ESPResSo 4.0-an extensible software package for simulating soft matter systems
ESPResSo 4.0-an extensible software package for simulating soft matter systems
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DOI：
10.1140/epjst/e2019-800186-9
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发表时间：
2019-03-01
影响因子：
2.8
通讯作者：
Holm, Christian
中科院分区：
文献类型：
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作者：
Weik, Florian;Weeber, Rudolf;Holm, Christian
ESPResSo 是一个用于软物质研究的可扩展仿真包。这种多功能分子动力学程序最初是为带电系统的粗粒度模拟而开发的 [H.J. Limbach 等人，计算机。物理。交流。 174, 704 (2006)]。此后，该软件的范围已大大扩展：ESPResSo 现在可用于模拟长度尺度从分子到胶体的系统。例子包括活性物质中的自驱动颗粒、生物系统中的膜以及过程工程中烟灰颗粒的聚集。 ESPResSo 还包括连续介质和显式粒子级别上的流体动力学和电动问题的求解器。自从我们上次描述版本 3.1 [A. Arnold 等人，偏微分方程的无网格方法 VI，Lect。笔记计算。科学。工程师。 89, 1 (2013)]，软件进行了相当大的重组。最大的变化是用更强大的 Python 接口替换了 Tcl 脚本接口。此外，还实施了许多新的模拟方法。在本文中，我们重点介绍对界面和代码所做的更改和改进，以及新的模拟技术，使 ESPResSo 4.0 用户能够模拟处于软物质研究前沿的物理学。
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.