# Register now to access 7 million high quality study materials (What's Course Hero?) Course Hero is the premier provider of high quality online educational resources. With millions of study documents, online tutors, digital flashcards and free courseware, Course Hero is helping students learn more efficiently and effectively. Whether you're interested in exploring new subjects or mastering key topics for your next exam, Course Hero has the tools you need to achieve your goals.

22 Pages

### 01SurveyMD

Course: CS 653, Fall 2008
School: USC
Rating:

Word Count: 5641

#### Document Preview

Dynamics Molecular I: Principles Basics of the molecular-dynamics (MD) method1-3 are described, along with corresponding data structures in program, md.c. Newtons Second Law of Motion TRAJECTORY, COORDINATE, AND ACCELERATION Physical system = a set of atomic coordinates: r {ri = (xi ,yi ,zi ) | xi ,yi ,zi &quot; #,i = 0,...,N \$ 1} , where ! is the set of r numbers (in the program, represented by a double...

Register Now

#### Unformatted Document Excerpt

Coursehero >> California >> USC >> CS 653

Course Hero has millions of student submitted documents similar to the one
below including study guides, practice problems, reference materials, practice exams, textbook help and tutor support.

Course Hero has millions of student submitted documents similar to the one below including study guides, practice problems, reference materials, practice exams, textbook help and tutor support.

Find millions of documents on Course Hero - Study Guides, Lecture Notes, Reference Materials, Practice Exams and more. Course Hero has millions of course specific materials providing students with the best way to expand their education.

Below is a small sample set of documents:

USC - CS - 653
Minimal Complex Analysis Complex function: A mapping from a complex variable z = x + iy (i = f(z) C.&quot;1) to a complex numberDifferentiation: A complex function f(z) at z is differentiable if the quantity ! f (z + &quot;z) # f (z)&quot;zconverges to a
USC - CS - 653
JOURNALOF COMPUTATIONALPHYSICS73, 315-348 (1987)A Fast Algorithmfor ParticleANDSimulations*L. GREENCARDV. ROKHLINDepartment of Computer Science, Yale Lnipersiry, New Haven, Connecticut 06520 Received June 10. 1986; revised February
USC - CS - 653
ELSEYIER2s -/.-I@Computer Physics Communications Computer Physics Communications ( 1997)59-69 104Parallel multilevel preconditioned conjugate-gradient approach to variable-charge molecular dynamicsAiichiro Nakano Depurtment of Computer Scienc
USC - CS - 653
Computer Physics Communications 153 (2003) 445461 www.elsevier.com/locate/cpcScalable and portable implementation of the fast multipole method on parallel computers Shuji Ogata a , Timothy J. Campbell b , Rajiv K. Kalia c,d , Aiichiro Nakano c,d,
USC - CS - 653
Reversiblemultipletime scale moleculardynamicsM. Tuckermar?) G. J. Martynaand B. J. BerneDepartment of Chemistry, Columbia University, New York, New York 10027 Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvani
USC - CS - 653
Computer Physics CommunicationsELSEVIERComputer Physics Communications 83 (1994) 197214Multiresolution molecular dynamics algorithm for realistic materials modeling on parallel computersAiichiro Nakano, Rajiv K. Kalia, Priya VashishtaConcurrent
USC - CS - 653
Message Passing Interface (MPI) ProgrammingMPI (Message Passing Interface) is a standard message passing system that enables us to write and run applications on parallel computers. In 1992, MPI Forum was formed to develop a portable message passing
USC - CS - 653
OpenMP ProgrammingAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Department of Computer Science Department of Physics &amp; Astronomy Department of Chemical Engineering &amp; Materials Science University of Southern California Email: ana
USC - CS - 653
Hybrid MPI+OpenMP Parallel MDAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Department of Computer Science Department of Physics &amp; Astronomy Department of Chemical Engineering &amp; Materials Science University of Southern California
USC - CS - 653
Parallel Molecular DynamicsThis chapter explains the example parallel MD program, pmd.c, in detail.Spatial Decomposition Spatial decomposition: The physical system to be simulated is partitioned into subsystems of equal volume. Processors in a pa
USC - CS - 653
Parallel Molecular DynamicsAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Department of Computer Science Department of Physics &amp; Astronomy Department of Chemical Engineering &amp; Materials Science University of Southern California E
USC - CS - 653
Scalability Metrics for Parallel Molecular DynamicsParallel EfficiencyWe define the efficiency of a parallel program running on P processors to solve a problem of size W. Let T(W, P) be the execution time of this parallel program. Speed of the prog
USC - CS - 653
Anton, a Special-Purpose Machine for Molecular Dynamics SimulationDavid E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey S. Kuskin, Richard H. Larson, John K. Salmon, Cliff Young, Brannon Batson, Kevin J. Bowers, Jack C. Chao, Michael P. Eastwood,
USC - CS - 653
A Fast, Scalable Method for the Parallel Evaluation of Distance-Limited Pairwise Particle InteractionsDAVID E. SHAWD. E. Shaw Research and Development, LLC and Center for Computational Biology and Bioinformatics, Columbia University, 120 W. 45th S
USC - CS - 653
Divide-and-Conquer Parallelization ParadigmDivide-and-Conquer Simulation Algorithms Divide-and-conquer (DC) algorithms: Recursively partition a problem into subprogram of roughly equal size. If subprogram can be solved independently, there is a pos
USC - CS - 653
Divide-&amp;-Conquer ParallelismAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Department of Computer Science Department of Physics &amp; Astronomy Department of Chemical Engineering &amp; Materials Science University of Southern California
USC - CS - 653
Computational Materials Science 38 (2007) 642652 www.elsevier.com/locate/commatsciA divide-and-conquer/cellular-decomposition framework for million-to-billion atom simulations of chemical reactionsAiichiro Nakano a,*, Rajiv K. Kalia a, Ken-ichi No
USC - CS - 653
DE NOVO ULTRASCALE ATOMISTIC SIMULATIONS ON HIGH-END PARALLEL SUPERCOMPUTERSAiichiro Nakano Rajiv K. Kalia1 Ken-ichi Nomura1 Ashish Sharma1, 2 Priya Vashishta1 Fuyuki Shimojo1,3 4 Adri C. T. van Duin 4 William A. Goddard, III 5 Rupak Biswas Deepak S
USC - CS - 653
Load BalancingAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Department of Computer Science Department of Physics &amp; Astronomy Department of Chemical Engineering &amp; Materials Science University of Southern California Email: anakano
USC - CS - 653
Lanczos Method for EigensystemsAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Department of Computer Science Department of Physics &amp; Astronomy Department of Chemical Engineering &amp; Materials Science University of Southern Californ
USC - CS - 653
Supplementary Derivations for the Lanczos-Algorithm LectureSpectral representation The eigenvalues and eigenvectors satisfyn n\$ Aij q (&quot; ) = #&quot; qi(&quot; ) = \$ qi(&quot; ) #%&amp;%&quot; , jj=1%=1()(1)where &quot;#\$ = 1 (\$ = #); 0 (\$ % #). Define an orthogona
USC - CS - 653
C3P 913June 1990Performance of Dynamic Load Balancing Algorithms for Unstructured Mesh CalculationsRoy D. WilliamsConcurrent Supercomputing Facility California Institute of Technology Pasadena, CaliforniaAbstract If a nite element mesh has a
USC - CS - 653
SIAM J. SCI. COMPUT. Vol. 20, No. 1, pp. 359392c 1998 Society for Industrial and Applied MathematicsA FAST AND HIGH QUALITY MULTILEVEL SCHEME FOR PARTITIONING IRREGULAR GRAPHSGEORGE KARYPIS AND VIPIN KUMAR Abstract. Recently, a number of researc
USC - CS - 653
Applied Numerical Mathematics 52 (2005) 133152www.elsevier.com/locate/apnumNew challenges in dynamic load balancingKaren D. Devine a, , Erik G. Boman a , Robert T. Heaphy a , Bruce A. Hendrickson a , James D. Teresco b,1 , Jamal Faik c , Joseph E
USC - CS - 653
Hypergraph-based Dynamic Load Balancing for Adaptive Scientic ComputationsUmit V. Catalyurek, Erik G. Boman, Karen D. Devine, Doruk Bozda , Robert Heaphy, g and Lee Ann Riesen Ohio State University Sandia National Laboratories Dept. of Biomedical
USC - CS - 653
Optimizing Molecular DynamicsAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Department of Computer Science Department of Physics &amp; Astronomy Department of Chemical Engineering &amp; Materials Science University of Southern California
USC - CS - 653
Improving Memory Hierarchy Performance for Irregular Applications*John Mellor-Crummeyt, T Department of Computer Science, MS 132 Rice University 6100 Main Houston, TX 77005 David Whalleyz, Ken Kennedy?Cjohnmc,ken}@cs.rice.edu AbstractThe gap betw
USC - CS - 653
Metrics and Models for Reordering TransformationsMichelle Mills StroutMathematics and Computer Science Division Argonne National Laboratory Argonne, IL 60439 USAPaul D. HovlandMathematics and Computer Science Division Argonne National Laboratory
USC - CS - 653
SIAM REVIEW Vol. 46, No. 1, pp. 345c 2004 Society for Industrial and Applied MathematicsRecursive Blocked Algorithms and Hybrid Data Structures for Dense Matrix Library SoftwareErik Elmroth Fred Gustavson Isak Jonsson Bo K gstrom aAbstract. Ma
USC - CS - 653
Lattice-Boltzmann (LB) Fluid Simulation on a Playstation3 (PS3) ClusterKen-ichi Nomura, Liu Peng &amp; Richard SeymourCollaboratory for Advanced Computing &amp; Simulations Dept. of Computer Science, Dept. of Physics &amp; Astronomy, Dept. of Chemical Engineer
USC - CS - 653
SCOP3A Rough Guide to Scientic Computing On the PlayStation 3Technical Report UT-CS-07-595 Version 0.1by Alfredo Buttari Piotr Luszczek Jakub Kurzak Jack Dongarra George Bosilca Innovative Computing Laboratory University of Tennessee Knoxville Ap
USC - CS - 653
Parallel Lattice Boltzmann Flow Simulation on a Low-cost PlayStation3 ClusterInternational Journal of Computational Science 1992-6669 (Print) 1992-6677 (Online) www.gip.hk/ijcs 2008 Global Information Publisher (H.K) Co., Ltd. All rights reserved.
USC - CS - 653
CTWatchISSN 1555-9874 VOLUME 3 NUMBER 1 FEBRUARY 2007Coming Multicore Revolution and its ImpactJACK DONGARRAGUEST EDITORthe Promise and Perils of theCTWatch Quarterly February 2007IntroductionOver the past few years, the familiar idea t
USC - CS - 653
Teraflops Research ChipMoores Law Motivates Multi-Core10945nm 45nm2007107More, better transistors Continued benefits from Moores Law+ More cores1051032Teraflops of performance operating on Terabytes of dataEntertainmentWhat is
USC - CS - 653
The Landscape of Parallel Computing Research: A View from BerkeleyKrste Asanovic Ras Bodik Bryan Christopher Catanzaro Joseph James Gebis Parry Husbands Kurt Keutzer David A. Patterson William Lester Plishker John Shalf Samuel Webb Williams Katheri
USC - CS - 653
Accelerating Molecular Modeling Applications with Graphics ProcessorsJOHN E. STONE,1* JAMES C. PHILLIPS,1* PETER L. FREDDOLINO,1,2* DAVID J. HARDY,1* LEONARDO G. TRABUCO,1,2 KLAUS SCHULTEN1,2,32Beckman Institute, University of Illinois at Urbana-
USC - CS - 653
Harvesting graphics power for MD simulationsarXiv:0709.3225v1 [cond-mat.other] 20 Sep 2007J.A. van Meel , A. Arnold , D. Frenkel , S.F. Portegies Zwart , R.G. Belleman February 2, 2008Abstract We discuss an implementation of molecular dynamics (M
USC - CS - 653
1 Quantum Dynamics BasicsIn this chapter, we will simulate the dynamics of a particle, such as an electron, which follows the law of quantum mechanics [1]. Basics of the quantum-dynamics (QD) method [2-5] are described, along with corresponding data
USC - CS - 653
Quantum Dynamics BasicsSpectral MethodIn this chapter, we will solve the time-dependent Schrdinger equation using another numerical technique, i.e., the spectral method, which is based on Fourier transformation.1.Discrete Fourier TransformCons
USC - CS - 653
Parallelizing Quantum DynamicsAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Department of Computer Science Department of Physics &amp; Astronomy Department of Chemical Engineering &amp; Materials Science University of Southern Californi
USC - CS - 653
Multiresolution MethodsAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Department of Computer Science Department of Physics &amp; Astronomy Department of Chemical Engineering &amp; Materials Science University of Southern California Email
USC - CS - 653
13.10 Wavelet Transforms591The splitting point b must be chosen large enough that the remaining integral over (b, ) is small. Successive terms in its asymptotic expansion are found by integrating by parts. The integral over (a, b) can be done usi
USC - CS - 653
Multiresolution Analysis Using WaveletsHAAR BASIS Consider a one dimensional image on 2 pixels: I[2] = (6, 2). We decompose this information into a smooth and a detailed components. The smooth component is an average of the two intensities:s= (6
USC - CS - 653
19.6 Multigrid Methods for Boundary Value Problems871standard tridiagonal algorithm. Given u n , one solves (19.5.36) for un+1/2 , substitutes on the right-hand side of (19.5.37), and then solves for u n+1 . The key question is how to choose the
USC - CS - 653
Computer Physics CommunicationsELSEVIER Computer Physics Communications 83 (1994) 181196Massively parallel algorithms for computational nanoelectronics based on quantum molecular dynamicsAiichiro Nakano, Priya Vashishta, Rajiv K. KaliaConcurrent
USC - CS - 653
Computer Physics Communications 167 (2005) 151164 www.elsevier.com/locate/cpcEmbedded divide-and-conquer algorithm on hierarchical real-space grids: parallel molecular dynamics simulation based on linear-scaling density functional theoryFuyuki Shi
USC - CS - 653
! ! !43 2 1
USC - CS - 653
Hybrid Particle-Continuum SimulationAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Department of Computer Science Department of Physics &amp; Astronomy Department of Chemical Engineering &amp; Materials Science University of Southern Cal
USC - CS - 653
RAPID COMMUNICATIONSPHYSICAL REVIEW B, VOLUME 64, 161102 RLinear scaling relaxation of the atomic positions in nanostructures Stefan Goedecker, Frederic Lancon, and Thierry Deutsch ` Departement de Recherche Fondamentale sur la Matiere Conden
USC - CS - 653
Computer Physics Communications 138 (2001) 143154 www.elsevier.com/locate/cpcHybrid nite-element/molecular-dynamics/ electronic-density-functional approach to materials simulations on parallel computersShuji Ogata a , Elefterios Lidorikis b , Fuyu
USC - CS - 653
PerspectiveEquation-Free: The Computer-Aided Analysis of Complex Multiscale SystemsIoannis G. KevrekidisDept. of Chemical Engineering, and PACM and Mathematics, Princeton University, Princeton, NJ 08544C. William GearDept. of Chemical Engineer
USC - CS - 653
ARTICLE IN PRESSJournal of the Mechanics and Physics of solids 53 (2005) 16501685 www.elsevier.com/locate/jmpsMultiscale modeling of the dynamics of solids at nite temperatureXiantao Lia, Weinan EbaProgram in Applied and Computational Mathema
USC - CS - 653
Comput. Methods Appl. Mech. Engrg. 196 (2007) 908922 www.elsevier.com/locate/cmaGeneralized mathematical homogenization of atomistic media at nite temperatures in three dimensionsJacob Fish *, Wen Chen, Renge LiRensselaer Polytechnic Institute, T
USC - CS - 653
VOLUME 93, NUMBER 17PHYSICA L R EVIEW LET T ERSweek ending 22 OCTOBER 2004Learn on the Fly: A Hybrid Classical and Quantum-Mechanical Molecular Dynamics Simulation Gabor Csa nyi,1 T. Albaret,3 M. C. Payne,1 and A. De Vita 2,3Cavendish Laborat
USC - CS - 653
Center for Turbulence Research Annual Research Briefs 200597A python approach to multi-code simulations: CHIMPSBy J. U. Schlter, X. Wu, E. v. d. Weide, S. Hahn, u M. Herrmann, J. J. Alonso A N D H. Pitsch1. IntroductionSimulations of real wor
USC - CS - 653
Visualizing Molecular Dynamics IWindowingGraphic LibraryOpenGL OpenGL: A standard, hardware-independent interface to graphics hardware (e.g., SGI InfiniteReality2 Graphics Engine). A set of graphics routines defined on the OpenGL virtual graphics
USC - CS - 653
Scientic Visualization BasicsAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Dept. of Computer Science, Dept. of Physics &amp; Astronomy, Dept. of Chemical Engineering &amp; Materials Science University of Southern California Email: anak
USC - CS - 653
Massive Dataset VisualizationAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Dept. of Computer Science, Dept. of Physics &amp; Astronomy, Dept. of Chemical Engineering &amp; Materials Science University of Southern California Email: anak
USC - CS - 653
Ashish Sharma sharmaa@usc.edu Collaboratory for Advanced Computing and Simulations Dept. of Computer Science Aiichiro Nakano anakano@usc.edu Dept. of Computer Science Rajiv K. Kalia rkalia@usc.edu Dept. of Physics &amp; Astronomy Priya Vashishta priyav@u