burke, Phys. Rev. Lett. 111, 073003 (2013).<br />
<!--* Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory, J Klimeš, A Michaelides, J. Chem. Phys. 137, 120901 (2012).--><br />
* An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases, V.R. Cooper, T. Thonhauser, and D.C. Langreth, J. Chem. Phys. 128, 204102 (2008).<br />
* On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit, B. Santra, A. Michaelides, and M. Scheffler, J. Chem. Phys. 127, 184104 (2007).<br />
* On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level, I. Dąbkowska, P. Jurečka, and P. Hobza, J. Chem. Phys. 122, 204322 (2005).<br />
<br />
=== Report ===<br />
<br />
Please write a report 5-10 pages containing and discussing your results and hand it in by Friday TBA.<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 2: [[Maria Fyta]], [[Narayanan Krishnamoorthy Anand]]: Atomistic Simulations of Co-Solutes in Aqueous Solutions ==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: 18.05.2018 in the ICP meeting room. <br />
<br />
Final meeting: 15.06.2018 in the ICP meeting room.<br />
<br />
Deadline for reports: 15.06.2018<br />
=== Description ===<br />
<br />
This module focuses on atomistic Molecular Dynamics simulations and the study of biological co-solutes like urea, ectoine or hydroxyectoine and their influence on aqueous solutions. Biological co-solutes, often also called osmolytes are omnipresent in biological cells. A main function of these small-weight organic <br />
molecules is given by the protection of protein structures under harsh environmental conditions (protein stabilizers) or the denaturation of proteins (protein denaturants). The underlying mechanism leading to these effects is still unknown. It has been often discussed that osmolytes have a significant impact on the aqueous solution.<br />
The module consists of model development, simulation, analysis and oral and written presentation part. <br />
<br />
=== Contact ===<br />
<br />
If you have any questions regarding the organization or content of this module, please do not hesitate to contact [[Narayanan Krishnamoorthy Anand]].<br />
<br />
=== Part 1: Osmolytes and Kirkwood-Buff Theory ===<br />
<br />
==== Description ====<br />
<br />
This part introduces the students to the field of osmolyte research. An important theory to study solvation and binding behavior is given by the Kirkwood-Buff theory which can be well applied to computer simulations.<br />
The students should study the literature given below and present their findings. The presentation should at a minimum contain an introduction to Kirkwood-Buff theory in the context of the simulations.<br />
<br />
==== Literature ====<br />
<br />
* D. R. Canchi and A. E. Garcia, "Co-solvent effects on protein stability", Ann. Rev. Phys. Chem. 64. 273 (2013)<br />
* J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951) <br />
* V. Pierce, M. Kang, M. Aburi, S. Weerasinghe and P. E. Smith, "Recent applications of Kirkwood–Buff theory to biological systems", Cell Biochem. Biophys. 50, 1 (2008)<br />
* S. Weerasinghe and P. E. Smith, "A Kirkwood–Buff derived force field for sodium chloride in water", The Journal of Chemical Physics 119, 11342 (2003).<br />
* J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)<br />
* J. Smiatek, "Osmolyte effects: Impact on the aqueous solution around charged and neutral spheres", J. Phys. Chem. B 118, 771 (2014)<br />
* T. Kobayashi <i>et al</i>, "The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches", Phys.Chem.Chem.Phys. 19, 18924 (2017)<br />
<br />
=== Part 2: Model Development and Simulations ===<br />
<br />
==== Description ====<br />
<br />
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will develop Generalized Amber Force Fields (GAFF) [http://ambermd.org/antechamber/gaff.html] with the help of the ACPYPE program [http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder] for the osmolytes (urea, hydroxyectoine, ectoine) which will be used for the study of solvent properties like the thermodynamics of hydrogen bonding ans the diffusivity according to J. Phys. Chem. B 118, 771 (2014).<br />
In comparison to pure water, the students will analyze several water parameters and elucidate the differences in presence of osmolytes and their concentration dependent behavior. The Kirkwood-Buff theory will be used to calculate derivatives of the activity coefficients and the derivative of the chemical activity for the osmolytes. <br />
<br />
==== Force Fields for ectoine and hydroxyectoine ====<br />
<br />
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}<br />
* {{Download| hectoinzwittmp2.gro |gro-File for Hydroxyectoine}}<br />
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}<br />
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}<br />
<br />
=== Part 3: Tasks ===<br />
1. Implement the developed force fields for the osmolytes (urea, ectoine and hydroxyectoine) in combination with the SPC/E water model. After energy minimization and warm up, run 20-30 ns simulations with GROMACS for osmolyte concentrations between c = 0 - 6 M.<br />
<br />
2. Study the following properties for the different osmolytes and concentrations:<br />
* diffusion coefficients<br />
* hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs<br />
* water mean relaxation times<br />
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?<br />
<br />
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.<br />
Use this information to compute the<br />
* Kirkwood-Buff integrals<br />
* derivatives of the chemical activity<br />
* derivatives of the activity coefficient<br />
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004). <br />
<br />
==== Literature ====<br />
<br />
* D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media", J. Phys. Chem. B 110, 4393 (2006)<br />
* J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem. 25, 1157 (2004)<br />
<br />
=== Report ===<br />
<br />
Please write a report of about 5 pages containing and discussing your results and hand it in until TBA.<br />
<br />
<!--Please hand in one report per group of 5 to 10 pages containing and discussing your results.--><br />
<br />
== Module 3: [[Christian Holm]], Electrostatics, Lattice Boltzmann, and Electrokinetics==<br />
<br />
<br />
=== Dates ===<br />
<br />
First meeting: TBA in the ICP meeting room. <br />
<br />
Final meeting: TBA in the ICP meeting room. <br />
<br />
=== Description ===<br />
<br />
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people.<br />
It consists of one lecture on electrostatic algorithms, simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation<br />
and hand in one report. The Module 3 consists of three parts:<br />
<br />
=== Contact ===<br />
If you have any questions regarding the organisation or content of this module please do not hesitate to contact [[Christian Holm]].<br />
For questions regarding the practical part of the module and technical help contact [[David Sean]].<br />
<br />
=== Part 1: Electrostatics ===<br />
==== Description ====<br />
This part is about the theory of electrostatic algorithms for molecular dynamics simulations.<br />
It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald<br />
methods. To this end the students should read the referenced literature. [[Christian Holm]] will give an hour long lecture. Afterwards we will discuss the content and try to resolve open questions. The presentation should foster the students understanding of the P3M method as well<br />
as give them an overview of its performance compared to other modern electrostatics methods.<br />
<br />
==== Literature ====<br />
:* C. Holm.<br />'''"Simulating Long range interactions".'''<br />''Institute for Computational Physics, Universitat Stuttgart,'' '''2018'''. <br /> [[Media:longrange.pdf|[PDF]]] (15.4 MB) <br /><br />
<bibentry>deserno98a,arnold13b,arnold05a</bibentry><br />
<br />
=== Part 2: Electro-Osmotic Flow ===<br />
==== Description ====<br />
[[File:Slitpore.png|550px|right|Electroosmotic flow in a slit pore]]<br />
This part is practical. It is concerned with the movement of ions in an charged slit pore.<br />
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]<br />
which is recommended reading. A slit pore consists of two infinite charge walls as shown<br />
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].<br />
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented<br />
by charge Week-Chandler-Anderson spheres.<br />
In addition to the charge on the walls, the ions are also subject to an external electrical field parallel to the walls.<br />
Electrostatics should be handled by the P3M algorithm with ELC.<br />
A set of realistic parameters and an more in detail description of the system can be found in the<br />
thesis.<br />
You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit<br />
pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high<br />
salt limit (Debye-Hueckel-Limit).<br />
Calculate the ion profiles in one or both of these cases and compare the results with the simulation.<br />
<br />
==== Instructions and Literature ====<br />
Some ESPResSo tutorials can be helpful.<br />
* General part and parts 4 & 6 of [https://github.com/espressomd/espresso/blob/python/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann.pdf the Lattice-Boltzmann tutorial] <br />
* Part 7 of the [https://github.com/espressomd/espresso/blob/python/doc/tutorials/02-charged_system/02-charged_system.pdf charged systems tutorial] to see how to setup proper electrostatics in quasi-2D geometry.<br />
<br />
* Georg Rempfer, {{Download|BSc_thesis_rempfer.pdf|"Lattice-Boltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart<br />
<br />
=== Part 3: Electrophoresis of Polyelectrolytes ===<br />
==== Description ====<br />
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions.<br />
Set up a system consisting of a charge polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled<br />
the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer<br />
for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and<br />
experimental results (see literature).<br />
<br />
==== Instructions and Literatur ====<br />
General part and part 5 of [[Media:04-lattice_boltzmann.pdf]]<br />
<br />
<bibentry>grass08a, grass09c</bibentry><br />
<br />
=== Report ===<br />
<br />
At the final meeting day of this module, one group will give a presentation about the learned and performed work. In addition, they write a report of about 5 pages containing and discussing the obtained results and hand it in together with the reports of the other modules at the end of the course (see above).<br />
<br />
The final report is due electronically Friday night, TBA<br />
<br />
<br />
<br />
<!--Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.--></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:Flory-DavidNotes.pdf&diff=23273File:Flory-DavidNotes.pdf2018-06-20T11:35:24Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2018&diff=23272Simulation Methods in Physics II SS 20182018-06-20T11:35:13Z<p>Dsean: /* 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 />
Thursday 02.08.2018 between 11am-2pm, <br><br />
Tuesday 11.09.2018 between 11am-2pm, <br><br />
Wednesday 12.09.2018 between 10am-2pm, <br><br />
Thursday 13.09.2018 between 11am-2pm, <br><br />
Monday 01.10.2018 between 11am-2pm, <br><br />
Tuesday 02.10.2018 between 10am-2pm, <br><br />
Thursday 04.10.2018 between 11am-2pm, <br><br />
<!-- Monday 22.10.2018 between 12pm-14pm, <br--><br />
Tuesday 23.10.2018 between 11am-2pm.<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 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; 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 in September or October 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://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]<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 />
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.--><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 />
| 12.04.2018 || Introduction/organisation, electronic structure || <!--{{ Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}} {{ Download|simmethodsII_ss16_lecture1notes.pdf|Lecture Notes}}--><br />
|- <br />
| 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || <!--{{ |Lecture Notes}} --><br />
|- <br />
| 26.04.2018 || Density Functional Theory (DFT) || <!--{{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}--><br />
|- <br />
| 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} <br />
|- <br />
| 10.05.2018 || Holiday (Christi Himmelfahrt) ||<br />
|-<br />
| 17.05.2018 || Classical force fields and water models || <br />
|- <br />
| 24.05.2018 || '' Holiday (Pfingsten) '' || <br />
|- <br />
| 31.05.2018 || Holiday (Fronleichnam) '' || <br />
|- <br />
| 07.06.2018 || Simulations of macromolecules and soft matter || <br />
|- <br />
| 14.06.2018 || Poisson-Boltzmann theory, charged polymers || {{Download|Poisson-Boltzmann-DavidNotes.pdf |Poisson-Boltzmann}} {{Download|Flory-DavidNotes.pdf|Polymer scaling}}<br />
|-<br />
| 21.06.2018 || Hydrodynamic methods I (Lattice-Boltzmann, Brownian Dynamics, DPD, SRD) ||<br />
|- <br />
| 28.06.2018 || Free energy methods ||<br />
|- <br />
| 05.07.2018 || Interatomic potentials (pair-potentials, EAM) (solid-state systems) ||<br />
|- <br />
| 12.07.2018 || Energy minimization||<br />
|- <br />
| 19.07.2018 ||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, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] )<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 18th. The deadline will be Wed. May 2nd. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout<br />
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}}<br />
* {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 4: Flow Between Plates and Free Energy ====<br />
* Deadline: '''June 19, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss17_template4.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 />
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====<br />
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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/2017</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 ([[Miriam Kohagen]] or [[David Sean]]).<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>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:Poisson-Boltzmann-DavidNotes.pdf&diff=23271File:Poisson-Boltzmann-DavidNotes.pdf2018-06-20T11:34:27Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2018&diff=23270Simulation Methods in Physics II SS 20182018-06-20T11:33:34Z<p>Dsean: /* 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 />
Thursday 02.08.2018 between 11am-2pm, <br><br />
Tuesday 11.09.2018 between 11am-2pm, <br><br />
Wednesday 12.09.2018 between 10am-2pm, <br><br />
Thursday 13.09.2018 between 11am-2pm, <br><br />
Monday 01.10.2018 between 11am-2pm, <br><br />
Tuesday 02.10.2018 between 10am-2pm, <br><br />
Thursday 04.10.2018 between 11am-2pm, <br><br />
<!-- Monday 22.10.2018 between 12pm-14pm, <br--><br />
Tuesday 23.10.2018 between 11am-2pm.<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 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; 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 in September or October 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://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]<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 />
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.--><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 />
| 12.04.2018 || Introduction/organisation, electronic structure || <!--{{ Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}} {{ Download|simmethodsII_ss16_lecture1notes.pdf|Lecture Notes}}--><br />
|- <br />
| 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || <!--{{ |Lecture Notes}} --><br />
|- <br />
| 26.04.2018 || Density Functional Theory (DFT) || <!--{{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}--><br />
|- <br />
| 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} <br />
|- <br />
| 10.05.2018 || Holiday (Christi Himmelfahrt) ||<br />
|-<br />
| 17.05.2018 || Classical force fields and water models || <br />
|- <br />
| 24.05.2018 || '' Holiday (Pfingsten) '' || <br />
|- <br />
| 31.05.2018 || Holiday (Fronleichnam) '' || <br />
|- <br />
| 07.06.2018 || Simulations of macromolecules and soft matter || <br />
|- <br />
| 14.06.2018 || Poisson-Boltzmann theory, charged polymers || {{Download|Poisson-Boltzmann-DavidNotes|Poisson-Boltzmann}} {{Download|Flory-DavidNotes.pdf|Polymer scaling}}<br />
|-<br />
| 21.06.2018 || Hydrodynamic methods I (Lattice-Boltzmann, Brownian Dynamics, DPD, SRD) ||<br />
|- <br />
| 28.06.2018 || Free energy methods ||<br />
|- <br />
| 05.07.2018 || Interatomic potentials (pair-potentials, EAM) (solid-state systems) ||<br />
|- <br />
| 12.07.2018 || Energy minimization||<br />
|- <br />
| 19.07.2018 ||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, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] )<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 18th. The deadline will be Wed. May 2nd. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout<br />
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}}<br />
* {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 4: Flow Between Plates and Free Energy ====<br />
* Deadline: '''June 19, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss17_template4.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 />
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====<br />
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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/2017</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 ([[Miriam Kohagen]] or [[David Sean]]).<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>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2018&diff=23269Simulation Methods in Physics II SS 20182018-06-20T11:33:10Z<p>Dsean: /* 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 />
Thursday 02.08.2018 between 11am-2pm, <br><br />
Tuesday 11.09.2018 between 11am-2pm, <br><br />
Wednesday 12.09.2018 between 10am-2pm, <br><br />
Thursday 13.09.2018 between 11am-2pm, <br><br />
Monday 01.10.2018 between 11am-2pm, <br><br />
Tuesday 02.10.2018 between 10am-2pm, <br><br />
Thursday 04.10.2018 between 11am-2pm, <br><br />
<!-- Monday 22.10.2018 between 12pm-14pm, <br--><br />
Tuesday 23.10.2018 between 11am-2pm.<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 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; 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 in September or October 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://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]<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 />
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.--><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 />
| 12.04.2018 || Introduction/organisation, electronic structure || <!--{{ Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}} {{ Download|simmethodsII_ss16_lecture1notes.pdf|Lecture Notes}}--><br />
|- <br />
| 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || <!--{{ |Lecture Notes}} --><br />
|- <br />
| 26.04.2018 || Density Functional Theory (DFT) || <!--{{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}--><br />
|- <br />
| 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} <br />
|- <br />
| 10.05.2018 || Holiday (Christi Himmelfahrt) ||<br />
|-<br />
| 17.05.2018 || Classical force fields and water models || <br />
|- <br />
| 24.05.2018 || '' Holiday (Pfingsten) '' || <br />
|- <br />
| 31.05.2018 || Holiday (Fronleichnam) '' || <br />
|- <br />
| 07.06.2018 || Simulations of macromolecules and soft matter || <br />
|- <br />
| 14.06.2018 || Poisson-Boltzmann theory, charged polymers || {{Download|Poisson-Boltzmann-DavidNotes|Poisson-Boltzmann}}<br />
{{Download|Flory-DavidNotes.pdf|Polymer scaling}}<br />
|-<br />
| 21.06.2018 || Hydrodynamic methods I (Lattice-Boltzmann, Brownian Dynamics, DPD, SRD) ||<br />
|- <br />
| 28.06.2018 || Free energy methods ||<br />
|- <br />
| 05.07.2018 || Interatomic potentials (pair-potentials, EAM) (solid-state systems) ||<br />
|- <br />
| 12.07.2018 || Energy minimization||<br />
|- <br />
| 19.07.2018 ||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, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] )<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 18th. The deadline will be Wed. May 2nd. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout<br />
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}}<br />
* {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 4: Flow Between Plates and Free Energy ====<br />
* Deadline: '''June 19, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss17_template4.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 />
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====<br />
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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/2017</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 ([[Miriam Kohagen]] or [[David Sean]]).<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>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss18_template5.py&diff=23266File:SimmethodsII ss18 template5.py2018-06-19T09:01:16Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2018&diff=23265Simulation Methods in Physics II SS 20182018-06-19T09:01:00Z<p>Dsean: /* Worksheet 5: Charge distribution around a charged rod */</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 />
Thursday 02.08.2018 between 11am-2pm, <br><br />
Tuesday 11.09.2018 between 11am-2pm, <br><br />
Wednesday 12.09.2018 between 10am-2pm, <br><br />
Thursday 13.09.2018 between 11am-2pm, <br><br />
Monday 01.10.2018 between 11am-2pm, <br><br />
Tuesday 02.10.2018 between 10am-2pm, <br><br />
Thursday 04.10.2018 between 11am-2pm, <br><br />
<!-- Monday 22.10.2018 between 12pm-14pm, <br--><br />
Tuesday 23.10.2018 between 11am-2pm.<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 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; 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 in September or October 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://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]<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 />
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.--><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 />
| 12.04.2018 || Introduction/organisation, electronic structure || <!--{{ Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}} {{ Download|simmethodsII_ss16_lecture1notes.pdf|Lecture Notes}}--><br />
|- <br />
| 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || <!--{{ |Lecture Notes}} --><br />
|- <br />
| 26.04.2018 || Density Functional Theory (DFT) || <!--{{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}--><br />
|- <br />
| 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} <br />
|- <br />
| 10.05.2018 || Holiday (Christi Himmelfahrt) ||<br />
|-<br />
| 17.05.2018 || Classical force fields and water models || <br />
|- <br />
| 24.05.2018 || '' Holiday (Pfingsten) '' || <br />
|- <br />
| 31.05.2018 || Holiday (Fronleichnam) '' || <br />
|- <br />
| 07.06.2018 || Simulations of macromolecules and soft matter || <br />
|- <br />
| 14.06.2018 || Poisson-Boltzmann theory, charged polymers || <br />
|-<br />
| 21.06.2018 || Hydrodynamic methods I (Lattice-Boltzmann, Brownian Dynamics, DPD, SRD) ||<br />
|- <br />
| 28.06.2018 || Free energy methods ||<br />
|- <br />
| 05.07.2018 || Interatomic potentials (pair-potentials, EAM) (solid-state systems) ||<br />
|- <br />
| 12.07.2018 || Energy minimization||<br />
|- <br />
| 19.07.2018 ||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, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] )<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 18th. The deadline will be Wed. May 2nd. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout<br />
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}}<br />
* {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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|Worksheet}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 4: Flow Between Plates and Free Energy ====<br />
* Deadline: '''June 19, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet4.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss17_template4.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 />
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====<br />
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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/2017</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 ([[Miriam Kohagen]] or [[David Sean]]).<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>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2018&diff=23263Simulation Methods in Physics II SS 20182018-06-19T08:59:52Z<p>Dsean: /* Worksheets */</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 />
Thursday 02.08.2018 between 11am-2pm, <br><br />
Tuesday 11.09.2018 between 11am-2pm, <br><br />
Wednesday 12.09.2018 between 10am-2pm, <br><br />
Thursday 13.09.2018 between 11am-2pm, <br><br />
Monday 01.10.2018 between 11am-2pm, <br><br />
Tuesday 02.10.2018 between 10am-2pm, <br><br />
Thursday 04.10.2018 between 11am-2pm, <br><br />
<!-- Monday 22.10.2018 between 12pm-14pm, <br--><br />
Tuesday 23.10.2018 between 11am-2pm.<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 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; 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 in September or October 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://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]<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 />
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.--><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 />
| 12.04.2018 || Introduction/organisation, electronic structure || <!--{{ Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}} {{ Download|simmethodsII_ss16_lecture1notes.pdf|Lecture Notes}}--><br />
|- <br />
| 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || <!--{{ |Lecture Notes}} --><br />
|- <br />
| 26.04.2018 || Density Functional Theory (DFT) || <!--{{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}--><br />
|- <br />
| 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} <br />
|- <br />
| 10.05.2018 || Holiday (Christi Himmelfahrt) ||<br />
|-<br />
| 17.05.2018 || Classical force fields and water models || <br />
|- <br />
| 24.05.2018 || '' Holiday (Pfingsten) '' || <br />
|- <br />
| 31.05.2018 || Holiday (Fronleichnam) '' || <br />
|- <br />
| 07.06.2018 || Simulations of macromolecules and soft matter || <br />
|- <br />
| 14.06.2018 || Poisson-Boltzmann theory, charged polymers || <br />
|-<br />
| 21.06.2018 || Hydrodynamic methods I (Lattice-Boltzmann, Brownian Dynamics, DPD, SRD) ||<br />
|- <br />
| 28.06.2018 || Free energy methods ||<br />
|- <br />
| 05.07.2018 || Interatomic potentials (pair-potentials, EAM) (solid-state systems) ||<br />
|- <br />
| 12.07.2018 || Energy minimization||<br />
|- <br />
| 19.07.2018 ||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, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] )<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 18th. The deadline will be Wed. May 2nd. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout<br />
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}}<br />
* {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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|Worksheet 3}}<br />
* {{Download|SimmethodsII_ss18_template5.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
<br />
<!--<br />
==== Worksheet 4: Flow Between Plates and Free Energy ====<br />
* Deadline: '''June 19, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet4.pdf|Worksheet 4}}<br />
* {{Download|SimmethodsII_ss17_template4.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 />
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====<br />
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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/2017</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 ([[Miriam Kohagen]] or [[David Sean]]).<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>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Open_Positions&diff=23258Open Positions2018-06-18T09:27:58Z<p>Dsean: position filled</p>
<hr />
<div>__TOC__<br />
<br />
<strong>Topics for Diploma/Master/Bachelor-Theses can be found [[Theses|here]].</strong><br />
<br />
== Ph.D. positions ==<br />
<br />
=== Simulations and theoretical work in the area of soft matter systems ===<br />
<br />
The Institute for Computational Physics works in the fields of research of simulations and theory of soft matter and biophysical systems, e.g. subjects like ''nucleation, ionic systems, ferrofluids, hydrogels, as well as colloids, polymers or biomolecules''.<br />
<br />
At present we have no open positions. However, we can support applications of exceptionally good candidates for funding in other projects. These positions would be in the groups of [[Maria Fyta]], [[Jens Smiatek]], and [[Christian Holm]].<br />
<br />
Common to all applicants should be a strong background in statistical physics and MD or MC simulation strategies, and knowledge of basic soft matter background (polymers, colloids) or knowledge in atomistic modelling (biomolecules, proteins). The simulations will be performed using the software package {{ES}}, GROMACS, or self-written codes. We are also active in the field of algorithm and code development, in particular for electrostatic and hydrodynamic interactions.<br />
<br />
There will be ample opportunity to interact with other researchers at Stuttgart, the Max Planck Institute for metals research, the {{MPIP}}, and the [http://www.uni-stuttgart.de University of Stuttgart].<br />
<br />
All positions are initially for one year, renewable upon mutual agreement. Candidates should have the relevant background in a quantitative discipline (see above) and a keen interest in several of the lab's research areas. Applicants should submit: <br />
<br />
* resume (including date of birth, grades, awards, publications), <br />
* statement of research interests (up to 2 pages), <br />
* names and email addresses of 2-3 references <br />
* links to their thesis and/or publications <br />
<br />
Positions will remain open until filled. Please send applications via email to [{{SERVER}}/nmt.php?page=application application _at_ icp.uni-stuttgart.de], or if you are located in Stuttgart, simply drop by our institute.<br />
<br />
=== Doktorandenstelle: Physik poröser Medien ===<br />
<br />
Am Institut für Computerphysik ist eine '''Doktorandenstelle''' (TVL E13 2/3) im Fach "Theoretische Physik" in der Arbeitsgruppe Physik poröser Medien zu besetzen.<br />
<br />
Das Institut für Computerphysik der Universität Stuttgart sucht Diplom/M.Sc.-Studenten, die ihre Doktorarbeit über ein Thema auf dem Gebiet der rechnergestützten statistischen Physik schreiben möchten. Die geplante Dissertation befasst sich mit der Simulation mehrskaliger poröser Medien. Das Projekt wird im Rahmen des Sonderforschungsbereichs 716 durchgeführt. Interessierte Studenten sollten einen überdurchschnittlichen Diplom-, Magister (M.Sc.) oder äquivalenten Abschluss in Physik oder Mathematik vorweisen können. Programmierkenntnisse sind erforderlich. Fähigkeit und Bereitschaft zur Zusammenarbeit mit anderen Doktoranden und Projekten auf demselben Arbeitsgebiet sowie überdurchschnittliche Einsatzbereitschaft werden erwartet. Interessenten senden bitte Ihre Bewerbungsunterlagen (Lebenslauf, Anschreiben, Zeugnisse etc) an.<br />
<br />
Prof. Dr. R. Hilfer<br /><br />
Institut für Computerphysik<br /><br />
Universität Stuttgart<br /><br />
Allmandring 3<br /><br /><br />
70569 Stuttgart<br />
<br />
Tel: +49 711 685-67607<br /><br />
Fax: +49 711 685-63658<br /><br />
hilfer@icp.uni-stuttgart.de<br />
<br />
Die Einstellung erfolgt durch das Rektoramt der Universität Stuttgart.<br />
<br />
<!--=== PhD position: Modeling biologically modified materials===<br />
<br />
<br />
A graduate student position is available at the Institute of Computational Physics, University of Stuttgart under the guidance of JunProf. Dr. Maria Fyta. The position is funded by the collaborative grant SFB716 "Dynamic simulation of systems with large particle numbers" of the University of Stuttgart, Germany. The specific project will deal with integrating biomolecules and materials to make biofunctional materials. The research will be conducted by means of theoretical and computational tools. Specifically, a wide range of computational schemes, ranging from first principles quantum dynamics simulations up to coarse grained approaches will be used to model biomolecules grafted on materials. A comparative study of a wide range of biologically modified materials will be complemented by the in depth investigation of their optical, electronic, and mechanical properties, as well as the functionality of these biomaterials for potential applications. The applicant should have a strong background in Physics, Chemistry, Biology or Materials Science and an overall strong motivation. Computational skills are a prerequisite, as well as experience in scientific computing. Previous experience in UNIX/Linux environment and programming in either Fortran and/or C/C++ and/or Python is essential. Ability to work independently and also function as an active and efficient team player is also important. Please send a CV, a research statement, and two reference letters to JunProf. Dr. Maria Fyta (mfyta@icp.uni-stuttgart.de).--><br />
<br />
== Studentische Hilfskräfte ==<br />
<br />
We also have a number of open positions for student helpers.<br />
<!-- === Unterstützung der Institutsleitung ===<br />
Wir suchen studentische Hilfskräfte zur Unterstützung des Institutsleiters. Kenntnisse in MS Office und sicheres Deutsch sind Voraussetzung, Englischkenntnisse sind wünschenswert. Zeitlicher Umfang nach Absprache.<br />
<br />
Weitere Informationen: [[Media:Stellenanzeige_Hiwi.pdf|Stellenanzeige_Hiwi.pdf]]<br />
<br />
Bei Interesse wenden Sie sich bitte an Henriette Patzelt, Tel: 0711 685 63593, E-mail: [mailto:sekretariat@icp.uni-stuttgart.de sekretariat@icp.uni-stuttgart.de]<br />
--><br />
<!-- === Programmieren und Visualisierung ===<br />
We are constantly looking for motivated HiWis (student helpers) who can do basic programming tasks in C, and can help with producing animated videos and graphics, using VMD. Write an email to [mailto:sekretariat@icp.uni-stuttgart.de sekretariat@icp.uni-stuttgart.de]<br />
--><br />
<br />
<br />
=== Modellierung von biomodifizierten Oberflächen/Modeling biomodified surfaces ===<br />
<br />
* Eine HiWi Stelle zur Unterstützung der Modellierung von biologisch modifizierten Materialien ist frei. Interessenten bitte eine E-mail an [[Maria Fyta]] (mfyta_at_icp.uni-stuttgart.de) schicken.<br />
<br />
* There is currently an opening for a HiWi (student assistant) in the field of computer simulations of modified surfaces (molecules adsorbed on surfaces). In case you are interested in bachelor or master projects, please contact [[Maria Fyta]] (mfyta_at_icp.uni-stuttgart.de). <br />
<br />
<!-- === Studentische Hilfskraft zur Unterstützung des Institutsleiters ===<br />
<br />
* Die Aufgaben umfassen Internet- und Literaturrecherche, Unterstützung bei der Vorbereitung der Vorlesungen, Pflege der Literaturdatenbank und der Webseiten des Instituts, allgemeine Projektmitarbeit<br />
* Wir setzen voraus: Gültige Immatrikulationsbescheinigung, Kenntnisse in MS Office (v.a. Microsoft Word und Excel), Kenntnisse in LaTeX wünschenswert, sicheres Deutsch, gute Englischkenntnisse, Teamfähigkeit, Flexibilität und Zuverlässigkeit<br />
Beginn sofort; zeitlicher Umfang nach Absprache. Wir sind an einer mehrjährigen Zusammmenarbeit interessiert. <br />
<br />
Bewerbungsunterlagen (Lebenslauf) an das Sekretariat des ICP, Henriette Patzelt, Tel: 0711 685 63593, E-mail: Sekretariat@icp.uni-stuttgart.de --><br />
<br />
<br />
<!--=== Typesetting a course script/preparing problem sets === <br />
<br />
There are two openings for HiWi jobs related to the Simulation Methods in Physics course.<br />
<br />
The first opening concerns a HiWi position for typesetting the course script in LaTeX and in English. There is already a hand-written version of the script.<br />
<br />
The task of the second HiWi job is the preparation and testing of new exercises for the course. For this computational skills are needed. --><br />
<!--=== Unterstützung der Modellierung biologisch modifizierten Materialien ===<br />
Wir suchen eine studentische Hilfskraft zur Unterstützung des Projektes für die Modellierung von biologisch modifizierten Materialien. <br />
<br />
Weitere Informationen: [[Media:Stellenanzeige_Hiwi_biomater.pdf|Stellenanzeige_Hiwi_biomater.pdf]]<br />
<br />
Bei Interesse wenden Sie sich bitte an Maria Fyta, Tel: 0711 / 685 63935, E-mail: [mailto:mfyta@icp.uni-stuttgart.de mfyta@icp.uni-stuttgart.de]--></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2018&diff=23237Simulation Methods in Physics II SS 20182018-06-06T10:29:10Z<p>Dsean: /* 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 10am-2pm, <br><br />
Wednesday 01.08.2018 between 10am-2pm, <br><br />
Thursday 02.08.2018 between 10am-2pm, <br><br />
Tuesday 11.09.2018 between 10am-2pm, <br><br />
Wednesday 12.09.2018 between 10am-2pm, <br><br />
Thursday 13.09.2018 between 10am-2pm, <br><br />
Monday 01.10.2018 between 10am-2pm, <br><br />
Tuesday 02.10.2018 between 10am-2pm, <br><br />
Thursday 04.10.2018 between 10am-2pm.<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 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; 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 in September or October 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://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]<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 />
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.--><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 />
| 12.04.2018 || Introduction/organisation, electronic structure || <!--{{ Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}} {{ Download|simmethodsII_ss16_lecture1notes.pdf|Lecture Notes}}--><br />
|- <br />
| 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || <!--{{ |Lecture Notes}} --><br />
|- <br />
| 26.04.2018 || Density Functional Theory (DFT) || <!--{{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}--><br />
|- <br />
| 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} <br />
|- <br />
| 10.05.2018 || Holiday (Christi Himmelfahrt) ||<br />
|-<br />
| 17.05.2018 || Classical force fields and water models || <br />
|- <br />
| 24.05.2018 || '' Holiday (Pfingsten) '' || <br />
|- <br />
| 31.05.2018 || Holiday (Fronleichnam) '' || <br />
|- <br />
| 07.06.2018 || Simulations of macromolecules and soft matter || <br />
|- <br />
| 14.06.2018 || Poisson-Boltzmann theory, charged polymers || <br />
|-<br />
| 21.06.2018 || Hydrodynamic methods I (Lattice-Boltzmann, Brownian Dynamics, DPD, SRD) ||<br />
|- <br />
| 28.06.2018 || Free energy methods ||<br />
|- <br />
| 05.07.2018 || Interatomic potentials (pair-potentials, EAM) (solid-state systems) ||<br />
|- <br />
| 12.07.2018 || Energy minimization||<br />
|- <br />
| 19.07.2018 ||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, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] )<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 18th. The deadline will be Wed. May 2nd. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout<br />
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}}<br />
* {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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 6: Advanced MD/MC: The Widom insertion method ====<br />
* Available online: June 27, 2016<br />
* Deadline: '''July 11, 2016'''<br />
* {{Download|SS_2016_SM2_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SS_2016_SM2_worksheet6_template.tcl|template.tcl|txt}} - ESPResSo sample script<br />
* {{Download|SS_2016_SM2_WS6_solution.pdf|Solution|pdf}} - Sample solution<br />
<br />
==== Worksheet 2: Diffusion processes and properties of atomistic water models ====<br />
* Deadline: '''May 9, 2016'''<br />
* {{Download|SimmethodsII ss16 worksheet2.pdf|Worksheet 2}}<br />
* {{Download|SS_2015_SM2_worksheet2_templates.tar.gz|templates.tar.gz|tgz}} - Archive containing GROMACS input files<br />
* {{Download|SS_2016_SM2_WS2_solution.pdf|Solution|pdf}} - Sample solution<br />
--><br />
<!--<br />
==== Worksheet 1: Properties and Fitting of Atomistic Water models ====<br />
* Deadline: '''May 1, 2017'''<br />
* {{Download|SimmethodsII_ss17_worksheet1.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss17_worksheet1_templates.tar.gz|templates.tar.gz|tgz}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
--><br />
<br />
<!--<br />
* {{Download|SS_2015_SM2_WS1_solution.tar.gz|solution.tar.gz|tgz}} - Archive containing the sample solution<br />
--><br />
<br />
<!--<br />
==== Worksheet 2: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''May 15, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet2.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss17_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 />
<!--<br />
==== Worksheet 3: Charge distribution around a charged rod ====<br />
* Deadline: '''May 29, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|SimmethodsII_ss17_template3.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
--><br />
<br />
<!--<br />
==== Worksheet 4: Flow Between Plates and Free Energy ====<br />
* Deadline: '''June 19, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet4.pdf|Worksheet 4}}<br />
* {{Download|SimmethodsII_ss17_template4.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 />
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====<br />
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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/2017</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 ([[Miriam Kohagen]] or [[David Sean]]).<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>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss18_template.py&diff=23236File:SimmethodsII ss18 template.py2018-06-06T10:27:32Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:SimmethodsII_ss18_worksheet4.pdf&diff=23235File:SimmethodsII ss18 worksheet4.pdf2018-06-06T10:26:47Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_II_SS_2018&diff=23234Simulation Methods in Physics II SS 20182018-06-06T10:26:14Z<p>Dsean: /* Tutorials */</p>
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<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 10am-2pm, <br><br />
Wednesday 01.08.2018 between 10am-2pm, <br><br />
Thursday 02.08.2018 between 10am-2pm, <br><br />
Tuesday 11.09.2018 between 10am-2pm, <br><br />
Wednesday 12.09.2018 between 10am-2pm, <br><br />
Thursday 13.09.2018 between 10am-2pm, <br><br />
Monday 01.10.2018 between 10am-2pm, <br><br />
Tuesday 02.10.2018 between 10am-2pm, <br><br />
Thursday 04.10.2018 between 10am-2pm.<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 (Tutors: Dr. [[Miriam Kohagen]], Dr. [[David Sean]]; 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 in September or October 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://lcbc.epfl.ch/files/content/users/232236/files/Script_IESM_2015-1.pdf]<br />
<br />
* E-Book: Kieron Burke et al.,University of California, 2007: [http://www.chem.uci.edu/~kieron/dftold2/materials/bookABCDFT/gamma/g1.pdf E-Book: The ABC of DFT.]<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 />
<!--To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.--><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 />
| 12.04.2018 || Introduction/organisation, electronic structure || <!--{{ Download|simmethodsII_ss16_lecture1.pdf|Lecture Notes}} {{ Download|simmethodsII_ss16_lecture1notes.pdf|Lecture Notes}}--><br />
|- <br />
| 19.04.2018 || Hartree and Hartree-Fock (HF) approximations, post HF || <!--{{ |Lecture Notes}} --><br />
|- <br />
| 26.04.2018 || Density Functional Theory (DFT) || <!--{{DownloadExt|/teaching/2015-ss-sim_methods/lecture05_notes.pdf|Lecture Notes}}--><br />
|- <br />
| 03.05.2018 || <i>ab initio</i> MD, QM/MM|| {{Download|simmethodsII_ss18_lecture4.pdf|Lecture Notes}} <br />
|- <br />
| 10.05.2018 || Holiday (Christi Himmelfahrt) ||<br />
|-<br />
| 17.05.2018 || Classical force fields and water models || <br />
|- <br />
| 24.05.2018 || '' Holiday (Pfingsten) '' || <br />
|- <br />
| 31.05.2018 || Holiday (Fronleichnam) '' || <br />
|- <br />
| 07.06.2018 || Simulations of macromolecules and soft matter || <br />
|- <br />
| 14.06.2018 || Poisson-Boltzmann theory, charged polymers || <br />
|-<br />
| 21.06.2018 || Hydrodynamic methods I (Lattice-Boltzmann, Brownian Dynamics, DPD, SRD) ||<br />
|- <br />
| 28.06.2018 || Free energy methods ||<br />
|- <br />
| 05.07.2018 || Interatomic potentials (pair-potentials, EAM) (solid-state systems) ||<br />
|- <br />
| 12.07.2018 || Energy minimization||<br />
|- <br />
| 19.07.2018 ||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, 15:45 – 17:15 (Tutors: [[Miriam Kohagen]] / [[David Sean]] )<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 18th. The deadline will be Wed. May 2nd. </b><br />
<br />
<br />
==== Worksheet 1: Quantum chemistry and simple models ====<br />
* Deadline: '''May 2, 2018, 12:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_01''' as subject line.<br />
* {{Download|SMII_SS2018_WS1.pdf|Worksheet 1}}<br />
* {{Download|templates_SMII_SS2018_WS1.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 2: Density Functional Theory ====<br />
* additional reading on CIP pool machines under: /group/sm/2018/tutorial_02/handout<br />
* Deadline: '''May 16, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet2.pdf|Worksheet 2}}<br />
* {{Download|templates_SMII_SS2018_WS2.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
==== Worksheet 3: properties and fitting of atomistic water models and ab initio molecular dynamics of water monomer/dimer ====<br />
* Deadline: '''May 30, 2018, 13:00 noon''' by email to [[Miriam Kohagen]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_SS18_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|templates_SMII_SS2018_WS3.zip|template}} - input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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_ss18_espresso_install.sh|ESPResSo install}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
<br />
<!--<br />
==== Worksheet 6: Advanced MD/MC: The Widom insertion method ====<br />
* Available online: June 27, 2016<br />
* Deadline: '''July 11, 2016'''<br />
* {{Download|SS_2016_SM2_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SS_2016_SM2_worksheet6_template.tcl|template.tcl|txt}} - ESPResSo sample script<br />
* {{Download|SS_2016_SM2_WS6_solution.pdf|Solution|pdf}} - Sample solution<br />
<br />
==== Worksheet 2: Diffusion processes and properties of atomistic water models ====<br />
* Deadline: '''May 9, 2016'''<br />
* {{Download|SimmethodsII ss16 worksheet2.pdf|Worksheet 2}}<br />
* {{Download|SS_2015_SM2_worksheet2_templates.tar.gz|templates.tar.gz|tgz}} - Archive containing GROMACS input files<br />
* {{Download|SS_2016_SM2_WS2_solution.pdf|Solution|pdf}} - Sample solution<br />
--><br />
<!--<br />
==== Worksheet 1: Properties and Fitting of Atomistic Water models ====<br />
* Deadline: '''May 1, 2017'''<br />
* {{Download|SimmethodsII_ss17_worksheet1.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss17_worksheet1_templates.tar.gz|templates.tar.gz|tgz}}<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<br />
--><br />
<br />
<!--<br />
* {{Download|SS_2015_SM2_WS1_solution.tar.gz|solution.tar.gz|tgz}} - Archive containing the sample solution<br />
--><br />
<br />
<!--<br />
==== Worksheet 2: Properties of Coarse-grained Polymers ====<br />
* Deadline: '''May 15, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_02''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet2.pdf|Worksheet}}<br />
* {{Download|SimmethodsII_ss17_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 />
<!--<br />
==== Worksheet 3: Charge distribution around a charged rod ====<br />
* Deadline: '''May 29, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_03''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet3.pdf|Worksheet 3}}<br />
* {{Download|SimmethodsII_ss17_template3.py|template}} - ESPResSo sample script<br />
* {{Download|espresso_install_script_rod.sh|ESPResSo install}}<br />
--><br />
<br />
<!--<br />
==== Worksheet 4: Flow Between Plates and Free Energy ====<br />
* Deadline: '''June 19, 2017, 12:00 noon''' by email to [[David Sean]] use '''SM2_04''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet4.pdf|Worksheet 4}}<br />
* {{Download|SimmethodsII_ss17_template4.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 />
==== Worksheet 6: Density functional theory and ab initio molecular dynamics ====<br />
* Deadline: '''July 17, 2017, 12:00 noon''' by email to [[Frank Uhlig]] use '''SM2_06''' as subject line.<br />
* {{Download|SimmethodsII_ss17_worksheet6.pdf|Worksheet 6}}<br />
* {{Download|SimmethodsII_ss17_template6.tar.gz|template}} - CP2K input files<br />
* {{Download|latex-template.tex|latex-template.tex|txt}} - LaTeX template for the report<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/2017</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 ([[Miriam Kohagen]] or [[David Sean]]).<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>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Open_Positions&diff=23077Open Positions2018-03-23T15:49:41Z<p>Dsean: /* Software Developer */</p>
<hr />
<div>__TOC__<br />
<br />
<strong>Topics for Diploma/Master/Bachelor-Theses can be found [[Theses|here]].</strong><br />
<br />
== Ph.D. positions ==<br />
<br />
=== Simulations and theoretical work in the area of soft matter systems ===<br />
<br />
The Institute for Computational Physics works in the fields of research of simulations and theory of soft matter and biophysical systems, e.g. subjects like ''nucleation, ionic systems, ferrofluids, hydrogels, as well as colloids, polymers or biomolecules''.<br />
<br />
At present we have no open positions. However, we can support applications of exceptionally good candidates for funding in other projects. These positions would be in the groups of [[Maria Fyta]], [[Jens Smiatek]], and [[Christian Holm]].<br />
<br />
Common to all applicants should be a strong background in statistical physics and MD or MC simulation strategies, and knowledge of basic soft matter background (polymers, colloids) or knowledge in atomistic modelling (biomolecules, proteins). The simulations will be performed using the software package {{ES}}, GROMACS, or self-written codes. We are also active in the field of algorithm and code development, in particular for electrostatic and hydrodynamic interactions.<br />
<br />
There will be ample opportunity to interact with other researchers at Stuttgart, the Max Planck Institute for metals research, the {{MPIP}}, and the [http://www.uni-stuttgart.de University of Stuttgart].<br />
<br />
All positions are initially for one year, renewable upon mutual agreement. Candidates should have the relevant background in a quantitative discipline (see above) and a keen interest in several of the lab's research areas. Applicants should submit: <br />
<br />
* resume (including date of birth, grades, awards, publications), <br />
* statement of research interests (up to 2 pages), <br />
* names and email addresses of 2-3 references <br />
* links to their thesis and/or publications <br />
<br />
Positions will remain open until filled. Please send applications via email to [{{SERVER}}/nmt.php?page=application application _at_ icp.uni-stuttgart.de], or if you are located in Stuttgart, simply drop by our institute.<br />
<br />
=== Doktorandenstelle: Physik poröser Medien ===<br />
<br />
Am Institut für Computerphysik ist eine '''Doktorandenstelle''' (TVL E13 2/3) im Fach "Theoretische Physik" in der Arbeitsgruppe Physik poröser Medien zu besetzen.<br />
<br />
Das Institut für Computerphysik der Universität Stuttgart sucht Diplom/M.Sc.-Studenten, die ihre Doktorarbeit über ein Thema auf dem Gebiet der rechnergestützten statistischen Physik schreiben möchten. Die geplante Dissertation befasst sich mit der Simulation mehrskaliger poröser Medien. Das Projekt wird im Rahmen des Sonderforschungsbereichs 716 durchgeführt. Interessierte Studenten sollten einen überdurchschnittlichen Diplom-, Magister (M.Sc.) oder äquivalenten Abschluss in Physik oder Mathematik vorweisen können. Programmierkenntnisse sind erforderlich. Fähigkeit und Bereitschaft zur Zusammenarbeit mit anderen Doktoranden und Projekten auf demselben Arbeitsgebiet sowie überdurchschnittliche Einsatzbereitschaft werden erwartet. Interessenten senden bitte Ihre Bewerbungsunterlagen (Lebenslauf, Anschreiben, Zeugnisse etc) an.<br />
<br />
Prof. Dr. R. Hilfer<br /><br />
Institut für Computerphysik<br /><br />
Universität Stuttgart<br /><br />
Allmandring 3<br /><br /><br />
70569 Stuttgart<br />
<br />
Tel: +49 711 685-67607<br /><br />
Fax: +49 711 685-63658<br /><br />
hilfer@icp.uni-stuttgart.de<br />
<br />
Die Einstellung erfolgt durch das Rektoramt der Universität Stuttgart.<br />
<br />
<!--=== PhD position: Modeling biologically modified materials===<br />
<br />
<br />
A graduate student position is available at the Institute of Computational Physics, University of Stuttgart under the guidance of JunProf. Dr. Maria Fyta. The position is funded by the collaborative grant SFB716 "Dynamic simulation of systems with large particle numbers" of the University of Stuttgart, Germany. The specific project will deal with integrating biomolecules and materials to make biofunctional materials. The research will be conducted by means of theoretical and computational tools. Specifically, a wide range of computational schemes, ranging from first principles quantum dynamics simulations up to coarse grained approaches will be used to model biomolecules grafted on materials. A comparative study of a wide range of biologically modified materials will be complemented by the in depth investigation of their optical, electronic, and mechanical properties, as well as the functionality of these biomaterials for potential applications. The applicant should have a strong background in Physics, Chemistry, Biology or Materials Science and an overall strong motivation. Computational skills are a prerequisite, as well as experience in scientific computing. Previous experience in UNIX/Linux environment and programming in either Fortran and/or C/C++ and/or Python is essential. Ability to work independently and also function as an active and efficient team player is also important. Please send a CV, a research statement, and two reference letters to JunProf. Dr. Maria Fyta (mfyta@icp.uni-stuttgart.de).--><br />
<br />
== Studentische Hilfskräfte ==<br />
<br />
We also have a number of open positions for student helpers.<br />
<!-- === Unterstützung der Institutsleitung ===<br />
Wir suchen studentische Hilfskräfte zur Unterstützung des Institutsleiters. Kenntnisse in MS Office und sicheres Deutsch sind Voraussetzung, Englischkenntnisse sind wünschenswert. Zeitlicher Umfang nach Absprache.<br />
<br />
Weitere Informationen: [[Media:Stellenanzeige_Hiwi.pdf|Stellenanzeige_Hiwi.pdf]]<br />
<br />
Bei Interesse wenden Sie sich bitte an Henriette Patzelt, Tel: 0711 685 63593, E-mail: [mailto:sekretariat@icp.uni-stuttgart.de sekretariat@icp.uni-stuttgart.de]<br />
--><br />
<!-- === Programmieren und Visualisierung ===<br />
We are constantly looking for motivated HiWis (student helpers) who can do basic programming tasks in C, and can help with producing animated videos and graphics, using VMD. Write an email to [mailto:sekretariat@icp.uni-stuttgart.de sekretariat@icp.uni-stuttgart.de]<br />
--><br />
<br />
<br />
=== Modellierung von biomodifizierten Oberflächen/Modeling biomodified surfaces ===<br />
<br />
* Eine HiWi Stelle zur Unterstützung der Modellierung von biologisch modifizierten Materialien ist frei. Interessenten bitte eine E-mail an [[Maria Fyta]] (mfyta_at_icp.uni-stuttgart.de) schicken.<br />
<br />
* There is currently an opening for a HiWi (student assistant) in the field of computer simulations of modified surfaces (molecules adsorbed on surfaces). In case you are interested in bachelor or master projects, please contact [[Maria Fyta]] (mfyta_at_icp.uni-stuttgart.de). <br />
<br />
<!-- === Studentische Hilfskraft zur Unterstützung des Institutsleiters ===<br />
<br />
* Die Aufgaben umfassen Internet- und Literaturrecherche, Unterstützung bei der Vorbereitung der Vorlesungen, Pflege der Literaturdatenbank und der Webseiten des Instituts, allgemeine Projektmitarbeit<br />
* Wir setzen voraus: Gültige Immatrikulationsbescheinigung, Kenntnisse in MS Office (v.a. Microsoft Word und Excel), Kenntnisse in LaTeX wünschenswert, sicheres Deutsch, gute Englischkenntnisse, Teamfähigkeit, Flexibilität und Zuverlässigkeit<br />
Beginn sofort; zeitlicher Umfang nach Absprache. Wir sind an einer mehrjährigen Zusammmenarbeit interessiert. <br />
<br />
Bewerbungsunterlagen (Lebenslauf) an das Sekretariat des ICP, Henriette Patzelt, Tel: 0711 685 63593, E-mail: Sekretariat@icp.uni-stuttgart.de --><br />
<br />
<br />
<!--=== Typesetting a course script/preparing problem sets === <br />
<br />
There are two openings for HiWi jobs related to the Simulation Methods in Physics course.<br />
<br />
The first opening concerns a HiWi position for typesetting the course script in LaTeX and in English. There is already a hand-written version of the script.<br />
<br />
The task of the second HiWi job is the preparation and testing of new exercises for the course. For this computational skills are needed. --><br />
<!--=== Unterstützung der Modellierung biologisch modifizierten Materialien ===<br />
Wir suchen eine studentische Hilfskraft zur Unterstützung des Projektes für die Modellierung von biologisch modifizierten Materialien. <br />
<br />
Weitere Informationen: [[Media:Stellenanzeige_Hiwi_biomater.pdf|Stellenanzeige_Hiwi_biomater.pdf]]<br />
<br />
Bei Interesse wenden Sie sich bitte an Maria Fyta, Tel: 0711 / 685 63935, E-mail: [mailto:mfyta@icp.uni-stuttgart.de mfyta@icp.uni-stuttgart.de]--><br />
<br />
== Misc. positions ==<br />
=== Software Developer ===<br />
<br />
We are seeking a software developer for the software ESPResSo ([http://espressomd.org espressomd.org]). It is mainly used to perform particle-based<br />
MD simulations in the fields of statistical and biological physics and<br />
process engineering. Its main strength is to combine a large number of<br />
simulation schemes, including hydrodynamic and long-range<br />
electrostatic solvers, with coarse-grained particle-based molecular<br />
dynamics.<br />
It combines a C/C++ core with a Python interface.<br />
<br />
'''What we are looking for'''<br />
* Strong skills in C++ and Python<br />
* Experience in scientific computing<br />
* Experience in software engineering concepts<br />
* Experience in development tools for continuous integration, such as Git and a CI testing platform such as Travis or Gitlab-CI<br />
* Degree in Computer Science, software engineering, natural sciences or a similar subject<br />
* PhD is of advantage<br />
* If your degree is in an other field, proven interest in natural sciences (e.g., as a side-subject in a computer science degree, or previous involvement in a natural science project)<br />
* Strong communication skills in English, both oral and written<br />
<br />
'''What we are offering'''<br />
* Full-time 3-year position in the TV-LE 13 remuneration group of the German states<br />
* Possibility to earn a PhD if desired<br />
* The ability to work on a simulation package used world wide for published scientific projects<br />
* The opportunity to get to know a broad variety of simulation techniques and their applications<br />
* Close interaction with the scientists using the software<br />
* The possibility to visit and interact with scientific groups using the software<br />
<br />
The deadline for the application is 15.4.2018 or until position is filled. The desired starting date is as soon as possible. Send your application as a PDF via email to: application@icp.uni-stuttgart.de</div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Open_Positions&diff=23076Open Positions2018-03-23T15:44:35Z<p>Dsean: added ESPResSo call</p>
<hr />
<div>__TOC__<br />
<br />
<strong>Topics for Diploma/Master/Bachelor-Theses can be found [[Theses|here]].</strong><br />
<br />
== Ph.D. positions ==<br />
<br />
=== Simulations and theoretical work in the area of soft matter systems ===<br />
<br />
The Institute for Computational Physics works in the fields of research of simulations and theory of soft matter and biophysical systems, e.g. subjects like ''nucleation, ionic systems, ferrofluids, hydrogels, as well as colloids, polymers or biomolecules''.<br />
<br />
At present we have no open positions. However, we can support applications of exceptionally good candidates for funding in other projects. These positions would be in the groups of [[Maria Fyta]], [[Jens Smiatek]], and [[Christian Holm]].<br />
<br />
Common to all applicants should be a strong background in statistical physics and MD or MC simulation strategies, and knowledge of basic soft matter background (polymers, colloids) or knowledge in atomistic modelling (biomolecules, proteins). The simulations will be performed using the software package {{ES}}, GROMACS, or self-written codes. We are also active in the field of algorithm and code development, in particular for electrostatic and hydrodynamic interactions.<br />
<br />
There will be ample opportunity to interact with other researchers at Stuttgart, the Max Planck Institute for metals research, the {{MPIP}}, and the [http://www.uni-stuttgart.de University of Stuttgart].<br />
<br />
All positions are initially for one year, renewable upon mutual agreement. Candidates should have the relevant background in a quantitative discipline (see above) and a keen interest in several of the lab's research areas. Applicants should submit: <br />
<br />
* resume (including date of birth, grades, awards, publications), <br />
* statement of research interests (up to 2 pages), <br />
* names and email addresses of 2-3 references <br />
* links to their thesis and/or publications <br />
<br />
Positions will remain open until filled. Please send applications via email to [{{SERVER}}/nmt.php?page=application application _at_ icp.uni-stuttgart.de], or if you are located in Stuttgart, simply drop by our institute.<br />
<br />
=== Doktorandenstelle: Physik poröser Medien ===<br />
<br />
Am Institut für Computerphysik ist eine '''Doktorandenstelle''' (TVL E13 2/3) im Fach "Theoretische Physik" in der Arbeitsgruppe Physik poröser Medien zu besetzen.<br />
<br />
Das Institut für Computerphysik der Universität Stuttgart sucht Diplom/M.Sc.-Studenten, die ihre Doktorarbeit über ein Thema auf dem Gebiet der rechnergestützten statistischen Physik schreiben möchten. Die geplante Dissertation befasst sich mit der Simulation mehrskaliger poröser Medien. Das Projekt wird im Rahmen des Sonderforschungsbereichs 716 durchgeführt. Interessierte Studenten sollten einen überdurchschnittlichen Diplom-, Magister (M.Sc.) oder äquivalenten Abschluss in Physik oder Mathematik vorweisen können. Programmierkenntnisse sind erforderlich. Fähigkeit und Bereitschaft zur Zusammenarbeit mit anderen Doktoranden und Projekten auf demselben Arbeitsgebiet sowie überdurchschnittliche Einsatzbereitschaft werden erwartet. Interessenten senden bitte Ihre Bewerbungsunterlagen (Lebenslauf, Anschreiben, Zeugnisse etc) an.<br />
<br />
Prof. Dr. R. Hilfer<br /><br />
Institut für Computerphysik<br /><br />
Universität Stuttgart<br /><br />
Allmandring 3<br /><br /><br />
70569 Stuttgart<br />
<br />
Tel: +49 711 685-67607<br /><br />
Fax: +49 711 685-63658<br /><br />
hilfer@icp.uni-stuttgart.de<br />
<br />
Die Einstellung erfolgt durch das Rektoramt der Universität Stuttgart.<br />
<br />
<!--=== PhD position: Modeling biologically modified materials===<br />
<br />
<br />
A graduate student position is available at the Institute of Computational Physics, University of Stuttgart under the guidance of JunProf. Dr. Maria Fyta. The position is funded by the collaborative grant SFB716 "Dynamic simulation of systems with large particle numbers" of the University of Stuttgart, Germany. The specific project will deal with integrating biomolecules and materials to make biofunctional materials. The research will be conducted by means of theoretical and computational tools. Specifically, a wide range of computational schemes, ranging from first principles quantum dynamics simulations up to coarse grained approaches will be used to model biomolecules grafted on materials. A comparative study of a wide range of biologically modified materials will be complemented by the in depth investigation of their optical, electronic, and mechanical properties, as well as the functionality of these biomaterials for potential applications. The applicant should have a strong background in Physics, Chemistry, Biology or Materials Science and an overall strong motivation. Computational skills are a prerequisite, as well as experience in scientific computing. Previous experience in UNIX/Linux environment and programming in either Fortran and/or C/C++ and/or Python is essential. Ability to work independently and also function as an active and efficient team player is also important. Please send a CV, a research statement, and two reference letters to JunProf. Dr. Maria Fyta (mfyta@icp.uni-stuttgart.de).--><br />
<br />
== Studentische Hilfskräfte ==<br />
<br />
We also have a number of open positions for student helpers.<br />
<!-- === Unterstützung der Institutsleitung ===<br />
Wir suchen studentische Hilfskräfte zur Unterstützung des Institutsleiters. Kenntnisse in MS Office und sicheres Deutsch sind Voraussetzung, Englischkenntnisse sind wünschenswert. Zeitlicher Umfang nach Absprache.<br />
<br />
Weitere Informationen: [[Media:Stellenanzeige_Hiwi.pdf|Stellenanzeige_Hiwi.pdf]]<br />
<br />
Bei Interesse wenden Sie sich bitte an Henriette Patzelt, Tel: 0711 685 63593, E-mail: [mailto:sekretariat@icp.uni-stuttgart.de sekretariat@icp.uni-stuttgart.de]<br />
--><br />
<!-- === Programmieren und Visualisierung ===<br />
We are constantly looking for motivated HiWis (student helpers) who can do basic programming tasks in C, and can help with producing animated videos and graphics, using VMD. Write an email to [mailto:sekretariat@icp.uni-stuttgart.de sekretariat@icp.uni-stuttgart.de]<br />
--><br />
<br />
<br />
=== Modellierung von biomodifizierten Oberflächen/Modeling biomodified surfaces ===<br />
<br />
* Eine HiWi Stelle zur Unterstützung der Modellierung von biologisch modifizierten Materialien ist frei. Interessenten bitte eine E-mail an [[Maria Fyta]] (mfyta_at_icp.uni-stuttgart.de) schicken.<br />
<br />
* There is currently an opening for a HiWi (student assistant) in the field of computer simulations of modified surfaces (molecules adsorbed on surfaces). In case you are interested in bachelor or master projects, please contact [[Maria Fyta]] (mfyta_at_icp.uni-stuttgart.de). <br />
<br />
<!-- === Studentische Hilfskraft zur Unterstützung des Institutsleiters ===<br />
<br />
* Die Aufgaben umfassen Internet- und Literaturrecherche, Unterstützung bei der Vorbereitung der Vorlesungen, Pflege der Literaturdatenbank und der Webseiten des Instituts, allgemeine Projektmitarbeit<br />
* Wir setzen voraus: Gültige Immatrikulationsbescheinigung, Kenntnisse in MS Office (v.a. Microsoft Word und Excel), Kenntnisse in LaTeX wünschenswert, sicheres Deutsch, gute Englischkenntnisse, Teamfähigkeit, Flexibilität und Zuverlässigkeit<br />
Beginn sofort; zeitlicher Umfang nach Absprache. Wir sind an einer mehrjährigen Zusammmenarbeit interessiert. <br />
<br />
Bewerbungsunterlagen (Lebenslauf) an das Sekretariat des ICP, Henriette Patzelt, Tel: 0711 685 63593, E-mail: Sekretariat@icp.uni-stuttgart.de --><br />
<br />
<br />
<!--=== Typesetting a course script/preparing problem sets === <br />
<br />
There are two openings for HiWi jobs related to the Simulation Methods in Physics course.<br />
<br />
The first opening concerns a HiWi position for typesetting the course script in LaTeX and in English. There is already a hand-written version of the script.<br />
<br />
The task of the second HiWi job is the preparation and testing of new exercises for the course. For this computational skills are needed. --><br />
<!--=== Unterstützung der Modellierung biologisch modifizierten Materialien ===<br />
Wir suchen eine studentische Hilfskraft zur Unterstützung des Projektes für die Modellierung von biologisch modifizierten Materialien. <br />
<br />
Weitere Informationen: [[Media:Stellenanzeige_Hiwi_biomater.pdf|Stellenanzeige_Hiwi_biomater.pdf]]<br />
<br />
Bei Interesse wenden Sie sich bitte an Maria Fyta, Tel: 0711 / 685 63935, E-mail: [mailto:mfyta@icp.uni-stuttgart.de mfyta@icp.uni-stuttgart.de]--><br />
<br />
== Misc. positions ==<br />
=== Software Developer ===<br />
<br />
We are seeking a software developer for the software ESPResSo ([http://espressomd.org espressomd.org]). It is mainly used to perform particle-based<br />
MD simulations in the fields of statistical and biological physics and<br />
process engineering. Its main strength is to combine a large number of<br />
simulation schemes, including hydrodynamic and long-range<br />
electrostatic solvers, with coarse-grained particle-based molecular<br />
dynamics.<br />
It combines a C/C++ core with a Python interface.<br />
<br />
'''What we are looking for'''<br />
* Strong skills in C++ and Python<br />
* Experience in scientific computing<br />
* Experience in software engineering concepts<br />
* Experience in development tools for continuous integration, such as<br />
Git and a CI testing platform such as Travis or Gitlab-CI<br />
* Degree in Computer Science, software engineering, natural sciences<br />
or a similar subject<br />
* PhD is of advantage<br />
* If your degree is in an other field, proven interest in natural<br />
sciences (e.g., as a side-subject in a computer science degree, or<br />
previous involvement in a natural science project)<br />
* Strong communication skills in English, both oral and written<br />
<br />
'''What we are offering'''<br />
* Full-time 3-year position in the TV-LE 13 remuneration group of the<br />
German states<br />
* Possibility to earn a PhD if desired<br />
* The ability to work on a simulation package used world wide for<br />
published scientific projects<br />
* The opportunity to get to know a broad variety of simulation<br />
techniques and their applications<br />
* Close interaction with the scientists using the software<br />
* The possibility to visit and interact with scientific groups using<br />
the software<br />
<br />
The deadline for the application is 15.4.2018 or until position is filled. The desired starting date is as soon as possible. Send your application as a PDF via email to: application@icp.uni-stuttgart.de</div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2017/2018&diff=23000Simulation Methods in Physics I WS 2017/20182018-02-02T12:44:40Z<p>Dsean: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Wed, 15:45-17:15 (Tutor: [[David Sean]]) and Fri, 14:00-15:30 (Tutor: [[Michael Kuron]]); ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating a problem, hence we will not go too to deep into specific details but rather try to cover a broad range of methods. In more detail, the lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|2017-10-19 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2017-10-26 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-02 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-09 ||Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-16 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-23 ||Observables, Brownian motion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-30 || D, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-07 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-14 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-21 || B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|2018-01-11 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-18 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-25 || Critical Exponent ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-01 || Finite Size Scaling ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
|-<br />
|2018-02-08 || t.b.a. || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture15_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<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 />
== 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) on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[David Sean]])<br />
** Fridays 14:00-15:30 (Tutor: [[Michael Kuron]])<br />
* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators || 2017-11-13 12:00 || {{Download|WS_2017_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics || 2017-11-27 12:00 || {{Download|WS_2017_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables || 2017-12-11 12:00 || {{Download|WS_2017_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion || 2018-01-08 12:00 (both groups submit to Michael) || {{Download|WS_2017_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo || 2018-01-22 12:00 || {{Download|WS_2017_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling || 2018-02-05 12:00 (both groups submit to David) || {{Download|WS_2017_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<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 />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|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 />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<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.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download 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.<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 />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<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 hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics I, II" (240918-005):<br />
:* Obtain 50% of the possible points in the hand-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 I" (40520):<br />
:* Obtain 50% of the possible points in the hand-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 I" (35840):<br />
:* The marks for the module are the marks obtained in the excercises (BSL)<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [http://www.iris.uni-stuttgart.de/lehre/lehrveranstaltungen-wintersemester-20172018/kompaktkurs-programmieren-in-c.html C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:Lecture14_notes.pdf&diff=22998File:Lecture14 notes.pdf2018-02-01T22:05:23Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2017/2018&diff=22997Simulation Methods in Physics I WS 2017/20182018-02-01T22:05:03Z<p>Dsean: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Wed, 15:45-17:15 (Tutor: [[David Sean]]) and Fri, 14:00-15:30 (Tutor: [[Michael Kuron]]); ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating a problem, hence we will not go too to deep into specific details but rather try to cover a broad range of methods. In more detail, the lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|2017-10-19 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2017-10-26 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-02 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-09 ||Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-16 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-23 ||Observables, Brownian motion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-30 || D, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-07 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-14 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-21 || B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|2018-01-11 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-18 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-25 || Critical Exponent ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-01 || Finite Size Scaling , Binder Parameters || {{Download|lecture14_notes.pdf |Lecture Notes}} ||<br />
<br />
|-<br />
|2018-02-08 || t.b.a. || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture15_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<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 />
== 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) on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[David Sean]])<br />
** Fridays 14:00-15:30 (Tutor: [[Michael Kuron]])<br />
* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators || 2017-11-13 12:00 || {{Download|WS_2017_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics || 2017-11-27 12:00 || {{Download|WS_2017_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables || 2017-12-11 12:00 || {{Download|WS_2017_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion || 2018-01-08 12:00 (both groups submit to Michael) || {{Download|WS_2017_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo || 2018-01-22 12:00 || {{Download|WS_2017_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling || 2018-02-05 12:00 (both groups submit to David) || {{Download|WS_2017_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<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 />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|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 />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<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.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download 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.<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 />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<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 hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics I, II" (240918-005):<br />
:* Obtain 50% of the possible points in the hand-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 I" (40520):<br />
:* Obtain 50% of the possible points in the hand-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 I" (35840):<br />
:* The marks for the module are the marks obtained in the excercises (BSL)<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [http://www.iris.uni-stuttgart.de/lehre/lehrveranstaltungen-wintersemester-20172018/kompaktkurs-programmieren-in-c.html C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2017/2018&diff=22995Simulation Methods in Physics I WS 2017/20182018-02-01T22:04:08Z<p>Dsean: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Wed, 15:45-17:15 (Tutor: [[David Sean]]) and Fri, 14:00-15:30 (Tutor: [[Michael Kuron]]); ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating a problem, hence we will not go too to deep into specific details but rather try to cover a broad range of methods. In more detail, the lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|2017-10-19 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2017-10-26 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-02 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-09 ||Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-16 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-23 ||Observables, Brownian motion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-30 || D, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-07 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-14 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-21 || B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|2018-01-11 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-18 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-25 || Critical Exponent ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-01 || Finite Size Scaling , Binder Parameters || {{Download|lecture13_notes.pdf |Lecture Notes}} ||<br />
<br />
|-<br />
|2018-02-08 || t.b.a. || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture15_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<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 />
== 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) on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[David Sean]])<br />
** Fridays 14:00-15:30 (Tutor: [[Michael Kuron]])<br />
* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators || 2017-11-13 12:00 || {{Download|WS_2017_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics || 2017-11-27 12:00 || {{Download|WS_2017_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables || 2017-12-11 12:00 || {{Download|WS_2017_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion || 2018-01-08 12:00 (both groups submit to Michael) || {{Download|WS_2017_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo || 2018-01-22 12:00 || {{Download|WS_2017_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling || 2018-02-05 12:00 (both groups submit to David) || {{Download|WS_2017_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<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 />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|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 />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<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.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download 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.<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 />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<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 hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics I, II" (240918-005):<br />
:* Obtain 50% of the possible points in the hand-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 I" (40520):<br />
:* Obtain 50% of the possible points in the hand-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 I" (35840):<br />
:* The marks for the module are the marks obtained in the excercises (BSL)<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [http://www.iris.uni-stuttgart.de/lehre/lehrveranstaltungen-wintersemester-20172018/kompaktkurs-programmieren-in-c.html C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2017/2018&diff=22994Simulation Methods in Physics I WS 2017/20182018-02-01T22:02:25Z<p>Dsean: /* Course Material */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Wed, 15:45-17:15 (Tutor: [[David Sean]]) and Fri, 14:00-15:30 (Tutor: [[Michael Kuron]]); ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating a problem, hence we will not go too to deep into specific details but rather try to cover a broad range of methods. In more detail, the lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|2017-10-19 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2017-10-26 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-02 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-09 ||Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-16 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-23 ||Observables, Brownian motion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-30 || D, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-07 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-14 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-21 || B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|2018-01-11 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-18 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-25 || Critical Exponent ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-01 || Finite Size Scaling , Binder Parameters || [lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-08 || t.b.a. || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture15_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<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 />
== 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) on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[David Sean]])<br />
** Fridays 14:00-15:30 (Tutor: [[Michael Kuron]])<br />
* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators || 2017-11-13 12:00 || {{Download|WS_2017_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics || 2017-11-27 12:00 || {{Download|WS_2017_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables || 2017-12-11 12:00 || {{Download|WS_2017_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion || 2018-01-08 12:00 (both groups submit to Michael) || {{Download|WS_2017_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo || 2018-01-22 12:00 || {{Download|WS_2017_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling || 2018-02-05 12:00 (both groups submit to David) || {{Download|WS_2017_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<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 />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|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 />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<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.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download 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.<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 />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<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 hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics I, II" (240918-005):<br />
:* Obtain 50% of the possible points in the hand-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 I" (40520):<br />
:* Obtain 50% of the possible points in the hand-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 I" (35840):<br />
:* The marks for the module are the marks obtained in the excercises (BSL)<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [http://www.iris.uni-stuttgart.de/lehre/lehrveranstaltungen-wintersemester-20172018/kompaktkurs-programmieren-in-c.html C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2017/2018&diff=22966Simulation Methods in Physics I WS 2017/20182018-01-24T16:16:12Z<p>Dsean: /* Worksheets */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Wed, 15:45-17:15 (Tutor: [[David Sean]]) and Fri, 14:00-15:30 (Tutor: [[Michael Kuron]]); ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating a problem, hence we will not go too to deep into specific details but rather try to cover a broad range of methods. In more detail, the lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|2017-10-19 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2017-10-26 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-02 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-09 ||Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-16 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-23 ||Observables, Brownian motion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-30 || D, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-07 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-14 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-21 || B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|2018-01-11 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-18 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-25 || Finite Size Scaling ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-01 || Binder Parameters || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-08 || Error Analysis || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture15_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<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 />
== 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) on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[David Sean]])<br />
** Fridays 14:00-15:30 (Tutor: [[Michael Kuron]])<br />
* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators || 2017-11-13 12:00 || {{Download|WS_2017_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics || 2017-11-27 12:00 || {{Download|WS_2017_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables || 2017-12-11 12:00 || {{Download|WS_2017_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion || 2018-01-08 12:00 (both groups submit to Michael) || {{Download|WS_2017_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo || 2018-01-22 12:00 || {{Download|WS_2017_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling || 2018-02-05 12:00 (both groups submit to David) || {{Download|WS_2017_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
remeber to use: python setup.py build_ext -fi<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 />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|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 />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<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.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download 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.<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 />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<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 hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics I, II" (240918-005):<br />
:* Obtain 50% of the possible points in the hand-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 I" (40520):<br />
:* Obtain 50% of the possible points in the hand-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 I" (35840):<br />
:* The marks for the module are the marks obtained in the excercises (BSL)<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [http://www.iris.uni-stuttgart.de/lehre/lehrveranstaltungen-wintersemester-20172018/kompaktkurs-programmieren-in-c.html C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=Simulation_Methods_in_Physics_I_WS_2017/2018&diff=22965Simulation Methods in Physics I WS 2017/20182018-01-24T16:15:55Z<p>Dsean: /* Worksheets */</p>
<hr />
<div>== Overview ==<br />
<br />
;Type<br />
:Lecture (2 SWS) and Tutorials (2 SWS)<br />
;Lecturer<br />
:Prof. Dr. [[Christian Holm]]<br />
;Course language<br />
:English<br />
;Location and Time<br />
:'''Lecture''': Thu, 14:00 - 15:30; ICP, Allmandring 3, Seminar Room (room 01.079)<br />
:'''Tutorials''': Wed, 15:45-17:15 (Tutor: [[David Sean]]) and Fri, 14:00-15:30 (Tutor: [[Michael Kuron]]); ICP, Allmandring 3, CIP-Pool (room 01.033)<br />
; Prerequisites<br />
: We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, and partial differential equations, as well as knowledge of a programming language (Python and C).<br />
<br />
The lecture is accompanied by hands-on tutorials which will take place in the CIP-Pool of the ICP, Allmandring 3 (room 01.033). They consist of practical exercises at the computer such as small programming tasks, simulations, visualization and data analysis.<br />
The tutorials build upon each other, therefore continuous attendance is expected.<br />
<br />
== Lecture ==<br />
<br />
=== Scope ===<br />
<br />
The first part of the course intends to give an overview about modern simulation methods used in physics today. The focus of the lecture will be to introduce different approaches to simulating a problem, hence we will not go too to deep into specific details but rather try to cover a broad range of methods. In more detail, the lecture will consist of:<br />
<br />
; Molecular Dynamics<br />
:The first problem that comes to mind when thinking about simulating physics is solving Newtons equations of motion for particles with given interactions. From that perspective, we first introduce the most common numerical integrators. This approach quickly leads us to Molecular Dynamics (MD) simulations. Many of the complex problems of practical importance require us to take a closer look at statistical properties, ensembles and the macroscopic observables.<br />
:The goal is to be able to set up and run real MD simulations for different ensembles and understand and interpret the output.<br />
<br />
; Error Analysis<br />
:Autocorrelation, Jackknifing, Bootstrapping<br />
<br />
; Monte Carlo Simulations<br />
:Since their invention, the importance of Monte Carlo (MC) sampling has grown constantly. Nowadays it is applied to a wide class of problems in modern computational physics. We want to present the general idea and theory behind MC simulations and show some more properties using simple toy models such as the Ising model.<br />
<br />
; Critical exponents<br />
: Finite-size scaling, universality concept, how to determine critical exponent with lattice spin models<br />
<br />
=== Course Material ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Date !! Subject !! Resources !! Remarks<br />
<br />
|-<br />
|2017-10-19 || Course Content, Organization, Introduction || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture01_slides.pdf Slides] ||<br />
<br />
|-<br />
|2017-10-26 || MD: Integrators || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture02_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-02 || Basics of Statistical Mechanics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture03_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-09 ||Chaos, LJ-Potential, Units || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture04_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-16 || PBC, cell-lists, simple MD || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture05_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-23 ||Observables, Brownian motion || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture06_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-11-30 || D, Green-Kubo, Langevin Dynamics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture07_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-07 || Thermostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture08_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-14 || Thermostats, Barostats || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture09_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2017-12-21 || B.Sc. / M.Sc. thesis @ ICP: information & research topics || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/thesis_topics.pdf Slides] ||<br />
<br />
|-<br />
|2018-01-11 || Monte-Carlo Method ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture11_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-18 || Monte-Carlo and Critical Phenomena || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture12_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-01-25 || Finite Size Scaling ||[https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture13_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-01 || Binder Parameters || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture14_notes.pdf Lecture Notes] ||<br />
<br />
|-<br />
|2018-02-08 || Error Analysis || [https://www.icp.uni-stuttgart.de/~icp/html//teaching/2017-ws-sim_methods/lecture15_notes.pdf Lecture Notes] || <br />
<br />
|}<br />
<br />
=== Script ===<br />
A '''''preliminary''''' version of the script can be downloaded {{DownloadExt|/teaching/2015-ws-sim_methods/script.pdf|here}}.<br />
<br />
If you find any kind of mistake / error / typo / bad formatting / etc. in the script (you surely will!), please send an email to [[Johannes Zeman]].<br />
<br />
=== Recommended literature ===<br />
<bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a,thijssen07,tuckerman10</bibentry><br />
=== Useful online resources ===<br />
<br />
* Thermostats: Philippe H. Hünenberger, [http://link.springer.com/chapter/10.1007%2Fb99427 <i>Thermostat Algorithms for Molecular Dynamics Simulations</i>], Adv. Polym. Sci. (2005) 173:105–149.<br />
<br />
* Error analysis: W. Janke, [http://www.physik.uni-leipzig.de/~janke/Paper/nic10_423_2002.pdf <i>Statistical Analysis of Simulations:Data Correlations and Error Estimation</i>], Quantum Simulations of Complex Many-Body Systems:<br />
From Theory to Algorithms, Lecture Notes, (2002).<br />
<br />
* [http://homepage.tudelft.nl/v9k6y/imsst/index.html Introduction to Molecular Simulation and Statistical Thermodynamics (pdf textbook from TU Delft)]<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 />
== 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) on<br />
** Wednesdays, 15:45-17:15 (Tutor: [[David Sean]])<br />
** Fridays 14:00-15:30 (Tutor: [[Michael Kuron]])<br />
* The tutorials on November 1st and 3rd are canceled due to a holiday.<br />
* The Friday tutorial on November 14th is canceled due to the unavailability of the computer room.<br />
* The tutors are switched between the tutorials on December 13th and 15th.<br />
* The Friday tutorial on December 22nd will be held by [[Florian Weik]].<br />
* The Wednesday tutorial on January 10th will be held by [[Michael Kuron]]. Please submit your reports to him.<br />
* The Friday tutorial on February 8th will be held by [[David Sean]]. Please submit your reports to him.<br />
<br />
=== Worksheets ===<br />
<br />
{| class="wikitable"<br />
|-<br />
!Topic !! Deadline !! Worksheet !! Further Resources<br />
<br />
|-<br />
| 0. First steps with Linux, Python, and C || no submission required || {{Download|WS_2015_SM1_worksheet0.pdf|Worksheet 0|pdf}} || {{ipynb|PythonTutorial.ipynb|PythonTutorial.ipynb}}, {{ipynb|NumPyTutorial.ipynb|NumPyTutorial.ipynb}}.<br />
<br />
|-<br />
| 1. Integrators || 2017-11-13 12:00 || {{Download|WS_2017_SM1_worksheet1.pdf|Worksheet 1|pdf}} || {{Download|solar_system.pkl.gz|solar_system.pkl.gz|tgz}} {{Download|cannonball_template.png|cannonball_template.png}}<br />
<br />
<br />
|-<br />
| 2. Statistical mechanics and Molecular Dynamics || 2017-11-27 12:00 || {{Download|WS_2017_SM1_worksheet2.pdf|Worksheet 2|pdf}} || {{Download|Templates.tar.gz|Templates.tar.gz|tgz}} {{Download|SS_2012_PC_Cython.pdf|Cython Introduction}}<br />
<br />
<br />
|-<br />
| 3. Molecular Dynamics and Observables || 2017-12-11 12:00 || {{Download|WS_2017_SM1_worksheet3.pdf|Worksheet 3}} || {{Download|WS_2015_SM1_WS3_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 4. Thermostats and Diffusion || 2018-01-08 12:00 (both groups submit to Michael) || {{Download|WS_2017_SM1_worksheet4.pdf|Worksheet 4}} || {{Download|WS_2017_SM1_WS4_templates.tar.gz|templates.tar.gz|tgz}}<br />
<br />
<br />
|-<br />
| 5. Monte-Carlo || 2018-01-22 12:00 || {{Download|WS_2017_SM1_worksheet5.pdf|Worksheet 5}} || [https://www.icp.uni-stuttgart.de/~icp/bib//janke02a.pdf janke02.pdf]<br />
<br />
<br />
|-<br />
| 6. Ising Model and Finite Size Scaling || 2018-02-05 12:00 (both groups submit to David) || {{Download|WS_2017_SM1_worksheet6.pdf|Worksheet 6}} || {{Download|WS_2015_SM1_WS6_templates.tar.gz|templates.tar.gz|tgz}}<br />
rember to use: python setup.py build_ext -fi<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 />
* For the reports, we have a nice {{Download|latex-template.tex|latex-template.tex|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 />
* If you want to do the exercises on your own computer, the following tools are required. All of these packages should be readily available from your OS distribution, if it is not Windows.<br />
** Python<br />
** The following Python packages:<br />
*** IPython<br />
*** NumPy<br />
*** SciPy<br />
*** matplotlib<br />
** A C compiler (e.g. GCC) <br />
* We only have experience with Unix/Linux machines. Although most tools will probably also work on Windows, we cannot guarantee it, and we can also not help you to get it running there.<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.<br />
* Most participants need 50% of the points in the hands-in exercises to be admitted to the oral examination (see [[#Examination|Examination]] for details).<br />
<br />
=== What happens in a tutorial ===<br />
<br />
* The tutorials take place every week.<br />
* The new worksheet will be available for download 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.<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 />
=== Documentation ===<br />
<br />
==== Linux ====<br />
* {{Download|linuxcheatsheet.pdf|Linux Cheat Sheet}} ({{Download|linuxcheatsheet.odt|source}}) - the most important linux commands on a single page<br />
<br />
==== Python ====<br />
* Use the existing documentation of Python itself! To get help on the command <code>print</code>, use<br />
pydoc print<br />
* Or use the Web browser to read it. Start<br />
pydoc -p 4242<br />
:and visit the page http://localhost:4242<br />
* http://python.org/doc/ - the official Python documentation (including tutorials etc.)<br />
* {{Download|Byte_of_Python.pdf}} - the free eBook "A byte of Python" [http://www.swaroopch.com/notes/python/], also available in German[http://sourceforge.net/projects/abop-german.berlios/]<br />
<br />
==== NumPy ====<br />
* first of all, try to use<br />
pydoc numpy<br />
* http://numpy.scipy.org/ - the homepage of NumPy contains a lot of documentation<br />
* {{Download|SS_2014_PadC.pdf|Script of the lecture "Physik auf dem Computer" (German)}} - Numerics in Python using Numpy<br />
<br />
==== LaTeX ====<br />
* [http://ctan.tug.org/tex-archive/info/lshort/english/lshort.pdf The Not So Short Introduction to LaTeX]<br />
* [http://www.latex-project.org/guides/ Documentation list of the LaTeX project]<br />
<br />
=== Running Python on your own computer ===<br />
<br />
If you want to solve the problems on your own computer, you need to install Python along with a few extensions. This works differently depending on your operating system.<br />
<br />
==== Debian und Ubuntu Linux ====<br />
<pre><br />
sudo apt-get update<br />
sudo apt-get install python python-numpy python-scipy \<br />
python-matplotlib ipython ipython-notebook gcc g++ \<br />
cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== OpenSUSE Linux ====<br />
<pre><br />
sudo zypper install python python-numpy python-scipy \<br />
python-matplotlib IPython gcc python-Cython<br />
mkdir -p ~/.config/matplotlib<br />
echo 'backend: TkAgg' > ~/.config/matplotlib/matplotlibrc<br />
</pre><br />
<br />
==== Mac OS X ====<br />
First, install the C compiler:<br />
<pre><br />
xcode-select --install<br />
xcodebuild -license accept<br />
</pre><br />
Now download and install [https://www.macports.org/install.php MacPorts].<br />
Next, you can install the Python packages.<br />
<pre><br />
sudo port selfupdate<br />
sudo port install python27 py27-numpy py27-scipy \<br />
py27-matplotlib py27-ipython py27-jupyter py27-cython<br />
sudo port select python python27<br />
sudo port select ipython py27-ipython<br />
sudo port select cython cython27<br />
</pre><br />
<br />
==== Windows ====<br />
For Windows, we recommend [https://www.continuum.io/downloads#_windows Anaconda Python], an all-in-one package that includes all required Python modules.<br />
<br />
For the worksheets that use Cython, you will also need to install a [https://conda.io/docs/user-guide/tutorials/build-windows.html compatible C compiler]. If you chose Python 2.7, that is [http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe Visual Studio 2008 Express Edition] plus, if you are running 64-bit Windows, the [http://www.microsoft.com/downloads/details.aspx?FamilyId=F26B1AA4-741A-433A-9BE5-FA919850BDBF&displaylang=en Windows SDK 2008] (in the installer, select "Installation Options", "Developer Tools", "Visual C++ Compilers", "Install the Visual C++ 9.0 Compilers).<br />
If you chose Python 3.5 or 3.6, you need [https://e5.onthehub.com/WebStore/OfferingsOfMajorVersionList.aspx?pmv=a45a6d43-f81e-e711-9427-b8ca3a5db7a1&cmi_mnuMain=f764a1c9-eb5e-e011-971f-0030487d8897&ws=058d5379-10d2-e311-93fc-b8ca3a5db7a3&vsro=8 Visual Studio 2015 Community Edition] (in the installer, select "Custom" and on the next page, select "Common Tools for Visual C++ 2015" in the "Programming Languages" category and uncheck all the other components that we do not need).<br />
<br />
== Examination ==<br />
<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 hand-in excercises of this lecture and the second part of the lecture as a prerequisite for the examination (USL-V)<br />
:* 60 min of oral examination (PL)<br />
:** After the lecture "Simulation Methods in Physics II" in summer term (i.e. Summer 2016)<br />
:** Contents: both lectures and the excercises of "Simulation Methods in Physics I"<br />
; International MSc Physics, Elective Module "Simulation Techniques in Physics I, II" (240918-005):<br />
:* Obtain 50% of the possible points in the hand-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 I" (40520):<br />
:* Obtain 50% of the possible points in the hand-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 I" (35840):<br />
:* The marks for the module are the marks obtained in the excercises (BSL)<br />
<br />
== C++ Course ==<br />
The Computer Science department is offering a week-long [http://www.iris.uni-stuttgart.de/lehre/lehrveranstaltungen-wintersemester-20172018/kompaktkurs-programmieren-in-c.html C++ course] at the end of this semester. We recommend all students that plan on participating the ''Advanced Simulation Methods'' lecture in summer semester 2018 to take this course. We also recommend it to all students that are considering doing a master's or bachelor's thesis at the ICP.<br />
Current bachelor students might be able to take this course as ''Schlüsselqualifikation'' -- but please contact the organizing Professor beforehand to ensure that this is actually the case. Master students will be able to take this course as ''One Course (2 SWS) in an Application Field of Simulation Methods'' as part of the ''Fortgeschrittene Simulationsmethoden (Schwerpunkt)'' module, pending a change of the ''Modulhandbuch''. Note that even current bachelor students can already take the course in 2018 if they intend to enroll in the master programme (starting in fall 2018) and take Advanced Simulation Methods (in summer 2019). All students will need to present their _Schein_ at the Advanced Simulation Methods exam in order to prove that they successfully participated in the C++ course and completed all required exercises.</div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:WS_2017_SM1_WS4_templates.tar.gz&diff=22854File:WS 2017 SM1 WS4 templates.tar.gz2017-12-11T11:42:11Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:WS_2017_SM1_worksheet4.pdf&diff=22853File:WS 2017 SM1 worksheet4.pdf2017-12-11T11:40:58Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=David_Sean&diff=22809David Sean2017-12-04T10:10:40Z<p>Dsean: </p>
<hr />
<div>{{Person<br />
|name=Sean, David<br />
|status=Postdoc<br />
|phone=67609<br />
|room=1.036<br />
|email=david.sean<br />
|image=David_Sean.png<br />
|category=holm<br />
|topical=electrokinetics<br />
|topical2=gel<br />
|topical3=espresso<br />
}}</div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:WS_2017_SM1_worksheet3.pdf&diff=22772File:WS 2017 SM1 worksheet3.pdf2017-11-27T08:51:57Z<p>Dsean: </p>
<hr />
<div></div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=File:WS_2017_SM1_worksheet1.pdf&diff=22449File:WS 2017 SM1 worksheet1.pdf2017-10-16T13:37:48Z<p>Dsean: worksheet 1</p>
<hr />
<div>worksheet 1</div>Dseanhttps://www2.icp.uni-stuttgart.de/~icp/mediawiki/index.php?title=David_Sean&diff=22386David Sean2017-09-28T11:03:22Z<p>Dsean: </p>
<hr />
<div>{{Person<br />
|name=Sean, David<br />
|status=Postdoc<br />
|phone=63609<br />
|room=1.036<br />
|email=david.sean<br />
|image=David_Sean.png<br />
|category=holm<br />
|topical=electrokinetics<br />
|topical2=gel<br />
|topical3=espresso<br />
}}</div>Dsean