Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques

Aktulga, Hasan Metin; Fogarty, Joseph; Pandit, Sagar A.; Grama, Ananth

doi:10.1016/j.parco.2011.08.005

Cited by 820 publications

(541 citation statements)

References 28 publications

(45 reference statements)

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“…The 2005 functional form developed for RDX is the current version of ReaxFF distributed by the van Duin group (commonly referred to as 'standalone ReaxFF'), as well as integrated in the open-source LAMMPS code, 9 supported through Nanohub, (http://www.nanohub.org) and available through the PuReMD (Purdue Reactive Molecular Dynamics) code. [10][11][12] Apart from these open-source distributions, the ReaxFF method is also integrated in ADF 13 …”

Section: Development Of the Reaxff Methods History Of Reaxff Developmentmentioning

confidence: 99%

The ReaxFF reactive force-field: development, applications and future directions

et al. 2016

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The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFF method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. This article provides an overview of the development, application, and future directions of the ReaxFF method. INTRODUCTIONAtomistic-scale computational techniques provide a powerful means for exploring, developing and optimizing promising properties of novel materials. Simulation methods based on quantum mechanics (QM) have grown in popularity over recent decades due to the development of user-friendly software packages making QM level calculations widely accessible. Such availability has proved particularly relevant to material design, where QM frequently serves as a theoretical guide and screening tool. Unfortunately, the computational cost inherent to QM level calculations severely limits simulation scales. This limitation often excludes QM methods from considering the dynamic evolution of a system, thus hampering our theoretical understanding of key factors affecting the overall behaviour of a material. To alleviate this issue, QM structure and energy data are used to train empirical force fields that require significantly fewer computational resources, thereby enabling simulations to better describe dynamic processes. Such empirical methods, including reactive force-field (ReaxFF), 1 trade accuracy for lower computational expense, making it possible to reach simulation scales that are orders of magnitude beyond what is tractable for QM.Atomistic force-field methods utilise empirically determined interatomic potentials to calculate system energy as a function of atomic positions. Classical approximations are well suited for nonreactive interactions, such as angle-strain represented by harmonic potentials, dispersion represented by van der Waals potentials and Coulombic interactions represented by various polarisation schemes. However, such descriptions are inadequate for modelling changes in atom connectivity (i.e., for modelling chemical reactions as bonds break and form). This motivates the

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Section: Development Of the Reaxff Methods History Of Reaxff Developmentmentioning

confidence: 99%

The ReaxFF reactive force-field: development, applications and future directions

et al. 2016

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“…MD simulations were performed using LAMMPS 25,26 with the Velocity-Verlet algorithm at a 0.35 fs timestep. The atomic forces are computed using ReaxFF 27, 28 .…”

Section: Simulation Methodologymentioning

confidence: 99%

Reactive Molecular Dynamics Simulations of the Silanization of Silica Substrates by Methoxysilanes and Hydroxysilanes

2016

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Abstract:We perform reactive molecular dynamics simulations of monolayer formation by silanes on hydroxylated silica substrates. Solutions composed of alkylmethoxysilanes or alkylhydroxysilanes in hexane are placed in contact with a hydroxylated silica surface and simulated using a reactive force field (ReaxFF). In particular, we have modeled the deposition of butyl-, octyl-, and dodecyltrimethoxysilane to observe the dependence of alkylsilyl chain length on monolayer formation. We additionally modeled silanization using dodecyltrihydroxysilane, which allows for the comparison of two grafting mechanisms of alkoxysilanes: (1) direct condensation of alkoxysilane with surface bound silanols, and (2) a two-step hydrolysiscondensation mechanism. In order to emulate an infinite reservoir of reactive solution far away from the substrate, we have developed a method in which new precursor molecules are periodically added to a region of the simulation box located away from the surface. It is determined that the contact angle of alkyl tails bound to the surface is dependent on their grafting density. During the early stages of grafting alkoxy-and hydroxysilanes to the substrate, a preference is shown for silanes to condense with silanols further from the substrate surface, and also nearby to neighboring surface-bound silanols. The kinetics of silica silanization by hydroxysilanes were observed to be much faster than methoxysilanes. However, the as-deposited hydroxysilane monolayers show similar morphological characteristics as those formed by methoxysilanes.

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“…The classical MD code was LAMMPS 61,62 , with the ReaxFF potential 63 . The runs were carried out for 6 ns with time step of 0.1 fs.…”

Section: Methodsmentioning

confidence: 99%

Dirac Cones in two-dimensional conjugated polymer networks

et al. 2014

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Linear electronic band dispersion and the associated Dirac physics has to date been limited to special-case materials, notably graphene and the surfaces of three-dimensional (3D) topological insulators. Here we report that it is possible to create two-dimensional fully conjugated polymer networks with corresponding conical valence and conduction bands and linear energy dispersion at the Fermi level. This is possible for a wide range of polymer types and connectors, resulting in a versatile new family of experimentally realisable materials with unique tuneable electronic properties. We demonstrate their stability on substrates and possibilities for doping and Dirac cone distortion. Notably, the cones can be maintained in 3D-layered crystals. Resembling covalent organic frameworks, these materials represent a potentially exciting new field combining the unique Dirac physics of graphene with the structural flexibility and design opportunities of organic-conjugated polymer chemistry.

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Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques

Abstract: openAccessArticle: FalsePage Range: 245-245doi: 10.1016/j.parco.2011.08.005Harvest Date: 2016-01-12 15:10:37issueName:cover date: 2012-04-01pubType

Cited by 820 publications

References 28 publications

The ReaxFF reactive force-field: development, applications and future directions

The ReaxFF reactive force-field: development, applications and future directions

Reactive Molecular Dynamics Simulations of the Silanization of Silica Substrates by Methoxysilanes and Hydroxysilanes

Dirac Cones in two-dimensional conjugated polymer networks

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