检索结果-内蒙古大学图书馆

parallel molecular dynamics in a parallelizing SML compiler

IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS 2003年第9期E86D卷 1569-1576页

作者： Scaife, N Hayashi, R Horiguchi, S Grad. School of Information Science JAIST Ishikawa-ken 923-1292 Japan

We have constructed a parallelizing compiler for Standard ML (SML) based upon algorithmic skeletons [3]. We present an implementation of a parallel molecular dynamics (PMD) simulation in order to compare our functional approach with a traditional imperative approach. Although we present performance data, the principal benefits from our approach are in the modularity of the code and the ease of programming. Extant FORTRAN90 code for an O(N-2) algorithm is translated, firstly into imperative SML and then into purely functional SML which is then parallelized. The ease of programming and the performance of the FORTRAN90 and SML code are compared. Modest parallel performance is obtained from the parallel SML but with a much slower sequential execution time compared to the FORTRAN90. We then improve the implementation with a ring topology implementation which gives much closer performance to the FORTRAN90 implementation.

关键词： parallelizing compilers standard ML FORTRAN90 parallel molecular dynamics

来源：评论

学校读者我要写书评

暂无评论

Effect of interface modification on the mechanical behavior of carbon nanotube reinforced composites using parallel molecular dynamics simulations

引用

CMES-COMPUTER MODELING IN ENGINEERING & SCIENCES 2007年第3期22卷 189-202页

作者： Namilae, S. Chandra, U. Srinivasan, A. Chandra, N. Oak Ridge Natl Lab Oak Ridge TN 37831 USA Florida A&M Univ Dept Informat & Comp Sci Tallahassee FL 32307 USA Florida State Univ Dept Comp Sci Tallahassee FL 32306 USA Univ Nebraska Dept Mech Engn Lincoln NE 68588 USA

molecular dynamics (MD) simulations play an important predictive role in understanding the behavior of nanoscale systems. In this paper, parallel MD simulations are used to understand the mechanical behavior of interfaces in CNT based composites. We present an algorithm for parallel implementation of MD simulations of carbon nanotube (CNT) based systems using reactive bond order potentials. We then use that algorithm to model the CNT-polymer interfaces with various levels of interaction as (a) described only by long range Van Der Waals interactions (b) chemically bonded with fixed matrix and (c) chemically bonded with matrix explicitly modeled. It is shown that interface strength based on non bonded interactions is very low (of the order of few MPa) and it can be significantly improved through surface chemical modification of CNTs (to an order of a few GPa). It is further noted that chemical bonding between functionalized nanotube and matrix during processing is essential to obtain good interface strength and hence a better composite.

关键词： carbon nanotube composites interfaces parallel molecular dynamics

来源：评论

学校读者我要写书评

暂无评论

Structure of supercritical fluid krypton at small scattering angle using parallel molecular dynamics simulation

引用

molecular SIMULATION 2000年第4-5期23卷 293-306页

作者： Jakse, N Charpentier, I Inst Math Appl Grenoble Lab Modelisat & Calcul F-38041 Grenoble 9 France Univ Metz Lab Theorie Mat Condensee F-57078 Metz 3 France

We present a parallel algorithm for molecular dynamics involving short-range two- and three-body potentials and the pair-correlation function, g(r). The method is based on a spatial decomposition of the simulation box that takes advantage of a linked-cell list, and allows a load balanced partition of the computations of both the forces and g(r) over the processors. The tests of the program is conducted by evaluating the efficiency for both the thermalization phase and the production phase of the simulation. This method is successfully applied to the calculation of the direct correlation function of fluid krypton at small scattering angle along the T = 297 K supercritical isotherm.

关键词： krypton parallel molecular dynamics linked-cell list three-body potential fluids structure factor

来源：评论

学校读者我要写书评

暂无评论

Investigation of point defect clusters in silicon using parallel molecular dynamics

引用

Journal of Computer-Aided Materials Design 1997年第1期4卷 29-42页

作者： Sinno, Talid Von Gottberg, Friedrich Brown, Robert A. Department of Chemical Engineering Massachusetts Inst. of Technology Cambridge MA 02139 United States

A parallel molecular dynamics algorithm is presented for computing configurations of relatively large defects in crystalline silicon, as modelled by the Stillinger-Weber (SW) three-body interatomic potential. The algorithm is based on a partitioning of physical space among the N processors with atoms migrating freely between the partitions. Implementation on an eight-processor IBM SP2 computer shows the increased efficiency with simulation size expected because of the increased computational load per processor relative to communication overhead. The parallel efficiency reached 70% for 21 952 atoms. Calculations are presented for the thermodynamics of formation of interstitial and vacancy clusters containing up to seven point defects. The clusters were relaxed within a host lattice of about 3000 silicon atoms subjected to periodic boundary conditions. Free energies of formation for temperatures 500 K≤T≤1600 K were computed using thermodynamic integration. Computed equilibrium distributions for these clusters show a shift to the larger species at lower temperatures, as expected. The SW potential predicts greater driving forces for interstitial aggregation than vacancy aggregation across the entire temperature range. Model calculations for a large vacancy cluster are also presented to demonstrate the utility of the algorithm for exploring very large defects in silicon.

关键词： Aggregation parallel molecular dynamics Point defects Silicon

来源：评论

学校读者我要写书评

暂无评论

parallel implementation of molecular dynamics simulation for short-ranged interaction

引用

COMPUTER PHYSICS COMMUNICATIONS 2005年第2期170卷 175-185页

作者： Wu, JS Hsu, YL Lee, YM Natl Chiao Tung Univ Dept Mech Engn Hsinchu 30050 Taiwan

A parallel molecular dynamics simulation method, designed for large-scale problems, employing dynamic spatial domain decomposition for short-ranged molecular interactions is proposed. In this parallel cellular molecular dynamics (PCMD) simulation method, the link-cell data structure is used to reduce the searching time required for forming the cut-off neighbor list as well as for domain decomposition, which utilizes the multi-level graph-partitioning technique. A simple threshold scheme (STS), in which workload imbalance is monitored and compared with some threshold value during the runtime, is proposed to decide the proper time for repartitioning the domain. The simulation code is implemented and tested on the memory-distributed parallel machine, e.g., PC-cluster system. parallel performance is studied using approximately one million L-J atoms in the condensed, vaporized and supercritical states. Results show that fairly good parallel efficiency at 49 processors can be obtained for the condensed and supercritical states (similar to 60%), while it is comparably lower for the vaporized state (-40%). (c) 2005 Elsevier B.V. All rights reserved.

关键词： parallel molecular dynamics short-ranged interaction dynamic domain decomposition parallel efficiency simple threshold scheme

来源：评论

学校读者我要写书评

暂无评论

parallel COMPUTING AT CRS4

引用

INTERNATIONAL JOURNAL OF MODERN PHYSICS C-PHYSICS AND COMPUTERS 1993年第6期4卷 1315-1321页

作者： SCHEININE, AL Parallel Computing Group Center for Advanced Studies Research and Development in Sardinia via Nazario Sauro 10 I-09123 Cagliari Italy

An overview is given of parallel computing work being done at CRS4 (Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna). parallel computation projects include: parallelization of a simulation of the interaction of high energy particles with matter (GEANT), domain decomposition for numerical solution of partial differential equations, seismic migration for oil prospecting, finite-element structural analysis, parallel molecular dynamics, a C++ library for distributed processing of specific functions, and real-time visualization of a computer simulation that runs as distributed processes.

关键词： DOMAIN DECOMPOSITION GEANT SEISMIC MIGRATION parallel molecular dynamics

来源：评论

学校读者我要写书评

暂无评论

Analysis of scalable data-privatization threading algorithms for hybrid MPI/OpenMP parallelization of molecular dynamics

引用

JOURNAL OF SUPERCOMPUTING 2013年第1期66卷 406-430页

作者： Kunaseth, Manaschai Richards, David F. Glosli, James N. Kalia, Rajiv K. Nakano, Aiichiro Vashishta, Priya Univ So Calif Dept Comp Sci Collaboratory Adv Comp & Simulat Los Angeles CA 90089 USA Lawrence Livermore Natl Lab Livermore CA 94550 USA

We propose and analyze threading algorithms for hybrid MPI/OpenMP parallelization of a molecular-dynamics simulation, which are scalable on large multicore clusters. Two data-privatization thread scheduling algorithms via nucleation-growth allocation are introduced: (1) compact-volume allocation scheduling (CVAS);and (2) breadth-first allocation scheduling (BFAS). The algorithms combine fine-grain dynamic load balancing and minimal memory-footprint data privatization threading. We show that the computational costs of CVAS and BFAS are bounded by I similar to(n (5/3) p (-2/3)) and I similar to(n), respectively, for p threads working on n particles on a multicore compute node. Memory consumption per node of both algorithms scales as O(n+n (2/3) p (1/3)), but CVAS has smaller prefactors due to a geometric effect. Based on these analyses, we derive the selection criterion between the two algorithms in terms of the granularity, n/p. We observe that memory consumption is reduced by 75 % for p=16 and n=8,192 compared to a na < ve data privatization, while maintaining thread imbalance below 5 %. We obtain a strong-scaling speedup of 14.4 with 16-way threading on a four quad-core AMD Opteron node. In addition, our MPI/OpenMP code achieves 2.58x and 2.16x speedups over the MPI-only implementation on 32,768 cores of BlueGene/P for 0.84 and 1.68 million particle systems, respectively.

关键词： Hybrid MPI/OpenMP parallelization Thread scheduling Memory optimization Load balancing parallel molecular dynamics

来源：评论

学校读者我要写书评

暂无评论

SIMULATING COMPLEX FLUIDS

引用

molecular SIMULATION 1995年第4-5期14卷 259-274页

作者： ESSELINK, K HILBERS, PAJ KARABORNI, S SIEPMANN, JI SMIT, B AMSTERDAM SHELL RES BV KONINKLIJKE SHELL LAB1030 BN AMSTERDAMNETHERLANDS

In this Article, a review is given on the progress of simulating complex fluids. Two approaches are used to deal with the special requirements of simulations of complex fluids. molecular dynamics on massively parallel computers allow long simulations on very large systems. This makes it possible to simulate the self-assembly of micelles and the solubilization of a droplet of oil. For problems in which dynamics is not essential, it is shown that a novel method, configurational-bias Monte Carlo, can be used to simulate efficiently systems containing chain molecules. The use of this method is illustrated by a calculation of the vapour-liquid curve of an alkane as long as octatetracontane C-48.

关键词： COMPLEX FLUIDS parallel molecular dynamics CONFIGURATIONAL BIAS MONTE CARLO SURFACTANT SELF-ASSEMBLY PHASE EQUILIBRIA

来源：评论

学校读者我要写书评

暂无评论

Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing

引用

parallel COMPUTING 2016年 55卷 17-27页

作者： Stone, John E. Sener, Melih Vandivort, Kirby L. Barragan, Angela Singharoy, Abhishek Teo, Ivan Ribeiro, Joao V. Isralewitz, Barry Liu, Bo Goh, Boon Chong Phillips, James C. MacGregor-Chatwin, Craig Johnson, Matthew P. Kourkoutis, Lena F. Hunter, C. Neil Schulten, Klaus Univ Illinois Beckman Inst 405 N Mathews Ave Urbana IL 61801 USA Univ Illinois Dept Phys 1110 W Green St Urbana IL 61801 USA Cornell Univ Sch Appl & Engn Phys 271 Clark Hall Ithaca NY 14853 USA Kavli Inst Cornell Nanoscale Sci 420 Phys Sci Bldg Ithaca NY 14853 USA Univ Sheffield Dept Mol Biol & Biotechnol Western Bank Sheffield S10 2TN S Yorkshire England

The cellular process responsible for providing energy for most life on Earth, namely, photosynthetic light-harvesting, requires the cooperation of hundreds of proteins across an organelle, involving length and time scales spanning several orders of magnitude over quantum and classical regimes. Simulation and visualization of this fundamental energy conversion process pose many unique methodological and computational challenges. We present, in two accompanying movies, light-harvesting in the photosynthetic apparatus found in purple bacteria, the so-called chromatophore. The movies are the culmination of three decades of modeling efforts, featuring the collaboration of theoretical, experimental, and computational scientists. We describe the techniques that were used to build, simulate, analyze, and visualize the structures shown in the movies, and we highlight cases where scientific needs spurred the development of new parallel algorithms that efficiently harness GPU accelerators and petascale computers. (C) 2015 Elsevier B.V. All rights reserved.

关键词： Photosynthesis parallel molecular dynamics parallel ray tracing GPU computing

来源：评论

学校读者我要写书评

暂无评论

ESPResSo - an extensible simulation package for research on soft matter systems

引用

COMPUTER PHYSICS COMMUNICATIONS 2006年第9期174卷 704-727页

作者： Limbach, HJ Arnold, A Mann, BA Holm, C Max Planck Inst Polymer Res D-55128 Mainz Germany Goethe Univ Frankfurt FIAS D-60438 Frankfurt Germany

We describe a new program package that is designed to perform numerical molecular dynamics (MD) and Monte Carlo (MC) simulations for a broad class of soft matter systems in a parallel computing environment. Our main concept in developing ESPResSo was to provide a user friendly and fast simulation tool which serves at the same time as a research platform capable of rapidly incorporating the latest algorithmic developments in the field of soft matter sciences. A particular strength of ESPResSo is its efficient treatment of long range interactions for various geometries using sophisticated algorithms like (PM)-M-3, MMM2D, MMM1D and ELC. It is already equipped with a broad variety of interaction potentials, thermostats, and ensemble integrators;it offers the usage of constraints, masses and rotational degrees of freedom;it allows to move between different ensembles on-the-fly. An efficient MPI parallelization allows the usage of multi-processor architectures. Strict usage of ANSI-C for the core functions and a Tcl-script driven user interface makes ESPResSo platform independent. This also ensures easily modifiable interfaces to communicate with other MD/MC Packages, real-time visualization and other graphic programs. We tried to maintain a clear program structure to keep ESPResSo extensible for future enhancements and additions. ESPResSo is implemented as an open source project with the goal to stimulate researchers to contribute to the package. (C) 2005 Elsevier B.V. All rights reserved.

关键词： computer simulation parallel molecular dynamics benchmarks

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：