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arXiv 1802.08602cond-mat.mtrl-sci
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GATor:一种用于分子晶体结构预测的第一性原理遗传算法

GAtor: A First Principles Genetic Algorithm for Molecular Crystal Structure Prediction

Farren Curtis, Xiayue Li, Timothy Rose, Álvaro Vázquez-Mayagoitia, Saswata Bhattacharya, Luca M. Ghiringhelli, Noa Marom

摘要:

我们提出了一个大规模并行的,第一原理遗传算法(GA)的分子晶体结构预测的GATor的实现。GATor是用Python编写的,目前与FHI-aims代码接口,使用包含色散的密度泛函理论(DFT)执行局部优化和能量计算。GATor提供了各种适应度评估、选择、交叉和变异方案。专门为分子晶体设计的育种操作员在探索和开发之间提供了平衡。进化小生境实现GATor通过使用机器学习聚类的动态更新的人口结构相似性,然后采用基于聚类的适应度函数。进化小生境通过进化几个亚种群来促进势能面的均匀采样,这有助于克服初始池偏差和选择偏差(遗传漂变)。GATor提供的各种设置增加了定位许多低能量极小值的可能性,包括那些位于断开连接,难以到达的潜在能量景观区域的能量极小值。最好的结构产生的重新放松和重新排名使用层次结构的越来越准确的DFT泛函和分散的方法。GATor应用于一组化学多样的四个过去的盲测试目标,其特征在于不同类型的分子间相互作用。实验观察到的结构和其他低能量的结构被发现的所有四个目标。特别地,对于目标II,5-氰基-3-羟基噻吩,排名最高的推定晶体结构是具有P $\bar{1}$对称性和支架填充基序的$Z^\prime$ =2结构,这在以前没有报道过。

英文摘要:

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 sub-populations, 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 $Z^\prime$=2 structure with P$\bar{1}$ symmetry and a scaffold packing motif, which has not been reported previously.

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