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LUNAR: Automated Input Generation and Analysis for Reactive LAMMPS Simulations.

Josh Kemppainen1, Jacob R Gissinger2, S Gowtham1

  • 1Michigan Technological University, Houghton, Michigan 49931, United States.

Journal of Chemical Information and Modeling
|June 27, 2024
PubMed
Summary
This summary is machine-generated.

The LUNAR toolkit simplifies creating molecular models for LAMMPS molecular dynamics (MD) simulations. This automation accelerates materials design by handling atom types, bonds, and charges, enabling efficient computational materials development.

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Area of Science:

  • Materials Science
  • Computational Chemistry
  • Polymer Science

Background:

  • Generating simulation-ready molecular models for LAMMPS molecular dynamics (MD) is complex and hinders materials design.
  • Current methods often require manual assignment of atom types, bonded interactions, charges, and simulation parameters.

Purpose of the Study:

  • To introduce LUNAR, a novel toolkit for efficiently building molecular systems for LAMMPS simulations.
  • To automate the generation of molecular models, including atom typing, bond generation, and charge assignment.
  • To facilitate the incorporation of chemical reactivity and advanced postprocessing capabilities.

Main Methods:

  • LUNAR automatically assigns atom types, generates bonded interactions, and assigns charges.
  • It provides methods for generating large molecular systems and incorporates the REACTER protocol for chemical reactivity.
  • Postprocessing includes free volume calculations, cure characterization, and property predictions from MD outputs.

Main Results:

  • LUNAR was validated by building and simulating pure epoxy and cyanate ester polymer systems.
  • Predicted structures and properties were compared to benchmark values, including experimental data.
  • The toolkit successfully generated simulation-ready models and provided insightful postprocessing analyses.

Conclusions:

  • LUNAR significantly simplifies and accelerates the creation of molecular models for LAMMPS MD simulations.
  • It supports computationally driven materials development within Integrated Computational Materials Engineering (ICME) and Materials Genome Initiative (MGI) frameworks.
  • The toolkit is freely available and accessible via multiple interfaces, promoting wider adoption in materials research.