Difference between revisions of "Advanced Simulation Methods SS 2022"

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:Lecture and Tutorials (2 SWS in total)
 
:Lecture and Tutorials (2 SWS in total)
 
;Lecturer
 
;Lecturer
:Prof. Dr. [[Christian Holm]], PD. Dr. [[Jens Smiatek]], aplProf. Dr. [[Maria Fyta]]
+
:Prof. Dr. [[Christian Holm]], aplProf. Dr. [[Maria Fyta]], Dr. [[Alexander Schlaich]]
 
;Course language
 
;Course language
 
:English or German
 
:English or German
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The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]], PD. Dr. [[Jens Smiatek]], and aplProf. Dr. [[Maria Fyta]]. It will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all  modules.
 
The course will consist of three modules supervised by Prof. Dr. [[Christian Holm]], PD. Dr. [[Jens Smiatek]], and aplProf. Dr. [[Maria Fyta]]. It will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all  modules.
 
The students can work in groups. All groups should write a report of about 10 pages on each module, which they should submit to the responsible person for each module by the deadline set for each module.
 
The students can work in groups. All groups should write a report of about 10 pages on each module, which they should submit to the responsible person for each module by the deadline set for each module.
 
 
  
 
== Module 1: [[Maria Fyta]] and [[Samuel Tovey]]:  Machine-learned Interatomic Potentials ==
 
== Module 1: [[Maria Fyta]] and [[Samuel Tovey]]:  Machine-learned Interatomic Potentials ==
Line 59: Line 57:
 
* ...
 
* ...
  
== Module 2: [[Jens Smiatek]]: Molecular Theories of Solutions ==
+
== Module 2: [[Alexander Schlaich]]: Molecular modeling of electrode/electrolyte interfaces ==
  
  
 
=== Dates ===
 
=== Dates ===
  
First meeting: tba
+
First meeting: 13th of May, 22 in the Seminar Room
  
Final meeting and presentation: tba.
+
Final meeting and presentation: 10th of June, 22
  
Tutorials: tba.
+
If there are any questions regarding the exercise, contact [[Philipp Stärk]].
  
Deadline for reports: tba
+
Deadline for reports: 9th of June, 22. (For feedback, please hand in the first draft one week before!)
  
 
=== Description ===
 
=== Description ===
 +
This module focuses on molecular modeling of electrode interfaces and confinement effects thereof. Such interfaces are highly relevant for numerous applications such as energy storage and catalysis. We will introduce simulation approaches to study the electrochemical double layer and capacitative performance of different materials. The corresponding approaches will be applied to study the performance of aqueous electrolyte supercapacitors.
  
This module focuses on molecular theories of solution. I will outline the main principles of solvation processes and the corresponding interactions. As we will see, most mechanisms strongly differ from highly idealized assumptions such that more effective descriptions are needed. Such considerations are represented by the Kirkwood-Buff theory of solutions or in the framework of conceptual density functional theory. The corresponding theories will be applied for the study of water-ionic liquid mixtures.
+
=== Literature ===
  
=== Lecture Notes ===
+
==== Important Constant Potential References ====
[[Media:Molecular.pdf|Lecture Notes for Part: Molecular Theories of Solution]]
+
* Siepmann, J. I.; Sprik, M. Influence of Surface Topology and Electrostatic Potential on Water/Electrode Systems. J. Chem. Phys. 1995, 102 (1), 511–524. https://doi.org/10.1063/1.469429.
 +
* Scalfi, L.; T. Limmer, D.; Coretti, A.; Bonella, S.; A. Madden, P.; Salanne, M.; Rotenberg, B. Charge Fluctuations from Molecular Simulations in the Constant-Potential Ensemble. Physical Chemistry Chemical Physics 2020, 22 (19), 10480–10489. https://doi.org/10.1039/C9CP06285H.
 +
* Gingrich, T. R.; Wilson, M. On the Ewald Summation of Gaussian Charges for the Simulation of Metallic Surfaces. Chemical Physics Letters 2010, 500 (1), 178–183. https://doi.org/10.1016/j.cplett.2010.10.010.
 +
* Ahrens-Iwers, L. J. V.; Tee, S. R.; Meißner, R. H. ELECTRODE: An Electrochemistry Package for LAMMPS. arXiv:2203.15461 [physics] 2022.
  
[[Media:conceptual_DFT.pdf|Lecture Notes for Part: Conceptual Density Functional Theory]]
+
==== Further References for Interfacial Physics and Related Methods ====
 +
* Tyagi, S.; Süzen, M.; Sega, M.; Barbosa, M.; Kantorovich, S. S.; Holm, C. An Iterative, Fast, Linear-Scaling Method for Computing Induced Charges on Arbitrary Dielectric Boundaries. J. Chem. Phys. 2010, 132 (15), 154112. https://doi.org/10.1063/1.3376011.
 +
* Loche, P.; Wolde-Kidan, A.; Schlaich, A.; Bonthuis, D. J.; Netz, R. R. Comment on ``Hydrophobic Surface Enhances Electrostatic Interaction in Water’’. Phys. Rev. Lett. 2019, 123 (4), 049601. https://doi.org/10.1103/PhysRevLett.123.049601.
 +
* Kornyshev, A. A. On the Non-Local Electrostatic Theory of Hydration Force. Journal of electroanalytical chemistry and interfacial electrochemistry 1986, 204 (1–2), 79–84.
 +
* Breitsprecher, K.; Szuttor, K.; Holm, C. Electrode Models for Ionic Liquid-Based Capacitors. J. Phys. Chem. C 2015, 119 (39), 22445–22451. https://doi.org/10.1021/acs.jpcc.5b06046.
 +
* Bonthuis, D. J.; Gekle, S.; Netz, R. R. Profile of the Static Permittivity Tensor of Water at Interfaces: Consequences for Capacitance, Hydration Interaction and Ion Adsorption. Langmuir 2012, 28 (20), 7679–7694. https://doi.org/10.1021/la2051564.
  
 
=== Contact ===
 
=== Contact ===
  
If you have any questions regarding the organization or content of this module, please do not hesitate to contact ???.
+
If you have any questions regarding the organization or content of this module please do not hesitate to contact [[Alexander Schlaich]]. For practical guidance regarding the simulations [[Philipp Stärk]].
 
 
=== Part 1: Molecular Theories of Solution ===
 
 
 
==== Description ====
 
 
 
This part introduces the students to the field of solution 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.
 
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.
 
 
 
==== Literature ====
 
 
 
* J. G. Kirkwood and F. P. Buff. "The statistical mechanical theory of solutions. I." J. Chem. Phys. 19, 774 (1951)
 
* 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)
 
* J. Rösgen, B. M. Pettitt and D. W. Bolen, "Protein folding, stability, and solvation structure in osmolyte solutions", Biophys. J. 89, 2988 (2005)
 
* J. Smiatek, "Aqueous ionic liquids and their effects on protein structures: an overview on recent theoretical and experimental results", J. Phys. Condens. Matter 29, 233001 (2017)
 
* E. A. Oprzeska-Zingrebe and J. Smiatek, "Aqueous ionic liquids in comparison with standard co-solutes - Differences and common principles in their interaction with protein and DNA structures", Biophys. Rev. 10, 809 (2018)
 
* J. Smiatek, A. Heuer and M. Winter, "Properties of ion complexes and their impact on charge transport in organic solvent-based electrolyte solutions for lithium batteries: insights from a theoretical perspective", Batteries 4, 62 (2018)
 
* 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)
 
 
 
=== Part 2: Simulations ===
 
 
 
==== Description ====
 
 
 
This part is practical. The simulations will be conducted by the software package GROMACS [http://www.gromacs.org/]. The students will perform the simulations of ionic liquids(IL)-water mixtures at different water concentration in combination with the SPC/E water model and OPLSAA force field for EMImBF4. To generate the initial configuration of the simulation boxes, the software package Packmol [http://www.ime.unicamp.br/~martinez/packmol] will be used.
 
 
 
First the students simulate pure water and pure IL, and analyze the output data. Following properties will be calculated. The Kirkwood-Buff theory will be used to calculate the Kirkwood-Buff integrals. The student perform the different simulation box size to estimate the proper box size for calculating the properties.
 
* Kirkwood-Buff integrals
 
* diffusion coefficients
 
* mass densities
 
In addition to above, for water
 
* hydrogen bond life times and number of hydrogen bonds for water-water pairs
 
* water mean relaxation times
 
 
 
Next the student perform the IL-water mixtures at different water concentrations. After energy minimization and warm up, run 500 ns simulations with GROMACS for water mole fractions between X_H2O = 0 - 0.30.
 
 
In comparison to pure water/pure IL, the students will analyze several properties stated above and elucidate their water concentration dependent behavior.
 
Interpret the corresponding results with regard to the findings in Phys.Chem.Chem.Phys. 19, 18924 (2017). 
 
 
 
All the data needed for the exercise can be found in /group/sm/2019/Advsm_part2
 
 
 
<!--
 
==== Force Fields for IL(EMImBF4) ====
 
 
 
* {{Download| hectoinzwittmp2.itp |itp-File for Hydroxyectoine}}
 
* {{Download| hectoinzwittmp2.gro |gro-File for Hydroxyectoine}}
 
* {{Download| ectoinzwittmp2.itp |itp-File for Ectoine}}
 
* {{Download| ectoinzwittmp2.gro |gro-File for Ectoine}}
 
-->
 
 
 
<!--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.
 
 
 
2. Study the following properties for the different osmolytes and concentrations:
 
* diffusion coefficients
 
* hydrogen bond life times and number of hydrogen bonds for water-water, water-osmolyte and osmolyte-osmolyte pairs
 
* water mean relaxation times
 
Interpret the corresponding results. Are the molecules kosmotropes or chaotropes?
 
 
 
3. Calculate the radial distribution functions for all systems in terms of water-water, water-osmolyte and osmolyte-osmolyte pairs.
 
Use this information to compute the
 
 
 
* derivatives of the chemical activity
 
* derivatives of the activity coefficient
 
Interpret the corresponding results with regard to the findings in Biochemistry 43, 14472 (2004).
 
 
 
==== Literature ====
 
 
 
* 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)
 
* 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)
 
-->
 
  
 
== Module 3: [[Christian Holm]], [[Mariano Brito]]: Electrostatics, Lattice Boltzmann, and Electrokinetics==
 
== Module 3: [[Christian Holm]], [[Mariano Brito]]: Electrostatics, Lattice Boltzmann, and Electrokinetics==
Line 158: Line 97:
 
=== Dates ===
 
=== Dates ===
  
First meeting: TBA (around end June)
+
First meeting: Friday, June 24, 16:00 h.
  
 
Location: Final meeting and presentation in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).
 
Location: Final meeting and presentation in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).
  
Tutorials: TBA in the ICP CIP-Pool.
+
Tutorials: arrange with tutor.
  
 
Deadline for reports: TBA
 
Deadline for reports: TBA
Line 192: Line 131:
 
This part is practical. It is concerned with the movement of ions in an charged slit pore.
 
This part is practical. It is concerned with the movement of ions in an charged slit pore.
 
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]
 
It is similar to the systems that are discussed in the Bachelors thesis of [[Georg Rempfer]]
which is recommended reading. A slit pore consists of two infinite charge walls as shown
+
which is recommended reading. A slit pore consists of two infinite charged walls as shown
 
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].
 
in the figure to the right. In this exercise you should simulate such a system with [http://espressomd.org ESPResSo].
 
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented
 
You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented
Line 207: Line 146:
 
===== Worksheet =====
 
===== Worksheet =====
  
Worksheet 2021 {{Download|SS21_adv_sm_mod3_part2.pdf|Detailed worksheet}}
+
{{Download|AdvSimMet_2022_part2.pdf|Detailed worksheet}}
  
 
==== Literature ====
 
==== Literature ====
Line 227: Line 166:
  
 
==== Worksheet ====
 
==== Worksheet ====
{{Download|SS21_adv_sm_mod3_part3.pdf|Detailed worksheet}}
+
{{Download|AdvsimMet_2022_part3.pdf|Detailed worksheet}}
  
 
==== Instructions and Literature ====
 
==== Instructions and Literature ====

Latest revision as of 21:08, 24 June 2022

Overview

Type
Lecture and Tutorials (2 SWS in total)
Lecturer
Prof. Dr. Christian Holm, aplProf. Dr. Maria Fyta, Dr. Alexander Schlaich
Course language
English or German
Location
ICP, Allmandring 3; Room: ICP Meeting Room
Time
(see below)

The course will consist of three modules supervised by Prof. Dr. Christian Holm, PD. Dr. Jens Smiatek, and aplProf. Dr. Maria Fyta. It will contain exercises, presentations, discussion meetings, and written reports, worked out in groups. Each group will have to give a talk for all modules. The students can work in groups. All groups should write a report of about 10 pages on each module, which they should submit to the responsible person for each module by the deadline set for each module.

Module 1: Maria Fyta and Samuel Tovey: Machine-learned Interatomic Potentials

Dates

First meeting: Friday, April 23, 2021 at 10:00 (online or in person TBA) in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).

Final meeting and presentation: Friday, May 22; time tba in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).

Tutorials: Fridays 11:30-13:00 in the ICP CIP-Pool. The first tutorial will take place on tba

Deadline for reports: tba-->

Description

This exercise introduces student to the process of developing an inter-atomic potential for liquid argon using machine learning methods. You will follow the process from start to finish, using ab-initio MD methods to construct training data before fitting a model and deploying it in scaled up simulations.

Contact

If you have any questions regarding the organization or content of this module please do not hesitate to contact Christian Holm. For practical guidance regarding the simulations Samuel Tovey.

Part 1 -- DFT Simulations

In the first part of the exercise, you will use the CP2K simulation software to perform ab-initio molecular dynamics simulations on a system of liquid argon, in the process experimenting with configuring the interactions between atoms and seeing the results.

Part 2 -- Fitting a Potential

In this part, students will use the data generated in part 1 to fit a Gaussian process regression based machine learned inter-atomic potential. This task will allow the students to develop a deeper understanding of how these potentials are fit and the different parameters that need to be optimised in the process.

Part 3

In part 3, students use the machine-learned potential to perform scaled up molecular dynamics simulations using the LAMMPS simulation engine. These simulations are compared to the ab-initio data to demonstrate the retention of accuracy with the significantly improved performance.

Tutorial

Literature

  • Bartók, A. P., Payne, M. C., Kondor, R. & Gábor, C. Gaussian approximation potentials: the accuracy of quantum mechanics, without the electrons. Phys. Rev. Lett. 104, 136403 (2010).

Further reading (if interested)

  • ...

Module 2: Alexander Schlaich: Molecular modeling of electrode/electrolyte interfaces

Dates

First meeting: 13th of May, 22 in the Seminar Room

Final meeting and presentation: 10th of June, 22

If there are any questions regarding the exercise, contact Philipp Stärk.

Deadline for reports: 9th of June, 22. (For feedback, please hand in the first draft one week before!)

Description

This module focuses on molecular modeling of electrode interfaces and confinement effects thereof. Such interfaces are highly relevant for numerous applications such as energy storage and catalysis. We will introduce simulation approaches to study the electrochemical double layer and capacitative performance of different materials. The corresponding approaches will be applied to study the performance of aqueous electrolyte supercapacitors.

Literature

Important Constant Potential References

  • Siepmann, J. I.; Sprik, M. Influence of Surface Topology and Electrostatic Potential on Water/Electrode Systems. J. Chem. Phys. 1995, 102 (1), 511–524. https://doi.org/10.1063/1.469429.
  • Scalfi, L.; T. Limmer, D.; Coretti, A.; Bonella, S.; A. Madden, P.; Salanne, M.; Rotenberg, B. Charge Fluctuations from Molecular Simulations in the Constant-Potential Ensemble. Physical Chemistry Chemical Physics 2020, 22 (19), 10480–10489. https://doi.org/10.1039/C9CP06285H.
  • Gingrich, T. R.; Wilson, M. On the Ewald Summation of Gaussian Charges for the Simulation of Metallic Surfaces. Chemical Physics Letters 2010, 500 (1), 178–183. https://doi.org/10.1016/j.cplett.2010.10.010.
  • Ahrens-Iwers, L. J. V.; Tee, S. R.; Meißner, R. H. ELECTRODE: An Electrochemistry Package for LAMMPS. arXiv:2203.15461 [physics] 2022.

Further References for Interfacial Physics and Related Methods

  • Tyagi, S.; Süzen, M.; Sega, M.; Barbosa, M.; Kantorovich, S. S.; Holm, C. An Iterative, Fast, Linear-Scaling Method for Computing Induced Charges on Arbitrary Dielectric Boundaries. J. Chem. Phys. 2010, 132 (15), 154112. https://doi.org/10.1063/1.3376011.
  • Loche, P.; Wolde-Kidan, A.; Schlaich, A.; Bonthuis, D. J.; Netz, R. R. Comment on ``Hydrophobic Surface Enhances Electrostatic Interaction in Water’’. Phys. Rev. Lett. 2019, 123 (4), 049601. https://doi.org/10.1103/PhysRevLett.123.049601.
  • Kornyshev, A. A. On the Non-Local Electrostatic Theory of Hydration Force. Journal of electroanalytical chemistry and interfacial electrochemistry 1986, 204 (1–2), 79–84.
  • Breitsprecher, K.; Szuttor, K.; Holm, C. Electrode Models for Ionic Liquid-Based Capacitors. J. Phys. Chem. C 2015, 119 (39), 22445–22451. https://doi.org/10.1021/acs.jpcc.5b06046.
  • Bonthuis, D. J.; Gekle, S.; Netz, R. R. Profile of the Static Permittivity Tensor of Water at Interfaces: Consequences for Capacitance, Hydration Interaction and Ion Adsorption. Langmuir 2012, 28 (20), 7679–7694. https://doi.org/10.1021/la2051564.

Contact

If you have any questions regarding the organization or content of this module please do not hesitate to contact Alexander Schlaich. For practical guidance regarding the simulations Philipp Stärk.

Module 3: Christian Holm, Mariano Brito: Electrostatics, Lattice Boltzmann, and Electrokinetics

Dates

First meeting: Friday, June 24, 16:00 h.

Location: Final meeting and presentation in the ICP meeting room (Allmandring 3, 1st floor, room 1.095).

Tutorials: arrange with tutor.

Deadline for reports: TBA

Description

This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people. 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 and hand in one report. The Module 3 consists of three parts.

Contact

If you have any questions regarding the organisation or content of this module please do not hesitate to contact Christian Holm. For questions regarding the practical part of the module and technical help contact Mariano Brito.

Part 1: Electrostatics

Description

This part is about the theory of electrostatic algorithms for molecular dynamics simulations. It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald 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 as give them an overview of its performance compared to other modern electrostatics methods.

Literature

  • C. Holm.
    "Simulating Long range interactions".
    Institute for Computational Physics, Universitat Stuttgart, 2018.
    [PDF] (15.4 MB)


Part 2: Electro-Osmotic Flow

Description

Electroosmotic flow in a slit pore

This part is practical. It is concerned with the movement of ions in an charged slit pore. It is similar to the systems that are discussed in the Bachelors thesis of Georg Rempfer which is recommended reading. A slit pore consists of two infinite charged walls as shown in the figure to the right. In this exercise you should simulate such a system with ESPResSo. You are supposed to use a Lattice Boltzmann fluid coupled to explicit ions which are represented by charge Week-Chandler-Anderson spheres. In addition to the charge on the walls, the ions are also subject to an external electrical field parallel to the walls. Electrostatics should be handled by the P3M algorithm with ELC. A set of realistic parameters and an more in detail description of the system can be found in the thesis. You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high salt limit (Debye-Hueckel-Limit). Calculate the ion profiles in one or both of these cases and compare the results with the simulation.

Worksheet

application_pdf.pngDetailed worksheet (89 KB)Info circle.png

Literature

Some ESPResSo tutorials can be helpful.

Part 3: Electrophoresis of Polyelectrolytes

Description

In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions. 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 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 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 experimental results (see literature).


Worksheet

application_pdf.pngDetailed worksheet (98 KB)Info circle.png

Instructions and Literature

General part and part 5 of Media:04-lattice_boltzmann.pdf


Report

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).

The final report is due electronically TBA