原子结构的三维云组分分析
3D Cloud Component Analysis of Atomic Structures
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中文总结 AI 辅助
该研究提出将原子坐标转为三维密度场的方法，可分解原子结构为类块体组分与真空，结合神经原型分类器确定晶相、标记原子类型并检测缺陷，在多种体系上验证了方法有效性。
中文摘要 AI 辅助
我们提出一种将原子结构分解为具有物理意义的组分的方法，该方法通过将离散的原子坐标转换为连续的三维密度场来实现。每种元素由高斯平滑密度图表示，其值范围为0到1，通过分箱后模糊的方法结合周期性边界条件高效计算。所有元素密度之和截断为1，定义了材料区域；其补集定义了真空。首先从阈值以上存在的元素集合中为每个体素分配化学式；随后清理得到的化学式图，仅保留那些通过到自身边界的欧氏距离测量的、具有真实块体内部的区域作为组分。薄的表面终止层（例如GaAs上的Ga单分子层）以及两个晶体之间1至2个体素的边界层会被相邻的稳定区域吸收，因此分解结果仅包含类块体的化学式组分和真空，不含表面或界面组分。对于每个组分，我们使用神经原型分类器确定其晶体相：若可信的内部原子一致投票则为单一相；若分为两个置信组（例如晶态和非晶态Si）则为两相，此时将该组分分为两部分。随后将界面和表面定义为边界——材料-材料边界和材料-真空边界，每个原子被标记为块体、表面、界面或顶点，顶点保留用于组分的几何角。在晶态组分内部，通过配位数和局部密度偏差检测内部缺陷。我们在Si/GaAs、Si/SiO₂异质结、晶态/非晶硅结、含空位晶体及块体晶体上验证了该方法。
英文摘要
We present a method for decomposing atomic structures into physically meaningful components by converting discrete atomic coordinates into continuous three-dimensional density fields. Each element is represented by a Gaussian-smeared density map with values ranging from 0 to 1, computed efficiently through a bin-then-blur approach with periodic boundary conditions. The sum of all element densities, truncated at unity, defines the material region; its complement defines the vacuum. Every voxel is first assigned a chemical formula from the set of elements present above a threshold; the resulting formula map is then cleaned so that only regions with a genuine bulk interior-measured by the Euclidean distance to their own boundary-survive as components. Thin surface terminations (e.g., a Ga monolayer on GaAs) and one-to-two-voxel boundary layers between two crystals are absorbed by the neighboring stable region, so the decomposition contains exactly the bulk-like chemical-formula components and the vacuum, with no surface or interface components. For each component we determine the crystal phase with a neural prototype classifier: one phase if the trusted interior atoms vote unanimously, two phases (e.g., crystalline and amorphous Si) if they split into two confident groups, in which case the component is divided into two. Interfaces and surfaces are then derived as boundaries-material-material and material-vacuum-and every atom is labeled bulk, surface, interface, or vertex, with vertex reserved for geometric corners of a component. Inside crystalline components, inner defects are detected from coordination-number and local-density deviations. We demonstrate the approach on Si/GaAs and Si/SiO2 heterojunctions, crystalline/amorphous silicon junctions, vacancy-containing crystals, and bulk crystals.
