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Embedded divide-and-conquer algorithmon hierarchical real-space grids: parallelmolecular dynamics simulation based onlinear-scaling density functional theoryAuthors:Shimojo, Fuyuki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

Affiliation:AA(Collaboratory for Advanced Computing and Simulations, Department ofComputer Science, Department of Physics & Astronomy, Department of MaterialsScience & Engineering, University of Southern California, Los Angeles, CA90089-0242, USA; Department of Physics, Kumamoto University, Kumamoto860-8555, Japan), AB(Collaboratory for Advanced Computing and Simulations,Department of Computer Science, Department of Physics & Astronomy,

Department of Materials Science & Engineering, University of SouthernCalifornia, Los Angeles, CA 90089-0242, USA), AC(Collaboratory for AdvancedComputing and Simulations, Department of Computer Science, Department ofPhysics & Astronomy, Department of Materials Science & Engineering, Universityof Southern California, Los Angeles, CA 90089-0242, USA), AD(Collaboratory forAdvanced Computing and Simulations, Department of Computer Science,Department of Physics & Astronomy, Department of Materials Science &Engineering, University of Southern California, Los Angeles, CA 90089-0242,USA)Publication:Computer Physics Communications, Volume 167, Issue 3, p. 151-164.

Publication Date:05/2005

Origin:ELSEVIER

Keywords:02.70.-c, 02.70.Ns, 71.15.-m

Abstract Copyright:Elsevier B.V.

DOI:10.1016/j.cpc.2005.01.005

Bibliographic Code:2005CoPhC.167..151S

Abstract

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A linear-scaling algorithm has beendeveloped to perform large-scale molecular-dynamics (MD) simulations, in whichinteratomic forces are computed quantum mechanically in the framework of thedensity functional theory. A divide-and-conquer algorithm is used to compute theelectronic structure, where non-additive contribution to the kinetic energy isincluded with an embedded cluster scheme. Electronic wave functions arerepresented on a real-space grid, which is augmented with coarse multigrids toaccelerate the convergence of iterative solutions and adaptive fine grids aroundatoms to accurately calculate ionic pseudopotentials. Spatial decomposition is

employed to implement the hierarchical-grid algorith mon massively parallel computers. A converged solution to the electronic-structureproblem is obtained for a 32,768-atom amorphous CdSe system on 512 IBMPOWER4 processors. The total energy is well conserved during MD simulationsof liquid Rb, showing the applicability of this algorithm to first principles MDsimulations. The parallel efficiency is 0.985 on 128 Intel Xeo

n processors for a 65,536-atom CdSe system.--------------------------------------------------------------------------------

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