# Difference between revisions of "Axel Arnold"

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on a single PCIe-board. With the introduction of easy-to-use programming languages for | on a single PCIe-board. With the introduction of easy-to-use programming languages for | ||

the GPU hardware, this computational power can be harnessed for many | the GPU hardware, this computational power can be harnessed for many | ||

− | applications. Using NVidia's CUDA, Koos van Meel and I have demonstrated this for classical Molecular Dynamics simulations. However, GPUs are better suited for mesh-based algorithms such as the lattice Boltzmann method, and {{es}} now contains a GPU-accelerated LB code written by Dominic Röhm. For more information, see [[GPU Computing| here]]. | + | applications. Using NVidia's CUDA, Koos van Meel and I have demonstrated this for classical Molecular Dynamics simulations. However, GPUs are better suited for mesh-based algorithms such as the lattice Boltzmann method, and {{es}} now contains a GPU-accelerated LB code written by Dominic Röhm. For more information, see [[GPU Computing| here]]. A number of simple CUDA examples can be found [[CUDA examples | here]]. |

=== Calculation of the electrostatic potential === | === Calculation of the electrostatic potential === |

## Revision as of 15:33, 11 November 2012

**JP Dr. Axel Arnold**

Group leader

Office: | 1.036 |
---|---|

Phone: | +49 711 685-67609 |

Fax: | +49 711 685-63658 |

Email: | arnolda _at_ icp.uni-stuttgart.de |

Address: | JP Dr. Axel Arnold Institute for Computational Physics Universität Stuttgart Allmandring 3 70569 Stuttgart Germany |

## Contents

## GNU/Linux

- projector.sh (5 KB) is a script that you can use to switch between internal and external displays on laptops. In the simplest form, it just toggles between internal display only and both internal and external display, which is basically the functionality that you would expect from the display switch fn-key. I tested it both with xrandr and the Nvidia driver, so it should work with most hardware.
- mount.sh (1 KB) and umount.sh (1 KB) are two scripts that perform the respective operations semiautomatically using the udisks command of Ubuntu and other current Linux distributions. If you a tiling window manager such as awesome or ratpoison, you probably also want to be able to mount USB devices from the terminal. These scripts simplify this process.

mount does the following:

- without arguments, shows the mounted partitions, just as plain mount would do
- with parameter "-a" looks for the first unmounted, mountable partition and mounts it. The devices it looks for are /dev/sd*1 and /dev/mmcblk*p1, which is what you will typically find with USB sticks.
- otherwise, the parameter should be a partition to mount, e.g. /dev/sdb1

The partitions are mounted using udisks, so are mounted to a new mount point in /media as reported.

umount just takes this mount point to unmount the partition, just as a plain umount would do, but in a second step tries to detach the device. USB HDDs will typically retract their heads in this case and stop spinning, rather than performing the fast head retract that they do if they are just powered off.

### Awesome

Here are some useful enhanced widgets for Awesome.

- Battery monitor (2 KB). Based on acpitool like the version suggested on the Awesome wiki, but also supports broken laptops that do not report remaining time.
- Network monitor (3 KB). Displays throughput of network devices, e.g. to check that UMTS is still sending/receiving.
- Keyboard switching widget (1 KB). Based on the example in the Awesome wiki, but allows to also specify variants, such as "nodeadkeys" for the German keyboard layout.

## Research interests

### Reviewing

As it seems, one of my favorite activities is reviewing papers for the Journal of Chemical Physics. At least, I became one of their top 20 reviewers 2011.

### ESPResSo

ESPResSo stands for **E**xtensible **S**imulation **P**ackage for
**Res**arch on **So**ft matter systems, and is a simulation package
mainly for (charged) bead spring models of soft matter. Since the beginning in 2003, I am one of the core developers and am still involved in the current development here at ICP. Also, if you are interested in any of the algorithmic work I do/did - all is implemented in ESPResSo and therefore open source. In particular, my major contributions are:

- a good deal of ESPResSo's core functionality
- GPU accelerated lattice Boltzmann
- MMM2D / MMM1D
- ELC
- collision detection

### Using GPUs for numerical calculations

In the last couple of years, the computational power of graphics cards has grown much faster than that of conventional CPUs, although at the same time the graphics cards have become true general purpose processors. Recent graphics processors reach speeds of up to a Teraflop on a single PCIe-board. With the introduction of easy-to-use programming languages for the GPU hardware, this computational power can be harnessed for many applications. Using NVidia's CUDA, Koos van Meel and I have demonstrated this for classical Molecular Dynamics simulations. However, GPUs are better suited for mesh-based algorithms such as the lattice Boltzmann method, and ESPResSo now contains a GPU-accelerated LB code written by Dominic Röhm. For more information, see here. A number of simple CUDA examples can be found here.

### Calculation of the electrostatic potential

Due to its long-ranged nature, the electrostatic interaction is very difficult to calculate in periodic systems. However, these systems are often used in computer simulation studies of bulk systems. Therefore, there has been and still is much interest in fast algorithms to calculate the Coulomb sum in periodic boundary conditions. For 3D periodic boundary conditions, many optimized algorithms exist, from the classical Ewald summation to particle-mesh methods, where the best method scale linearly in the number of particles.

My interest is in the calculation of this interaction in 3D systems, where only one or two coordinates are periodically replicated. For these systems, the classical Ewald method is slow to evaluate, and alternative approaches are necessary. I have developed the MMM1D/2D algorithms, and J. de Joannis and I found the electrostatic layer correction (ELC) method. This method consists of a correction term that is fast to calculate and allows to use any method for 3D-periodic boundary conditions for a quasi-2D system.

All these methods are implemented in ESPResSo, if you want to try them out.

### (Charged) soft matter

Mostly using ESPResSo and the above-mentioned electrostatics methods, I investigated several systems of interest in soft matter physics. For example:

- attraction of like-charged rods in the presence of multivalent counterions (here, MMM1D was used).
- interactions of charged colloids (using MMM2D and ELC).
- segregation and relaxation of polymers in confinement.

Current research in soft matter is mainly on charged colloidal systems:

- homogeneous and heterogeneous nucleation of charged colloids
- influence of hydrodynamics on the nucleation rate

## Publications

- Marcello Sega, Sofia S. Kantorovich, Axel Arnold, and Christian Holm.
*On the Calculation of the Dielectric Properties of Liquid Ionic Systems*. In Y. P. Kalmykov, Recent Advances in Broadband Dielectric Spectroscopy, NATO Science for Peace and Security Series B: Physics and Biophysics, Springer, 2013.

- M. Weigel, A. Arnold, P. Virnau (Editors).
*Computer Simulations on Graphics Processing Units*. Eur. Phys. J. ST 210 (2012).

- T. Brandes, A. Arnold, T. Soddemann and D. Reith.
*CPU vs. GPU - Performance comparison for the Gram-Schmidt algorithm*. Eur. Phys. J. ST 210:73-88 (2012).

- D. Roehm and A. Arnold.
*Lattice Boltzmann simulations on GPUs with ESPResSo*. Eur. Phys. J. ST 210:89-100 (2012).

- N. Gribova, A. Arnold, T. Schilling, C. Holm.
*How Close to Two Dimensions Does a Lennard-Jones System Need to Be to Produce a Hexatic Phase?*. J. Chem. Phys. 135:054514 (2011).

- A. Arnold.
*Fourier Transformed-Based Methods for Long-Range Interactions: Ewald, P3M and More*. In G. Sutmann, P. Gibbon, and T. Lippert, Fast Methods for Long-Range Interactions in Complex Systems. IAS Series Vol. 6, FZ Jülich (2011).

- A. Arnold, O. Lenz und C. Holm.
*Simulating Charged Systems with ESPResSo*. In G. Sutmann, P. Gibbon, and T. Lippert, Fast Methods for Long-Range Interactions in Complex Systems. IAS Series Vol. 6, FZ Jülich (2011).

- V. Ballenegger, A. Arnold and J. J. Cerdà.
*Simulations of non-neutral slab systems with long-range electrostatic interactions in two-dimensional periodic boundary conditions*. J. Chem. Phys. 131:094107 (2009).

- T. Kalkbrenner, A. Arnold and S. Tans.
*Internal Dynamics of Supercoiled DNA Molecules*. Biophysical Journal 96:4951-4955 (2009).

- S. Tyagi, A. Arnold and C. Holm.
*Electrostatic layer correction with image charges: A linear scaling method to treat slab 2D+h systems with dielectric interfaces*. J. Chem. Phys. 129:204102 (2008).

- A. Arnold and C. Holm.
*Interactions of like-charged rods at low temperatures: Analytical theory vs. simulations*. Euro. Phys. J. E, DOI:10.1140/epje/i2007-10347-4, 2008.

- J. A. van Meel, A. Arnold, D. Frenkel, S. F. Portegies Zwart and R. G. Belleman.
*Harvesting graphics power for MD simulations*. Molecular Simulation 34(3):259-266, 2008.

- A. Arnold, B. Bozorgui, D. Frenkel, B.-Y. Ha and S. Jun.
*Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement*. J. Chem. Phys. 127:164903, 2007.

- S. Tyagi, A. Arnold and C. Holm.
*ICMMM2D: An accurate method to include planar dielectric interfaces via image charge summation*. J. Chem. Phys. 127:154723, 2007.

- A. Arnold and S. Jun.
*Time scale of entropic segregation of flexible polymers in confinement: Implications for chromosome segregation in filamentous bacteria*. Phys. Rev. E 76:031901, 2007.

- S. Jun, A. Arnold and B.-Y. Ha.
*Confined space and effective interactions of multiple self-avoiding chains*. Phys. Rev. Lett. 98:128303, 2007.

- H. Limbach, A. Arnold, B. A. Mann and C. Holm.
*ESPResSo - An Extensible Simulation Package for Research on Soft Matter Systems*. Comp. Phys. Comm. 174:704-727, 2006.

- A. Arnold, B. A. F. Mann and C. Holm.
*Simulating Charged Systems with ESPResSo*. In Lecture Notes in Physics, 703, Springer, 2006.

- A. Arnold and C. Holm.
*Efficient methods to compute long range interactions for soft matter systems*. In C. Holm and K. Kremer, Advanced Computer Simulation Approaches for Soft Matter Sciences II, 59-109, Springer, 2005.

- A. Arnold and C. Holm.
*MMM1D: A method for calculating electrostatic interactions in one-dimensional periodic geometries*. J. Chem. Phys. 123(14):144103, 2005.

- A. Arnold.
*Computer simulations of charged systems in partially periodic geometries*. Disseration, J. Gutenberg-Universität, Mainz, Germany, 2004.

- A. Naji, A. Arnold, C. Holm and R. R. Netz.
*Attraction and unbinding of like--charged rods*. Europhys. Lett. 67:130-136, 2004.

- M. Deserno, A. Arnold and C. Holm.
*Attraction and ionic correlations between charged stiff polyelectrolytes*. Macromolecules 36(1):249-259, 2003.

- A. Arnold and C. Holm.
*MMM2D: A fast and accurate summation method for electrostatic interactions in 2D slab geometries*. Comp. Phys. Comm. 148(3):327-348, 2002.

- J. de Joannis, A. Arnold and C. Holm.
*Electrostatics in Periodic Slab Geometries II*. J. Chem. Phys. 117:2503-2512, 2002.

- A. Arnold, J. de Joannis and C. Holm.
*Electrostatics in Periodic Slab Geometries I*. J. Chem. Phys. 117:2496-2502, 2002.

- A. Arnold and C. Holm.
*A novel method for calculating electrostatic interactions in 2D periodic slab geometries*. Chem. Phys. Lett. 354(3):324-330, 2002.

- A. Arnold.
*Berechnung der elektrostatischen Wechselwirkung in 2d+h periodischen Systemen*. Diploma thesis, J. Gutenberg-Universität, Mainz, Germany, 2001.

## Curriculum vitae

### Scientific education

since Jan. 2010 | Post-doctoral researcher at the ICP, University of Stuttgart, Germany |

Jan. 2008 - Dec. 2009 | Post-doctoral researcher at the Fraunhofer institute SCAI, St. Augustin, Germany |

Nov. 2005 - Dec. 2007 | Post-doctoral researcher at the FOM-institute AMOLF, Amsterdam, The Netherlands |

Dec. 2004 - Oct. 2005 | Post-doctoral researcher at the Max-Planck-Institute for Polymer Research and the Frankfurt Institute for Advanced Studies (FIAS) |

Dec. 2004 | Doctor rer. nat. awarded at the Johannes Gutenberg-University of Mainz. Thesis:
Computer simulations of charged systems in partially periodic geometries |

since 2003 | One of the core developers of ESPResSo |

Oct. 2001- Dec. 2004 | Doctorate studies at the Max-Planck-Institute for Polymer Research in Mainz, Germany |

Oct. 2001 | Diploma in Mathematics at the Johannes Gutenberg- University of Mainz. Thesis:
Berechnung der elektrostatischen Wechselwirkung in 2d+h periodischen Systemen |

Oct. 1996 - Oct.2001 | Studies of Mathematics at the Johannes Gutenberg-University of Mainz |

1998 - 2002 | Participating in the RoboCup, a worldwide competition on multi-agent systems, as member of the Mainz Rolling Brains |

### Other skills

- Languages: German and English (fluent), Russian, Dutch (beginner)
- Computing languages: C, C++, Tcl/Tk, Python, MPI, CUDA, shell scripting
- System administration: Unix (Linux, Tru64, AIX, Irix, Solaris), MacOS/Darwin, Windows