Surface detection, meshing and analysis during large molecular dynamics simulations

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New techniques are presented for the detection and analysis of surfaces and interfaces in atomistic simulations of solids. Atomistic and other particle-based simulations have no inherent notion of a surface, only atomic positions and interactions. The algorithms we introduce here provide an unambiguous means to determine which atoms constitute the surface, and the list of surface atoms and a tessellation (meshing) of the surface are determined simultaneously. The algorithms have been implemented and demonstrated to run automatically (on the fly) in a large-scale parallel molecular dynamics (MD) code on a supercomputer. We demonstrate the validity of the method in three ... continued below

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Dupuy, L M & Rudd, R E August 1, 2005.

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New techniques are presented for the detection and analysis of surfaces and interfaces in atomistic simulations of solids. Atomistic and other particle-based simulations have no inherent notion of a surface, only atomic positions and interactions. The algorithms we introduce here provide an unambiguous means to determine which atoms constitute the surface, and the list of surface atoms and a tessellation (meshing) of the surface are determined simultaneously. The algorithms have been implemented and demonstrated to run automatically (on the fly) in a large-scale parallel molecular dynamics (MD) code on a supercomputer. We demonstrate the validity of the method in three applications in which the surfaces and interfaces evolve: void surfaces in ductile fracture, the surface morphology due to significant plastic deformation of a nanoscale metal plate, and the interfaces (grain boundaries) and void surfaces in a nanoscale polycrystalline system undergoing ductile failure. The technique is found to be quite robust, even when the topology of the surfaces changes as in the case of void coalescence where two surfaces merge into one. It is found to add negligible computational overhead to an MD code, and is much less expensive than other techniques such as the solvent-accessible surface.

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PDF-file: 24 pages; size: 0 Kbytes

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  • Journal Name: Modelling and Simulations in Materials Science and Engineering; Journal Volume: 14; Journal Issue: 2

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  • Report No.: UCRL-JRNL-214271
  • Grant Number: W-7405-ENG-48
  • Office of Scientific & Technical Information Report Number: 884791
  • Archival Resource Key: ark:/67531/metadc873791

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

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  • August 1, 2005

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  • Sept. 21, 2016, 2:29 a.m.

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  • Dec. 2, 2016, 2:44 p.m.

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Dupuy, L M & Rudd, R E. Surface detection, meshing and analysis during large molecular dynamics simulations, article, August 1, 2005; Livermore, California. (digital.library.unt.edu/ark:/67531/metadc873791/: accessed October 23, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.