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

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.