渡线
计算机科学
晶体结构预测
最大值和最小值
适应度函数
遗传算法
Python(编程语言)
进化算法
人口
选择(遗传算法)
算法
人工智能
理论计算机科学
机器学习
晶体结构
数学
化学
结晶学
操作系统
数学分析
社会学
人口学
作者
Farren Curtis,Xiayue Li,Timothy Rose,Álvaro Vázquez‐Mayagoitia,Saswata Bhattacharya,Luca M. Ghiringhelli,Noa Marom
标识
DOI:10.1021/acs.jctc.7b01152
摘要
We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low-energy minima, including those located in disconnected, hard to reach regions of the potential energy landscape. The best structures generated are re-relaxed and re-ranked using a hierarchy of increasingly accurate DFT functionals and dispersion methods. GAtor is applied to a chemically diverse set of four past blind test targets, characterized by different types of intermolecular interactions. The experimentally observed structures and other low-energy structures are found for all four targets. In particular, for Target II, 5-cyano-3-hydroxythiophene, the top ranked putative crystal structure is a Z' = 2 structure with P1̅ symmetry and a scaffold packing motif, which has not been reported previously.
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