d‑SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations
journal contributionposted on 27.03.2020, 11:03 by Rohit Goswami, Amrita Goswami, Jayant K. Singh
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.
Read the peer-reviewed publication
silver-exposed β- AgI surfaceopen-source postprocessing engineStructural time evolutiond-SEAMSice structure determinationtopological network criteriabulk ice structure determinationmonolayer square ice formationice nucleationYAML-Lua scripting pipelineMolecular Simulations Structural analysesgraphics software suitesanalysis