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IEEE International Conference on computational Science and engineering, CSE

作者： Michael Burger Christian Bischof Christian Schröppel Jens Wackerfuß Graduate School of Computational Engineering TU Darmstadt Darmstadt Institute for Scientific Computing TU Darmstadt Darmstadt Institute for Structural Analysis University of Kassel Kassel Universitat Kassel Kassel Hessen DE

In this paper we present an extended and improved algorithm based on our previous work for simulating the mechanical behavior of super carbon nanotubes (SCNTs). On previously considered level 0 SCNTs the performance is improved by a factor higher than 2 when running in serial and a factor up to 4.4 when running in parallel on a 16 core SMP system. A new pre-processing step exploiting structural symmetry and an improved proximity-aware Matrix-Vector-Multiplication routine make this performance improvement possible while only consuming few additional memory. We also extend our symmetry considerations to SCNTs of order 1 and give an insight into the graph algebra based construction of these structures. Experimental results show that our new solver outperforms a compressed-row-storage based reference solver, on order 0 and 1 SCNTs, with and without deformations, while requiring only half the memory.

关键词： Carbon nanotubes mathematical model Junctions Electron tubes Algebra Symmetric matrices Indexes

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Madness: A multiresolution, adaptive numerical environment for scientific simulation

Madness: A multiresolution, adaptive numerical environment f...

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作者： Harrison, Robert J. Beylkin, Gregory Bischoff, Florian A. Calvin, Justus A. Fann, George I. Fosso-Tande, Jacob Galindo, Diego Hammond, Jeff R. Hartman-Baker, Rebecca Hill, Judith C. Jia, Jun Kottmann, Jakob S. Ou, M-J. Yvonne Pei, Junchen Ratcliff, Laura E. Reuter, Matthew G. Richie-Halford, Adam C. Romero, Nichols A. Sekino, Hideo Shelton, William A. Sundahl, Bryan E. Thornton, W. Scott Valeev, Edward F. Vázquez-Mayagoitia, Álvaro Vence, Nicholas Yanai, Takeshi Yokoi, Yukina Stony Brook University Stony BrookNY11794 United States University of Colorado at Boulder BoulderCO80309 United States Institut für Chemie Humboldt-Universität Zu Berlin Unter den Linden 6 Berlin10099 Germany Department of Chemistry Virginia Tech. BlacksburgVA24061 United States Oak Ridge National Laboratory Oak RidgeTN37831 United States Department of Chemistry and Biochemistry Florida State University TallahasseeFL32306 United States Parallel Computing Lab Intel Corporation PortlandOR97219 United States National Energy Research Scientific Computing Center Lawrence Berkeley National Laboratory BerkeleyCA94720 United States LinkedIn Mountain ViewCA94043 United States Department of Mathematical Sciences University of Delaware NewarkDE19716 United States State Key Laboratory of Nuclear Physics and Technology School of Physics Peking University Beijing100871 China Argonne Leadership Computing Facility Argonne National Laboratory ArgonneIL60439 United States Department of Physics University of Washington SeattleWA98195 United States Computer Science and Engineering Toyohashi University of Technology ToyohashiAichi441-8580 Japan Louisiana State University Baton RougeLA70803 United States Department of Physics LaSierra University RiversideCA92505 United States Theoretical and Computational Molecular Science Institute for Molecular Science OkazakiAichi444-8585 Japan

MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods with guaranteed precision that are based on multiresolution analysis and separated representations. Underpinning the numerical capabilities is a powerful petascale parallel programming environment that aims to increase both programmer productivity and code scalability. This paper describes the features and capabilities of MADNESS and briefly discusses some current applications in chemistry and several areas of physics. © 2016 Society for Industrial and Applied mathematics.

关键词： Multiresolution analysis

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Exploiting structural properties during carbon nanotube simulation

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2015年 9156卷 339-354页

作者： Burger, Michael Bischof, Christian Schröppel, Christian Wackerfuß, Jens Graduate School of Computational Engineering TU Darmstadt Dolivostr. 15 Darmstadt64293 Germany Institute for Scientific Computing TU Darmstadt Mornewegstr. 30 Darmstadt64293 Germany Institute for Structural Analysis University of Kassel Mönchebergstr. 7 Kassel34109 Germany

In this paper, we present a novel matrix-free algorithm for the simulation of the mechanical behavior of carbon nanotubes (CNTs). For small deformations, this algorithm is capable of exploiting the inherent symmetry within CNT structures. The symmetry information is encoded with a graph algebra (GA) construction process and preserved within a tuple based atom-indexing. The exploitation of symmetry leads to a reduction of the needed calculations by a factor of more than 100 in the case of larger CNTs. Combining the usage of symmetry information with a new potential caching mechanism, our software is able to store even large tubes in a compressed way with only a few megabytes of data. Altogether, our implementation allows a matrix-free, resourceaware simulation of CNTs. For larger cases it is only about the factor 1.45 -1.6 slower than the reference solution with a fully assembled stiffness matrix, but consumes twelve times less memory. Also first results of the parallelization of our new algorithm are presented. © Springer International Publishing Switzerland 2015.

关键词： Carbon nanotubes

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Analysis of Sparse Quasi-Newton Updates with Positive Definite Matrix Completion

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Journal of the Operations Research Society of China 2014年第1期2卷 39-56页

作者： Yu-Hong Dai Nobuo Yamashita State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesP.O.Box 2719Beijing 100080People’s Republic of China Department of Applied Mathematics and Physics Graduate School of InformaticsKyoto UniversityKyoto 606-8501Japan

Based on the idea of maximum determinant positive definite matrix completion,Yamashita(math Prog 115(1):1–30,2008)proposed a new sparse quasi-Newton update,called MCQN,for unconstrained optimization problems with sparse Hessian *** exchange of the relaxation of the secant equation,the MCQN update avoids solving difficult subproblems and overcomes the ill-conditioning of approximate Hessian ***,local and superlinear convergence results were only established for the MCQN update with the DFP *** this paper,we extend the convergence result to the MCQN update with the whole Broyden’s convex *** results are also reported,which suggest some efficient ways of choosing the parameter in the MCQN update the Broyden’s family.

关键词： Quasi-Newton method Large-scale problems Sparsity Positive definite matrix completion Superlinear convergence

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A Constrained Cauchy-Born Elasticity Accelerated Multigrid Method for Nanoindentation

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Communications in computational Physics 2014年第2期15卷 470-486页

作者： Jingrun Chen Pingbing Ming Jerry Zhijian Yang Institute of Computational Mathematics and Scientific/Engineering Computing AMSSChinese Academy of SciencesBeijing100190P.R.China. LSEC Institute of Computational Mathematics and Scientific/Engineering ComputingAMSSChinese Academy of SciencesNo.55 East Road Zhong-Guan-CunBeijing100190P.R.China. School of Mathematics and Statistics Wuhan UniversityWuhan430072P.R.China. South Hall 6705 Mathematics DepartmentUniversity of CaliforniaSanta BarbaraCA93106USA

We introduce a new multigrid method to study the lattice statics model arising from nanoindentation.A constrained Cauchy-Born elasticity model is used as the coarse-grid *** method accelerates the relaxation process and considerably reduces the computational *** particular,it saves quite a bit when dislocations nucleate and move,as demonstrated by the simulation results.

关键词： Multigrid method constrained Cauchy-Born elasticity nanoindentation CauchyBorn rule.

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Foreword

Proceedings of the 2016 International Conference on Image Pr...

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Proceedings of the 2016 International Conference on Image Processing, Computer Vision, and Pattern Recognition, IPCV 2016 2016年

作者： Abd-Wahab, Mohd Helmy Al-Bakry, Abbas Al-Holou, Nizar Arabnia, Hamid R. Bhattacharya, Mahua Martinez Castillo, Juan Jose Daimi, Kevin Deligiannidis, Leonidas Djoudi, Lamia Atma Duong, Trung Eshaghian-Wilner, Mary Mehrnoosh Gravvanis, George A. Huang, Ruizhu Jandieri, George Kim, Byung-Gyu Kim, Tai-hoon Korovin, Iakov Lai, Guoming Lee, Hyo Jong Bin Mansor, Muhammad Naufal Marsh, Andrew Mostafaeipour, Ali Park, James J. Patil, Shashikant Ponalagusamy, R. Schaefer, Gerald Singh, Akash Solo, Ashu M.G. Swee, Sim Kok Thomas, Jaya Tinetti, Fernando G. Vladimir, Hahanov Wang, Shiuh-Jeng Yang, Mary Yoe, Hyun You, Jane Zhao, Wenbing Department of Computer Engineering University Tun Hussein Onn Malaysia Malaysia University of IT and Communications Baghdad Iraq Electrical and Computer Engineering Department IEEE/SEM-Computer Chapter University of Detroit Mercy DetroitMI United States University of Georgia United States ABV Indian Institute of Information Technology and Management MHRD Government of India India Acantelys Alan Turing Nikola Tesla Research Group and GIPEB Universidad Nacional Abierta Venezuela Computer Science and Software Engineering Programs Department of Mathematics Computer Science and Software Engineering University of Detroit Mercy DetroitMI United States Department of Computer Information Systems Wentworth Institute of Technology BostonMA United States Synchrone Technologies France Rutgers University State University of New Jersey New Jersey United States University of Southern California California United States Electrical Engineering University of California Los Angeles Los Angeles [UCLA CA United States Advanced Scientific Computing Applied Math and Applications Research Group Applied Mathematics and Numerical Computing and Department of ECE School of Engineering Democritus University of Thrace Xanthi Greece Texas Advanced Computing Center University of Texas AustinTX United States Georgian Technical University Tbilisi Georgia Institute of Cybernetics Georgian Academy of Science Georgia Multimedia Processing CommunicationsLab.[MPCL Department of Computer Science and Engineering College of Engineering SunMoon University Korea Republic of School of Information and Computing Science University of Tasmania Australia Southern Federal University Russia Computer Science and Technology Sun Yat-Sen University Guangzhou China Center for Advanced Image and Information Technology Division of Computer Science and Engineering Chonbuk National University Korea Republic of Faculty of Engineering Technology Kampus Uniciti Alam Universiti Malaysia Perlis UniMAP Malaysi

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A software platform for finite element simulation of ion permeation in ion channel systems

A software platform for finite element simulation of ion per...

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8th IUPAP International Conference on Biological Physics(第八届IUPAP国际生物物理大会)

作者： Benzhuo Lu Bin Tu Yan Xie Linbo Zhang Minxin Chen Institute of Computational Mathematics and Scientific Engineering Computing CAS BeijingChina

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Finite element implicit solvent modeling of molecular solvation and ionic flows

Finite element implicit solvent modeling of molecular solvat...

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International Conference on Theoretical and High Performance computational Chemistry 2014

作者： Tu Bin Xie Yan Bai Shiyang Chen Minxin Zhang Linbo Lu Benzhuo Institute of Computational Mathematics and Scientific/Engineering Computing Chinese Academy of Sciences

We will present a atomic-continuum modeling framework based on unstructured mesh to study molecular solvation in aqueous salt solution, as well as nonequilibrium ionic flow in ion channel. Unstructured mesh allows employment of well-established finite element/boundary element methods and packages to achieve high computational speed, accuracy and expandability. We developed a robust molecular surface mesh generation software, TMSmesh, to handle complex and arbitrarily large biomolecular systems in PDB, which allows applying FEM/BEM to continuum molecular modeling for general biomolecular systems, especially for large-scale and complicate systems. With the surface mesh and our latest version of AFMPB combining a parallel adaptive new version fast multipole method and BEM, we can successfully compute the PB electrostatics of a virus molecule with more than one million atoms and with more than ten million triangles in the surface mesh. For nonlinear PB cases and more general non-equilibrium electro-diffusion processes described by the Poisson-Nernst-Planck equations, we resort to a parallel adaptive finite element method, and the PB can be treated as a special case of PNP model. PNP modeling tracks particle diffusion and time information, and allows convenient incorporation of more physical effects such as size effects and ion-ion correlations in the model. Examples of non-equilibrium simulation will be given on the diffusion controlled substrate-enzyme encounter dynamics and on ionic flow through an ion channel. In addition, we also specifically designed a visualization system, VCMM, to facilitate continuum modeling based on unstructured mesh, which is not supported by usual visual systems in molecular modeling community. VCMM is a comprehensive system for visualizing and analyzing data from generic continuum molecular modeling. It can visualize molecule, mesh(especially unstructured mesh), and numerical results all at once. With these highly technical approaches and a

关键词： Solvation,ion flow,continuum modeling,finite element/boundary element method,meshing

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On the Effect of Ghost Force in the Quasicontinuum Method:Dynamic Problems in One Dimension

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Communications in computational Physics 2014年第3期15卷 647-676页

作者： Xiantao Li Pingbing Ming Department of Mathematics the Pennsylvania State UniversityUniversity ParkPennsylvania16802USA LSEC Institute of Computational Mathematics and Scientific/Engineering ComputingAMSSChinese Academy of SciencesNo.55East Road Zhong-Guan-CunBeijing100190P.R.China

Numerical error caused by“ghost forces”in a quasicontinuum method is studied in the context of dynamic *** error in the discrete W^(1,∞)norm is analyzed for the time scale O(ε)and the time scale O(1)withεbeing th... 详细信息

关键词： Quasicontinuum methods ghost force dynamic problems

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Peridynamic State-Based Models and the Embedded-Atom Model

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Communications in computational Physics 2014年第1期15卷 179-205页

作者： Pablo Seleson Michael L.Parks Max Gunzburger Institute for Computational Engineering and Sciences 201 East 24th StStop C0200AustinTexas 78712-1229USA. Sandia National Laboratories Computing Research CenterP.O.Box 5800MS 1320AlbuquerqueNM 87185-1320USA. Department of Scientific Computing 400 Dirac Science LibraryFlorida State UniversityTallahasseeFL 32306-4120USA.

We investigate connections between nonlocal continuum models and molecular dynamics.A continuous upscaling of molecular dynamics models of the form of the embedded-atom model is presented,providing means for simulating molecular dynamics systems at greatly reduced *** are presented for structured and structureless material models,supported by computational *** nonlocal continuum models are shown to be instances of the state-based peridynamics *** relating multibody peridynamic models and upscaled nonlocal continuum models are derived.

关键词： Peridynamics multibody potentials embedded-atom molecular dynamics.

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