A Fuzzy Classification Framework to Identify Equivalent Atoms in Complex Materials and Molecules
| Autor: | Lai, King Chun, Matera, Sebastian, Scheurer, Christoph, Reuter, Karsten |
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| Rok vydání: | 2023 |
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| Druh dokumentu: | Working Paper |
| DOI: | 10.1063/5.0160369 |
| Popis: | The nature of an atom in a bonded structure -- such as in molecules, in nanoparticles or solids, at surfaces or interfaces -- depends on its local atomic environment. In atomic-scale modeling and simulation, identifying groups of atoms with equivalent environments is a frequent task, to gain an understanding of the material function, to interpret experimental results or to simply restrict demanding first-principles calculations. While routine, this task can often be challenging for complex molecules or non-ideal materials with breaks of symmetries or long-range order. To automatize this task, we here present a general machine-learning framework to identify groups of (nearly) equivalent atoms. The initial classification rests on the representation of the local atomic environment through a high-dimensional smooth overlap of atomic positions (SOAP) vector. Recognizing that not least thermal vibrations may lead to deviations from ideal positions, we then achieve a fuzzy classification by mean-shift clustering within a low-dimensional embedded representation of the SOAP points as obtained through multidimensional scaling. The performance of this classification framework is demonstrated for simple aromatic molecules and crystalline Pd surface examples. Comment: Accepted manuscript in Journal of Chemical Physics. Repositories of the package (DECAF): DOI:10.17617/3.U7VKBM or https://gitlab.mpcdf.mpg.de/klai/decaf |
| Databáze: | arXiv |
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