Abstract
ESPResSo is an extensible simulation package for research on soft matter. This versatile molecular dynamics program was originally developed for coarse-grained simulations of charged systems [H.J. Limbach et al., Comput. Phys. Commun. 174, 704 (2006)]. The scope of the software has since broadened considerably: ESPResSo can now be used to simulate systems with length scales spanning from the molecular to the colloidal. Examples include, self-propelled particles in active matter, membranes in biological systems, and the aggregation of soot particles in process engineering. ESPResSo also includes solvers for hydrodynamic and electrokinetic problems, both on the continuum and on the explicit particle level. Since our last description of version 3.1 [A. Arnold et al., Meshfree methods for partial di_erential equations VI, Lect. Notes Comput. Sci. Eng. 89, 1 (2013)], the software has undergone considerable restructuring. The biggest change is the replacement of the Tcl scripting interface with a much more powerful Python interface. In addition, many new simulation methods have been implemented. In this article, we highlight the changes and improvements made to the interface and code, as well as the new simulation techniques that enable a user of ESPResSo 4.0 to simulate physics that is at the forefront of soft matter research.
| Original language | English |
|---|---|
| Pages (from-to) | 1789-1816 |
| Number of pages | 28 |
| Journal | European Physical Journal: Special Topics |
| Volume | 227 |
| Issue number | 14 |
| DOIs | |
| Publication status | Published - 1 Mar 2019 |
Funding
The ESPResSo package was set up as an open software project, committed to open source development under the GNU General Public License (GPL), a practice that we continue to adhere to. Users of ESPResSo are supported through mailing lists6 and workshops, such as the annual ESPResSo summer schools, which have between 20 and 40 participants. These workshops are often run as CECAM7 tutorials, jointly funded through grants from the German Research Foundation through the SFB 716 and the cluster of excellence SimTech (EXC 310). The mailing lists and workshops also allow the developer team to announce new features implemented in the code base of ESPResSo to the global research community. We would like to acknowledge more than 100 researchers who contributed over the last fifteen years to the ESPResSo software, and whose names can be found on our website http: //espressomd.org or in the AUTHORS file distributed with ESPResSo. We are also grateful to our colleagues of the SFB 716 for numerous suggestions for extending the capabilities of ESPResSo and in helping us to improve our software. As part of a collaboration [108], Milena Smiljanic contributed code to the cluster analysis framework, particularly to the analysis routines on the single cluster level. CH, KS, and FW gratefully acknowledge funding by the German Science Foundation (DFG) through the collaborative research center SFB 716 within TP C5, the SimTech cluster of excellence (EXC 310), and grants HO 1108/25-1, HO 1108/26-1, AR 593/7-1, HO 1108/28-1. MK, JdG, and CH thank the DFG for funding through the SPP 1726 Microswimmers–From Single Particle Motion to Collective Behavior. JdG further acknowledges funding from an NWO Rubicon Grant (#680501210) and a Marie Sk lodowska-Curie Intra European Fellowship (G.A. No. 654916) within Horizon 2020. The simulations were partially performed on the bwUniCluster funded by the Ministry of Science, Research and Arts and the Universities of the State of Baden-Württemberg, Germany, within the framework program bwHPC.