论文标题
原子全局优化X:用于优化原子结构的Python软件包
Atomistic Global Optimization X: A Python package for optimization of atomistic structures
论文作者
论文摘要
建模和理解第一原理的材料的特性需要了解潜在的原子结构。这需要了解所有相关原子的个人身份和位置。获取有关宏观分子,纳米颗粒,簇以及无定形和固体材料的表面,界面和整体阶段的信息,这是一个困难的高维全局优化问题。但是,材料科学中机器学习技术的兴起已导致许多引人入胜的发展,这些发展可能会加快这种结构搜索的速度。新方法的复杂性确定了有效的方法来实验并将它们组装成全球优化算法的必要性。在本文中,我们介绍了原子全局优化X(AGOX)框架和代码,作为一种可自定义的方法来构建有效的全球优化算法。描述了表达全局优化算法的模块化方式,并使用现代编程实践来使该模块化在自由使用的Agox Python软件包中。分析了全局优化问题的两个示例:一个是计算便宜的,用于展示Agox可以表达多个全局优化算法。作为另一个例子,Agox用于解决嵌入石墨烯片中的金属纳米簇的复杂原子优化问题,如密度功能理论(DFT)水平所述。
Modelling and understanding properties of materials from first principles require knowledge of the underlying atomistic structure. This entails knowing the individual identity and position of all involved atoms. Obtaining such information for macro-molecules, nano-particles, clusters, and for the surface, interface, and bulk phases of amorphous and solid materials represents a difficult high dimensional global optimization problem. The rise of machine learning techniques in materials science has, however, led to many compelling developments that may speed up such structure searches. The complexity of the new methods have established the necessity for an efficient way of experimenting with and assembling them into global optimization algorithms. In this paper we introduce the Atomistic Global Optimization X (AGOX) framework and code, as a customizable approach to building efficient global optimization algorithms. A modular way of expressing global optimization algorithms is described and modern programming practices are used to enable that modularity in the freely available AGOX python package. Two examples of global optimization problems are analyzed: One that is computationally inexpensive which is used to showcase that AGOX enables the expression of multiple global optimization algorithms. As the other example, AGOX is used for solving a complex atomistic optimization problem for a metal-nitride nano-cluster embedded in a graphene sheet as described at the density functional theory (DFT) level.