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 postprocessing 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. We also propose and validate a new order parameter for identifying the building blocks of quasi-one-dimensional ice. Recognizing the need for customization in structural analysis, d-SEAMS has a unique code architecture built with nix and employing a YAML-Lua scripting pipeline. The software has been designed to be user-friendly and extensible. 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 heterogeneous ice nucleation on a silver-exposed β-AgI surface, homogeneous ice nucleation, flat monolayer square ice formation, and freezing of an ice nanotube.

中文翻译：

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d-SEAMS：用于分子模拟的递延结构解析分析。

结构分析是成核和过冷水计算研究不可或缺的部分，其准确性和效率会影响此类研究的有效性和可行性。这些冰冷的，易计算的过程的潜在分子机制可以通过使用适当的结构分析技术确定的冰状结构的演化来推断。我们提出了d-SEAMS，这是一种用于分析分子动力学轨迹的免费开源开源后处理引擎，它特别能够对强约束和大体积系统中的冰结构进行定性分类。第一次，用于封闭冰结构确定的最新算法，连同用于大块冰结构确定的拓扑网络标准一起被实施。我们还提出并验证了用于识别准一维冰的构造块的新的顺序参数。d-SEAMS认识到在结构分析中需要自定义的需求，因此具有使用nix构建并采用YAML-Lua脚本编制管道的独特代码架构。该软件已被设计为用户友好和可扩展的。引擎输出与流行的图形软件套件兼容，从而可以立即直观地了解所研究的系统。我们通过使用d-SEAMS来分析整体状态下的成核以及准一维和准二维系统，从而展示了d-SEAMS的功能。确定了结构时间演变和定量指标，以确定暴露于银的β-AgI表面上的非均质冰核化，均质冰核化，平坦的单层正方形冰形成，