The authors develop an efficient particle labeling procedure based on a linked cell algorithm which is shown to reduce the computing time for a molecular dynamics simulation by a factor of 3. They prove that the improvement of performance is due to the efficient fulfillment of both spatial and temporal locality principles, as implemented by the contiguity of labels corresponding to interacting atoms. Finally, they show that the present label reordering procedure can be used to devise an efficient parallel one-dimensional domain decomposition molecular dynamics scheme.
Abstract Motivation: With the potential availability of nanopore devices that can sense the bases of translocating single-stranded DNA (ssDNA), it is likely that ‘reads’ of leng...
CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. I...
Efficient use of a distributed memory parallel computer requires that the computational load be balanced across processors in a way that minimizes interprocessor communication. ...
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