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CPHYSICS
2008

A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations

11 years 1 months ago
A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations
A scalable parallel algorithm has been designed to perform multimillion-atom molecular dynamics (MD) simulations, in which first principlesbased reactive force fields (ReaxFF) describe chemical reactions. Environment-dependent bond orders associated with atomic pairs and their derivatives are reused extensively with the aid of linked-list cells to minimize the computation associated with atomic n-tuple interactions (n 4 explicitly and 6 due to chain-rule differentiation). These n-tuple computations are made modular, so that they can be reconfigured effectively with a multiple time-step integrator to further reduce the computation time. Atomic charges are updated dynamically with an electronegativity equalization method, by iteratively minimizing the electrostatic energy with the charge-neutrality constraint. The ReaxFF-MD simulation algorithm has been implemented on parallel computers based on a spatial decomposition scheme combined with distributed n-tuple data structures.
Ken-ichi Nomura, Rajiv K. Kalia, Aiichiro Nakano,
Added 10 Dec 2010
Updated 10 Dec 2010
Type Journal
Year 2008
Where CPHYSICS
Authors Ken-ichi Nomura, Rajiv K. Kalia, Aiichiro Nakano, Priya Vashishta
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