Toward Large Scale Parallelization for Molecular Dynamics of Small Chemical Systems: A Combined Parallel Tempering and Domain Decomposition Approach

2008 ◽  
Vol 4 (10) ◽  
pp. 1570-1575 ◽  
Author(s):  
Henk A. Slim ◽  
Mark R. Wilson
Keyword(s):  
Molecular Dynamics ◽  
Domain Decomposition ◽  
Large Scale ◽  
Parallel Tempering ◽  
Decomposition Approach ◽  
Chemical Systems ◽  
Small Chemical

A Parallel Domain Decomposition Boundary Element Method Technique for Large-Scale Transient Heat Conduction Problems

2004 ◽  
Author(s):  
Kevin Erhart ◽  
Eduardo Divo ◽  
Alain J. Kassab
Keyword(s):  
Heat Conduction ◽  
Domain Decomposition ◽  
Large Scale ◽  
Parallel Implementation ◽  
Transient Heat Conduction ◽  
Initial Guess ◽  
Decomposition Approach ◽  
Acceleration Methods ◽  
Decomposition Procedure ◽  
Original Domain

In this paper, we develop a parallel domain decomposition Laplace transform BEM algorithm for the solution of transient heat conduction problems. The original domain is decomposed into a number of sub-domains, a procedure is described to provide a good initial guess for the domain interface temperatures, and an iteration is carried out to satisfy continuity of temperature and heat flux at the domain interfaces. The decomposition procedure significantly reduces the size of any single problem to be tackled by the BEM, significantly reduces the overall storage and computational burden, and renders the application of the BEM to modeling large transient conduction problem feasible on modest computational platforms. The procedure is readily implemented in parallel and applicable to 3D problems. Moreover, as the approach described herein readily allows adaptation and integration of traditional BEM codes, it is expected that the domain decomposition approach coupled to parallel implementation should prove very competitive to alternatives proposed in the literature such as fast multipole acceleration methods that require a complete re-write of traditional BEM codes.

scholarly journals Scalable generation of large-scale unstructured meshes by a novel domain decomposition approach

2018 ◽  
Vol 121 ◽  
pp. 131-146 ◽  
Author(s):  
Jianjun Chen ◽  
Zhoufang Xiao ◽  
Yao Zheng ◽  
Jianfeng Zou ◽  
Dawei Zhao ◽  
...  
Keyword(s):  
Domain Decomposition ◽  
Large Scale ◽  
Unstructured Meshes ◽  
Decomposition Approach

Domain Decomposition for 3D Boundary Elements in Non-Linear Heat Conduction

2003 ◽  
Author(s):  
Eduardo Divo ◽  
Alain J. Kassab ◽  
Franklin Rodriguez
Keyword(s):  
Heat Conduction ◽  
Domain Decomposition ◽  
Parallel Computation ◽  
Large Scale ◽  
Initial Guess ◽  
Iteration Algorithm ◽  
Decomposition Approach ◽  
Linear Heat ◽  
Non Linear ◽  
Coarse Surface

In this paper, we develop a domain decomposition, or the artificial sub-sectioning technique, along with a region-by-region iteration algorithm particularly tailored for parallel computation to address storage and memory issues arising from large-scale boundary element models. A coarse surface grid solution coupled with an efficient physically-based procedure provides an effective initial guess for a fine surface grid model. The process converges very efficiently offering substantial savings in memory. We discuss the implementation of the iterative domain decomposition approach for parallel computation on a modest Windows XP Pentium P4 PC-cluster running under MPI. Results from 3-D BEM heat conduction models including models of upwards of 85,000 nodes demonstrate that the BEM can practically be used to solve large-scale linear- and non-linear heat conduction problems using this algorithm.

A finite-element-based domain-decomposition approach for plane wave 3D electromagnetic modeling

Geophysics ◽  
2014 ◽  
Vol 79 (6) ◽  
pp. E255-E268 ◽  
Author(s):  
Zhengyong Ren ◽  
Thomas Kalscheuer ◽  
Stewart Greenhalgh ◽  
Hansruedi Maurer
Keyword(s):  
Finite Element ◽  
Electric Field ◽  
Domain Decomposition ◽  
Lagrange Multipliers ◽  
Large Scale ◽  
Unstructured Meshes ◽  
Interface Problem ◽  
Electromagnetic Modeling ◽  
Heterogeneous Distribution ◽  
Decomposition Approach

We developed a novel parallel domain-decomposition approach for 3D large-scale electromagnetic induction modeling in the earth. We used the edge-based finite-element method and unstructured meshes. Unstructured meshes were divided into sets of nonoverlapping subdomains. We used the curl-curl electric field equation to carry out the analysis. In each subdomain, the electric field was discretized by first-order vector shape functions along the edges of tetrahedral elements. The tangential components of the magnetic field on the interfaces of the subdomains were defined as a set of Lagrange multipliers. The unknown Lagrange multipliers were solved from an interface problem defined on the interfaces of the subdomains. With the availability of the Lagrange multipliers, the electric field values in each subdomain were solved independently. Three synthetic examples were evaluated to verify our code. Excellent agreement with previously published solutions was obtained. Synthetic examples revealed that our domain decomposition technique is scalable with respect to the number of subdomains and robust with regard to frequency and the heterogeneous distribution of material parameters, i.e., electric conductivity, electric permittivity, and magnetic permeability.

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Large Scale ◽  
Methane Combustion ◽  
Combustion Method ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Computational Time ◽  
Combustion Mechanism ◽  
Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

Evolution of Metastable Structures in Bimetallic Catalysts from Microscopy and Machine-Learning Molecular Dynamics

2020 ◽  
Author(s):  
Jin Soo Lim ◽  
Jonathan Vandermause ◽  
Matthijs A. van Spronsen ◽  
Albert Musaelian ◽  
Christopher R. O’Connor ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Complete Characterization ◽  
Layer By Layer ◽  
Surface Restructuring ◽  
Metastable Structures ◽  
Mechanistic Investigation ◽  
Underlying Mechanisms

Restructuring of interface plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of the long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. Encapsulation of Pd by Ag always precedes layer-by-layer dissolution of Pd, resulting in significant Ag migration out of the surface and extensive vacancy pits. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. The underlying mechanisms are uncovered by performing fast and large-scale machine-learning molecular dynamics, followed by our newly developed method for complete characterization of atomic surface restructuring events. Our approach is broadly applicable to other multimetallic systems of interest and enables the previously impractical mechanistic investigation of restructuring dynamics.

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