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One of the major design verification challenges in the development of Anton, a massively parallel special-purpose machine for molecular dynamics, was to provide evidence that computations spanning more than a quadrillion clock cycles will produce valid scientific results. Our verification methodology addressed this problem by using a hierarchy of RTL, architectural, and numerical simulations. Block-...
Anton is a massively parallel special-purpose supercomputer designed to accelerate molecular dynamics (MD) simulations by several orders of magnitude, making possible for the first time the atomic-level simulation of many biologically important phenomena that take place over microsecond to millisecond time scales. The majority of the computation required for MD simulations involves the calculation...
Recent contributions to the 3-D vortex methods are presented. Following Cottet, the particles strength exchange (PSE) scheme for diffusion is modified in the vicinity of solid boundaries to avoid a spurious vorticity flux and to enforce a zero-normal component of vorticity during the convection/PSE step. The vortex sheet algorithm used to enforce the no-slip boundary condition through a vorticity...
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