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

• Published in: Journal of chemical theory and computation Vol. 14; no. 4; pp. 2246 - 2264
• Main Authors: Curtis, Farren, Li, Xiayue, Rose, Timothy, Vázquez-Mayagoitia, Álvaro, Bhattacharya, Saswata, Ghiringhelli, Luca M, Marom, Noa
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 10.04.2018
• Subjects: Clusters; Crystal structure; Density functional theory; Dispersion; Energy consumption; First principles; Fitness; Genetic algorithms; INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Machine learning; Molecular chains; Molecular structure; Potential energy
• ISSN: 1549-9618; 1549-9626; 1549-9626
• DOI: 10.1021/acs.jctc.7b01152

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.