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ESPResSo Summer School 2012

Simulating Soft Matter with ESPResSo, ESPResSo++ and VOTCA

October 8,  2012 to October 12, 2012

Institute for Computational Physics, Stuttgart University, Germany

Participants and Speakers of the ESPResSo Summer School 2012.

ESPResSo , ESPResSo++ and VOTCA are open-source program packages that have been designed specifically to study coarse-grained soft matter systems, and they are used by more than 100 institutions worldwide. The packages are developed at the ICP at Stuttgart University, Germany and the Max-Planck-Institute for Polymer Research in Mainz, Germany. All three applications are tools that make it significantly easier for PhD students and researchers in general to get started with their projects.

Between October 8-12, ICP, the SimTech Cluster of Excellence at Stuttgart  University and CECAM (Centre Européen de Calcul Atomique et Moléculaire) organize the SimTech-CECAM-ESPResSo Summer School 2012. The school provides a detailed and hands-on introduction to the software packages and their uses.

The school consists of Lectures and Hands-on Sessions in two tracks, both for beginners as well as for experienced users and developers of ESPResSo, ESPResSo++ and VOTCA. One track aims to introduce the general ideas and usage of ESPResSo and its most common features for the simulation of a broad variety of soft matter systems. The second track is offering a more in-depth look into the code of the software and additional algorithms and possibilities of ESPResSo++, VOTCA and ADResS. It is aimed to attract researchers who are already familiar with the basic ESPResSo features and want to build on that or want to extend and optimize the code to better match their simulation setups. Furthermore, there will be a Poster Session and Lightning Talks where participants have the opportunity to present their projects and ideas with the other participants and the speakers, and a number of Scientific Talks where scientists will present recent research projects that were done with any of the software packages. Another aim of this school is to give the developers of the software packages feedback on ongoing research on soft matter, so that design decisions better match the needs of the community.

Monday, October 8th

8:30 – 9:00 Registration
9:00 – 9:30 Welcome
Olaf Lenz (ICP Stuttgart, Germany)
Track 1 Track 2
9:30 – 12:30 Introduction to Soft Matter Simulations
Christian Holm, Olaf Lenz (ICP Stuttgart, Germany)

  • Soft Matter
  • Molecular Dynamics
  • Cell lists, Verlet lists, Parallelization, Domain Decomposition
  • Using VMD
ESPResSo under the hood
Axel Arnold , Olaf Lenz (ICP Stuttgart, Germany)

  • Code structure
  • Development
  • Implementation details
12:30 – 14:00 Lunch break
14:00 – 17:00 Introduction to Tcl
Pedro Sanchez (ICP Stuttgart, Germany)
Introduction to Python
Stefan Kesselheim, Tobias Steinle (ICP Stuttgart, Germany)
17:00 – 18:00 Lightning Talks

Tuesday, October 9th

Track 1 Track 2
9:00 – 12:30 Introduction to ESPResSo
Olaf Lenz (ICP Stuttgart, Germany)

  • Compiling ESPResSo
  • Lennard-Jones fluid
  • Kremer-Grest polymer melt
  • Features of ESPResSo
Introduction to ESPResSo++
Torsten Stühn (MPIP Mainz, Germany)

  • Compiling ESPResSo++
  • Lennard-Jones fluid
  • Kremer-Grest polymer melt
  • ESPResSo++ class structure
  • Implementing new potentials
12:30 – 14:00 Lunch break
14:00 – 17:30 Recent and Future Developments of ESPResSo
Olaf Lenz (ICP), Stefan Kesselheim (ICP), Rudolf Weeber (ICP), Peter Kosovan (ICP)
ESPResSo++ and AdResS (Adaptive Resolution Scheme)
Torsten Stühn (MPIP Mainz, Germany), Christoph Junghans (Los Alamos National Laboratory, USA), Staš Bevc (National Institute of Chemistry, Ljubljana, Slovenia)
17:30 – Poster Sessionand BBQ

Wednesday, October 10th

9:00 – 12:30 Data Analysis and Visualization
Gaël Varoquaux (INRIA, France)
12:30 – 14:00 Lunch break
Track 1 Track 2
14:00 – 17:30 Electrostatic interactions in ESPResSo
Axel Arnold (ICP Stuttgart, Germany)

  • Ewald, P3M
  • Simulating charged systems
  • Partial periodicity: MMM*D, ELC
  • Maggswell Equation Molecular Dynamics
Systematic Coarse-Graining with VOTCA
Victor Rühle (Cambridge, UK), Christoph Junghans (Los Alamos National Laboratory, USA)
17:30 – Conference Dinner

Thursday, October 11th

Track 1 Track 2
9:00 – 12:30 Hydrodynamics in ESPResSo
Ulf Schiller (FZ Jülich, Germany), Jens Smiatek (ICP Stuttgart, Germany)

  • Lattice-Boltzmann (LB)
  • Dissipative Particle Dynamics (DPD)
Systematic Coarse-Graining with VOTCA 2
Victor Rühle (Cambridge, UK), Christoph Junghans (Los Alamos National Laboratory, USA)
12:30 – 14:00 Lunch break
14:00 – 17:30 Simulating Membranes in ESPResSo
Mingyang Hu, Patrick Diggins (Carnegie-Mellon University, USA)
Rare event sampling with FRESHS
Kai Kratzer (ICP Stuttgart, Germany)

Friday, October 12th (Scientific Talks)

9:00 – 9:45 Magnetic Soft Matter: A Simulational Approach
Christian Holm (ICP, Germany)
9:45 – 10:30 Determining the Gaussian curvature modulus of lipid membranes in simulations:
A comparative study via global shape transformations and local stress distributions
Mingyang Hu (Carnegie-Mellon University, USA)
10:30 – 11:00 Coffee Break
11:00 – 11:45 Agglomeration of nano- and micron-sized particles
Andreas Kronenburg (Institut für Technische Verbrennung, Universität Stuttgart, Germany)
11:45 – 12:30 Tracer diffusion in polymers and gels
Peter Kosovan (ICP, Germany)
12:30 – 13:00 Wrap-up
Olaf Lenz, Axel Arnold, Christian Holm (ICP, Germany)

Monday, 8th

Tuesday, 9th

Wednesday, 10th

Thursday, 11th

Friday, 12th

Participants and Speakers of the ESPResSo Summer School 2012.

Speakers

  1. Axel Arnold, Institute for Computational Physics, Universität Stuttgart, Germany
  2. Stas Bevc, National Institute of Chemistry, Ljubljana, Slovenia
  3. Patrick Diggins, Carnegie-Mellon University, Pittsburgh, USA
  4. Florian Fahrenberger, Institute for Computational Physics, Universität Stuttgart, Germany
  5. Christoph Junghans, Los Alamos National Laboratory, USA
  6. Christian Holm, Institute for Computational Physics, Universität Stuttgart, Germany
  7. Mingyang Hu, Carnegie-Mellon University, Pittsburgh, USA
  8. Stefan Kesselheim, Institute for Computational Physics, Universität Stuttgart, Germany
  9. Peter Kosovan, Institute for Computational Physics, Universität Stuttgart, Germany
  10. Kai Kratzer, Institute for Computational Physics, Universität Stuttgart, Germany
  11. Andreas Kronenburg, Institut für Technische Verbrennung, Universität Stuttgart, Germany
  12. Olaf Lenz, Institute for Computational Physics, Universität Stuttgart, Germany
  13. Dominic Röhm, Institute for Computational Physics, Universität Stuttgart, Germany
  14. Victor Rühle, Department of Chemistry, University of Cambridge, United Kingdom
  15. Pedro Sanchez, Institute for Computational Physics, Universität Stuttgart, Germany
  16. Ulf Schiller, Forschungszentrum Jülich, Germany
  17. Jens Smiatek, Institute for Computational Physics, Universität Stuttgart, Germany
  18. Torsten Stühn, Max Planck Institute for Polymer Research, Mainz, Germany
  19. Gael Varoquaux, INRIA, France
  20. Rudolf Weeber, Institute for Computational Physics, Universität Stuttgart, Germany

Participants

  1. Enrique Abad, Institut für Theoretische Chemie, Universität Stuttgart, Germany
  2. Bibek Adhikari, Institute for Computational Physics, Universität Stuttgart, Germany
  3. Arash Azari, Korea Institute for Advanced Study, Seoul, Korea
  4. Eduardo Robert Cruz-Chu, ETH Zürich, Switzerland
  5. Gernot Bauer, Institut für technische Thermodynamik, Universität Stuttgart, Germany
  6. Richard Bingham, Centre for Molecular Nanoscience, University of Leeds, United Kingdom
  7. José Rafael Bordin, Institute for Computational Physics, Universität Stuttgart, Germany
  8. Konrad Breitsprecher, Institute for Computational Physics, Universität Stuttgart, Germany
  9. Manuel Camargo, Universidad Antonio Nariño, Bogota, Columbia
  10. Rajarshi Chakrabarti, Institute for Computational Physics, Universität Stuttgart, Germany
  11. Hwan Won Chung, Korea Institute of Science and Technology, South Korea
  12. Oliver Dannemann, Universität Stuttgart, Germany
  13. Daniel Förster, Universität Stuttgart, Germany
  14. Joost de Graaf, Institute for Computational Physics, Universität Stuttgart, Germany
  15. Owen Hickey, Institute for Computational Physics, Universität Stuttgart, Germany
  16. Jaanus Karo, Institute of Cybernetics, Tallinn University of Technology, Estonia
  17. Tarun Khanna, Birla Institute of Technology & Science, Pilani, India
  18. Karsten Kreis, Max-Planck-Institute for Polymer Research, Mainz, Germany
  19. Robert Mackenzie, Centre for Biomolecular Sciences, University of Nottingham, United Kingdom
  20. Henri Menke, Institute for Computational Physics, Universität Stuttgart, Germany
  21. Andreas Michel, Institute for Computational Physics, Universität Stuttgart, Germany
  22. Elena Minina, Institute for Computational Physics, Universität Stuttgart, Germany
  23. Narges Nikoofard, Institute for Advanced Studies in Basic Sciences, Zanjan, Iran
  24. Harald Oberhofer, Technische Universität München, Germany
  25. Dusan Racko, Polymer Institute of the Slovak Academy of Sciences, Bratislava, Slovak Republic
  26. Shervin Rafatnia, Institute for Computational Physics, Universität Stuttgart, Germany
  27. Georg Rempfer, Institute for Computational Physics, Universität Stuttgart, Germany
  28. Tobias Richter, Institute for Computational Physics, Universität Stuttgart, Germany
  29. Jalal Sarabadani, Max-Planck-Institute for Polymer Research, Mainz, Germany
  30. Christoph Scheurer, Lehrstuhl für Theoretische Chemie, Technische Universität München, Germany
  31. Karel Sindelka, Faculty of Science, Charles University in Prague, Czech Republic
  32. Lucie Sucha, Faculty of Science, Charles University in Prague, Czech Republic
  33. Martin Vögele, Universität Stuttgart, Germany
  34. Florian Weik, Institute for Computational Physics, Universität Stuttgart, Germany
  35. Johannes Zemann, Institute for Computational Physics, Universität Stuttgart, Germany
  36. Heng Zhang, Theory of Soft Condensed Matter, University of Luxembourg, Luxembourg