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This work investigates the origins of cation ordering of double perovskites using first-principles theory computations combined with machine learning (ML) and causal relations. We have considered various oxidation states of A, A', B, and B' from the family of transition metal ions to construct a diverse compositional space. A conventional framework employing traditional ML classification algorithms such as Random Forest (RF) coupled with appropriate features including geometry-driven and key structural modes leads to highly accurate prediction (~98%) of A-site cation ordering. We have evaluated the accuracy of ML models by entailing analyses of decision paths, assignments of probabilistic confidence bound, and finally introducing a direct non-Gaussian acyclic structural equation model to investigate causality. Our study suggests that the structural modes are the most important features for classifying layered, columnar and rock-salt ordering. For clear layered ordering, the charge difference between the A and A' is the most important feature which in turn depends on the B, B' charge separation. Based on the outputs from ML models, we have designed functional forms with these features to derive energy differences forming clear layered ordering. The trilinear coupling between tilt, rotation, and A-site antiferroelectric displacement in Landau free-energy expansion becomes the necessary condition behind the formation of A-site cation ordering.