LAMMPS lb/fluid fix version 2: Improved hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid

Denniston, Colin; Afrasiabian, Navid; Cole-André, M.G.; Mackay, F. E.; Ollila, Santtu T. T.; Whitehead, Tyson

doi:10.1016/j.cpc.2022.108318

Cited by 5 publications

(2 citation statements)

References 38 publications

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“…It was designed to efficiently run on parallel computers and to be easy to extend and modify. For simulation, it can be viscosity, diffusion coefficient, energy, radial distribution function, melting and solidification of spherical or ellipsoidal particles (https://docs.lammps.org/ Manual.html) (Plimpton 1995;Denniston & Navid 2022). The model parameters are set as follows: SiC and SiO atoms were uniformly scattered with an initial spacing of 2 Å in a simulation box sized 20 × 20 × 20 Å 3 with periodic boundaries.…”

Section: Models and Methodsmentioning

confidence: 99%

Dust Condensation of SiC, SiO in Asymptotic Giant Branch Stellar Winds-SiC Spectrum

Wu,

Zhu,

Lü

et al. 2024

Res. Astron. Astrophys.

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We have chosen the Large Scale Atomic/Molecular Massively ParallelSimulator (LAMMPS) code to calculate the coalescence of silicon carbide (SiC), siliconoxide dust (SiO) in the AGB stellar wind. LAMMPS is a classical molecular dynamics(MD) simulation code. At the same time, we consider the effect of temperature on the evo lution of molecular dynamics. We also calculated the temperature change of non-sphericalSiC, SiO dust coalescence. The condensation temperature range of SiC dust in the AGBstellar wind is [300-500]k and [900-1100]k for SiO. Finally, the infrared spectrum of SiCwas calculated using Gaussian 16 software. The 77SiC, 70Si3C3, and 121Si3C3 modelshave clearly characteristic peaks of infrared spectra responding at 5, 8.6, 11.3, 15, 19, and37 µm.

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Section: Models and Methodsmentioning

confidence: 99%

Dust Condensation of SiC, SiO in Asymptotic Giant Branch Stellar Winds-SiC Spectrum

Wu,

Zhu,

Lü

et al. 2024

Res. Astron. Astrophys.

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“…The simulations used the open-source Molecular Dynamics software LAMMPS . For the fluid, we use a fluctuating Lattice–Boltzmann model (LB fluid) implemented in LAMMPS. − This algorithm solves the discrete Boltzmann equation on a rectangular mesh ∂ normalt f i + e i α ∂ α f i = prefix− 1 τ ( f i − f i eq ) + W i where f i is the discrete fluid distribution function (particle population), and e i α is the α component of the corresponding velocity by which the distribution f i travels to the neighboring sites. The first term on the right-hand side is the Bhatnagar–Gross–Krook (BGK) approximation of the Boltzmann collision operator, where f i eq is the equilibrium distribution function and τ is the relaxation time.…”

Section: Methodsmentioning

confidence: 99%

Enhanced Pulley Effect for Translocation: The Interplay of Electrostatic and Hydrodynamic Forces

2023

Self Cite

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Solid-state nanopore sensors remain a promising solution to the rising global demand for genome sequencing. These single-molecule sensing technologies require single-file translocation for high resolution and accurate detection. In a previous publication, we discovered a hairpin unraveling mechanism, namely, the pulley effect, in a pressure-driven translocation system. In this paper, we further investigate the pulley effect in the presence of pressure-driven fluid flow and an opposing force provided by an electrostatic field as an approach to increase single-file capture probability. A hydrodynamic flow is used to move the polymer forward, and two oppositely charged electrostatic square loops are used to create an opposing force. By optimizing the balance between forces, we show that the single-file capture can be amplified from about 50% to almost 95%. The force location, force strength, and flow rate are used as the optimizing variables.

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Implementation of a ternary lattice Boltzmann model in LAMMPS

Arumugam Kumar,

Andrews,

Schiller

2024

Computer Physics Communications

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LAMMPS lb/fluid fix version 2: Improved hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid

Cited by 5 publications

References 38 publications

Dust Condensation of SiC, SiO in Asymptotic Giant Branch Stellar Winds-SiC Spectrum

Dust Condensation of SiC, SiO in Asymptotic Giant Branch Stellar Winds-SiC Spectrum

Enhanced Pulley Effect for Translocation: The Interplay of Electrostatic and Hydrodynamic Forces

Implementation of a ternary lattice Boltzmann model in LAMMPS

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