A Topology-Preserving Python Framework for Reliable Initialization of Star and Cyclic Polymer Architectures in Molecular Dynamics (LAMMPS) Simulations
Accurate initialization of polymer architectures remains a critical yet underappreciated determinant of reliability in molecular dynamics simulations of soft matter systems. Errors in coordinate generation and connectivity assignment frequently introduce artificial stresses, topological inconsistencies, and numerical instabilities that propagate throughout simulation trajectories. Here, we present a topology-preserving Python framework for generating star and cyclic polymer architectures with deterministic bond connectivity, exact ring closure, excluded volume enforcement, and spatial-hashing-based overlap detection. The algorithm produces LAMMPS-compatible data files under atom style full without reliance on third-party libraries. We demonstrate that the generated structures exhibit mechanical stability at initialization, suppressed artificial energy spikes, and consistent thermodynamic behavior during equilibration. Benchmark comparisons against naive random placement schemes reveal significant reductions in overlap-induced instabilities and improved reproducibility of structural and dynamical observables. The presented framework establishes initialization as a controlled physical boundary condition rather than a stochastic preprocessing step, thereby enhancing the reliability and reproducibility of polymer molecular dynamics simulations.