Pothos: A Python Package for Polymer Chain Orientation and Microstructure Evolution Monitoring.

IF 5.7 1区化学 Q2 CHEMISTRY, PHYSICAL

Journal of Chemical Theory and Computation Pub Date : 2024-12-23 DOI:10.1021/acs.jctc.4c01216

Thomas J Barrett, Marilyn L Minus

引用次数: 0

Abstract

In the pursuit of informing experimental techniques with in silico optimizations, we propose a pip deployable Python package, pothos, to easily determine polymer crystallites within molecular dynamic melts and the chain orientation parameters of atomistic and coarse-grained simulations. The package supports the commonly used ⟨P₂⟩, ⟨P₄⟩, and ⟨P₆⟩ order parameters based on the chain chord vector and utilizes a modified DBSCAN algorithm to determine crystalline regions. The results of analysis are written to text and LAMMPS dump files for visualization and analysis.

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来源期刊

Journal of Chemical Theory and Computation 化学-物理：原子、分子和化学物理

CiteScore

9.90

自引率

16.40%

发文量

568

审稿时长

1 months

期刊介绍： The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.