Massively parallel dual control volume grand canonical molecular dynamics with LADERA I. Gradient driven diffusion in Lennard-Jones fluids

1998 ◽  
Vol 94 (4) ◽  
pp. 659-671 ◽  
Author(s):  
GRANT S. HEFFELFINGER ◽  
DAVID M. FORD
Keyword(s):  
Molecular Dynamics ◽  
Control Volume ◽  
Massively Parallel ◽  
Dual Control ◽  
Lennard Jones ◽  
Grand Canonical

Molecular Dynamics Computer Simulations of Diffusion in Porous Silicates

1994 ◽  
Vol 366 ◽  
Author(s):  
Grant S. Heffelfinger ◽  
Phillip I. Pohl ◽  
Laura J. D. Frink
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Chemical Potential ◽  
Control Volume ◽  
Dual Control ◽  
Cylindrical Pore ◽  
Knudsen Effect ◽  
State Pressure ◽  
Molecular Sieving ◽  
Grand Canonical

ABSTRACTIn this work a newly developed dual control volume grand canonical molecular dynamics technique simulates the diffusion of gas in a cylindrical pore. This allows spatial variation of chemical potential and hence an accurate simulation of steady state pressure driven diffusion. The molecular sieving nature of imicroporous imogolite models and the Knudsen effect are discussed and compared with experimental data.

Gradient-Driven Diffusion Using Dual Control Volume Grand Canonical Molecular Dynamics (DCV-GCMD)

1995 ◽  
Vol 408 ◽  
Author(s):  
Frank Van Swol ◽  
Grant S. Heffelfinger
Keyword(s):  
Molecular Dynamics ◽  
Chemical Potential ◽  
Control Volume ◽  
Simulation Method ◽  
Steady State Mode ◽  
Transient Phenomena ◽  
Insertion And Deletion ◽  
Separate Control ◽  
Control Volumes ◽  
Grand Canonical

AbstractRecently we developed a new nonequilibrium molecular simulation method [1] that allows the direct study of interdiffusion in multicomponent mixtures. The method combines stochastic insertion and deletion moves characteristic of grand canonical (GC) simulations with molecular dynamics (MD) to control the chemical potential μi of a species i. Restricting the insertions and deletions to two separate control volumes (CV's) one can apply different μ's in distinct locations, and thus create chemical potential gradients. DCV-GCMD can be used to study transient phenomena such as the filling of micropores or used in steady-state mode to determine the diffusion coefficients in multicomponent fluid mixtures. We report on the effects of molecular interactions and demonstrate how in a sufficiently nonideal ternary mixture this can lead to up-hill or reverse diffusion. In addition we introduce a novel extension of DCV-GCMD that is specifically designed for the study of gradient-driven diffusion of molecules that are simply too large to be inserted and deleted.

scholarly journals TRILLION-ATOM MOLECULAR DYNAMICS BECOMES A REALITY

2008 ◽  
Vol 19 (09) ◽  
pp. 1315-1319 ◽  
Author(s):  
TIMOTHY C. GERMANN ◽  
KAI KADAU
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Shear Instability ◽  
Dynamics Simulation ◽  
Massively Parallel ◽  
Lennard Jones ◽  
Simple Cubic ◽  
Simple Cubic Lattice ◽  
Future Potential ◽  
Large Scale Simulations

By utilizing the molecular dynamics code SPaSM on Livermore's BlueGene/L architecture, consisting of 212 992 IBM PowerPC440 700 MHz processors, a molecular dynamics simulation was run with one trillion atoms. To demonstrate the practicality and future potential of such ultra large-scale simulations, the onset of the mechanical shear instability occurring in a system of Lennard-Jones particles arranged in a simple cubic lattice was simulated. The evolution of the instability was analyzed on-the-fly using the in-house developed massively parallel graphical object-rendering code MD_render.

Massively Parallel Molecular Dynamics Simulation of Gas Permeation across Molecular Sieving Porous Membranes

1996 ◽  
Vol 464 ◽  
Author(s):  
Phillip I. Pohl ◽  
Grant S. Heffelfinger
Keyword(s):  
Molecular Dynamics ◽  
Chemical Potential ◽  
Control Volume ◽  
Sol Gel ◽  
Gas Permeation ◽  
Dynamics Simulation ◽  
Massively Parallel ◽  
Solid Models ◽  
Parallel Supercomputers ◽  
Molecular Sieving

AbstractIn this work we simulate the diffusion of gases in a microporous solid models using a newly developed dual control volume grand canonical molecular dynamics technique. This allows spatial variation of chemical potential and hence an accurate simulation of steady-state pressure driven diffusion. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica from sol-gel methods. Massively parallel supercomputers allow a quick and insightful study of these microporous structures.

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

2019 ◽  
Author(s):  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Étienne Derat ◽  
Jean-Philip Piquemal
Keyword(s):  
Molecular Dynamics ◽  
Parallel Implementation ◽  
Steered Molecular Dynamics ◽  
Massively Parallel

This paper is dedicated to the massively parallel implementation of Steered Molecular Dynamics in the Tinker-HP softwtare. It allows for direct comparisons of polarizable and non-polarizable simulations of realistic systems.

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