@article{Goswami2020,
author = {Goswami, Rohit and Goswami, Amrita and Singh, Jayant Kumar},
title = {d-SEAMS: Deferred Structural Elucidation Analysis for
Molecular Simulations},
journal = {Journal of Chemical Information and Modeling},
year = {2020},
month = {3},
day = {20},
publisher = {American Chemical Society},
abstract = {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. We also propose and
validate a new order parameter for identifying the building
blocks of quasi-two-dimensional ice. 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 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 heterogenous ice
nucleation on a silver-exposed b-AgI surface, homogenous ice
nucleation, flat monolayer square ice formation and freezing
of an ice nanotube.},
issn = {1549-9596},
doi = {10.1021/acs.jcim.0c00031},
archivePrefix = {arXiv},
eprint = {1909.09830},
eprinttype = {arxiv},
keywords = {journal, selected},
}