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Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir.通过与内部粒子库耦合实现自适应分辨率分子动力学模拟。
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使用光滑耗散粒子动力学的混合分子-连续介质模拟

Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics.

作者信息

Petsev Nikolai D, Leal L Gary, Shell M Scott

机构信息

Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080, USA.

出版信息

J Chem Phys. 2015 Jan 28;142(4):044101. doi: 10.1063/1.4905720.

DOI:10.1063/1.4905720
PMID:25637963
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5848718/
Abstract

We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.

摘要

我们提出了一种新的多尺度模拟方法,用于将通过分子动力学(MD)模拟的具有原子细节的区域与从平滑耗散粒子动力学(SDPD)获得的波动纳维 - 斯托克斯方程的数值解相耦合。在这种方法中,由于整个系统内分辨率的差异会出现化学势梯度,通过在两个域之间的缓冲区域内引入成对的热力学力来减小这种梯度,在该缓冲区域中粒子从MD类型转变为SDPD类型。当与多分辨率SDPD方法(如Kulkarni等人 [《化学物理杂志》138, 234105 (2013)] 提出的方法)相结合时,该方法能够将原子模型系统地耦合到以具有不同分辨率的SDPD流体建模的任意粗粒度连续域。我们通过证明该技术能正确再现简单 Lennard-Jones 流体在整个模拟域的热力学性质来测试此技术。此外,我们通过将其应用于剪切流启动的模拟来证明该方法也适用于非平衡问题。该方法的稳健性通过两种不同的流动场景得以说明,在这两种场景中,剪切力分别沿平行和垂直于分隔连续域和原子域的界面的方向作用。在这两种情况下,我们都获得了正确的瞬态速度分布。我们还进行了三尺度剪切流模拟,其中除了一个MD域外还包括两个具有不同分辨率的SDPD区域,说明了三尺度耦合的可行性。