PAPRECA: A parallel hybrid off-lattice kinetic MonteCarlo/molecular dynamics simulator

Stavros Ntioudis; James P. Ewen; Daniele Dini; C. Heath Turner

doi:10.21105/joss.06714

PAPRECA: A parallel hybrid off-lattice kinetic MonteCarlo/molecular dynamics simulator

Stavros Ntioudis, James P. Ewen, Daniele Dini, C. Heath Turner

Department of Mechanical Engineering

Research output: Contribution to journal › Article › peer-review

Abstract

Kinetic Monte Carlo (kMC) is an atomistic and stochastic simulation technique that captures the temporal evolution of various systems in materials science, chemistry, physics, biology, and engineering. Several open-source kMC packages are currently distributed online. Nevertheless, such implementations are typically lattice-based and are mostly designed to study ordered, crystalline materials. In this work, we present PArallel PREdefined CAtalog (PAPRECA), an easy-to-use and completely lattice-free open-source kMC software suitable for simulations on
amorphous materials or systems characterized by a low degree of crystallinity. PAPRECA is a parallel C++ software using the Message Passing Interface (MPI) protocol and coupled with the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) (Thompson et al., 2022) to enable pure kMC runs as well as hybrid kMC/Molecular Dynamics (MD) simulations.

Original language	English
Number of pages	6
Journal	The Journal of Open Source Software
Volume	9
Issue number	98
DOIs	https://doi.org/10.21105/joss.06714
Publication status	Published - 13 Jun 2024

Acknowledgements

S.N., J.P.E., and D.D. thank Shell and the Engineering and Physical Sciences Research Council, United Kingdom (EPSRC) for funding via the InFUSE Prosperity Partnership (EP/V038044/1). J.P.E. acknowledges the support of the Royal Academy of Engineering (RAEng) for support through their Research Fellowship scheme. D.D. acknowledges a Shell/RAEng Research Chair in Complex Engineering Interfaces. We acknowledge computational resources and support provided by the Imperial College Research Computing Service.

Keywords

Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)
Message Passing Interface (MPI)
Computational Materials Science
Off-lattice kinetic Monte Carlo
Molecular Dynamics

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Cite this

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title = "PAPRECA: A parallel hybrid off-lattice kinetic MonteCarlo/molecular dynamics simulator",

abstract = "Kinetic Monte Carlo (kMC) is an atomistic and stochastic simulation technique that captures the temporal evolution of various systems in materials science, chemistry, physics, biology, and engineering. Several open-source kMC packages are currently distributed online. Nevertheless, such implementations are typically lattice-based and are mostly designed to study ordered, crystalline materials. In this work, we present PArallel PREdefined CAtalog (PAPRECA), an easy-to-use and completely lattice-free open-source kMC software suitable for simulations on amorphous materials or systems characterized by a low degree of crystallinity. PAPRECA is a parallel C++ software using the Message Passing Interface (MPI) protocol and coupled with the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) (Thompson et al., 2022) to enable pure kMC runs as well as hybrid kMC/Molecular Dynamics (MD) simulations.",

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PAPRECA: A parallel hybrid off-lattice kinetic MonteCarlo/molecular dynamics simulator

Abstract

Acknowledgements

Keywords

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