d-SEAMS：用于分子模拟的延迟结构解析分析
d-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations
AI总结：
本研究推出免费开源的分子模拟后处理引擎d-SEAMS，可定性分类体相及受限体系冰结构，支持定制扩展，输出兼容主流图形软件，并通过多体系成核分析验证了其功能。
摘要：
结构分析是成核与过冷水计算研究中不可或缺的组成部分，其准确性与效率会影响此类研究的有效性与可行性。这些通常难以观测且计算成本高昂的过程的潜在分子机制，可通过类冰结构的演化推断，而类冰结构需借助合适的结构分析技术确定。我们推出d-SEAMS，这是一款用于分析分子动力学轨迹的免费开源后处理引擎，专门能够对强受限体系和体相体系中的冰结构进行定性分类。该引擎首次实现了用于受限冰结构测定的最新算法，以及用于体相冰结构测定的拓扑网络判据。考虑到结构分析中存在定制化需求，d-SEAMS采用独特的代码架构，基于nix构建，运用YAML-Lua脚本流水线。该软件设计为用户友好且易于扩展。引擎的输出结果与主流图形软件套件兼容，可对所研究的体系实现即时可视化洞察。我们通过分析体相区域以及准一维、准二维体系中的成核过程，展示了d-SEAMS的功能。针对银暴露的β-AgI表面上的异质冰成核、均质冰成核、平面单层方形冰形成以及冰纳米管冻结过程，测定了结构随时间的演化及定量指标。
英文摘要：
Structural analyses are an integral part of computational research on nucleation and supercooled water, whose accuracy and efficiency can impact the validity and feasibility of such studies. The underlying molecular mechanisms of these often elusive and computationally expensive processes can be inferred from the evolution of ice-like structures, determined using appropriate structural analysis techniques. We present d-SEAMS, a free and open-source post-processing engine for the analysis of molecular dynamics trajectories, which is specifically able to qualitatively classify ice structures, in both strong confinement and bulk systems. For the first time, recent algorithms for confined ice structure determination have been implemented, along with topological network criteria for bulk ice structure determination. Recognizing the need for customization in structural analysis, d-SEAMS has a unique code architecture, built with `nix`, employing a `YAML`-`Lua` scripting pipeline. The software has been designed to be user-friendly and easy to extend. The engine outputs are compatible with popular graphics software suites, allowing for immediate visual insights into the systems studied. We demonstrate the features of d-SEAMS by using it to analyze nucleation in the bulk regime and for quasi-one and quasi-two-dimensional systems. Structural time evolution and quantitative metrics are determined for heterogenous ice nucleation on a silver-exposed $β$-AgI surface, homogenous ice nucleation, flat monolayer square ice formation and freezing of an ice nanotube.
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