The ENUF method-Ewald summation based on nonuniform fast Fourier transform: Implementation, parallelization, and application
| Autor: | Aatto Laaksonen, Yong-Lei Wang, You-Liang Zhu, Bin Li, Sheng-Chun Yang |
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| Rok vydání: | 2020 |
| Předmět: |
Floating point
Computational complexity theory Fast Fourier transform FOS: Physical sciences Condensed Matter - Soft Condensed Matter 010402 general chemistry 01 natural sciences Ewald summation Physics - Chemical Physics 0103 physical sciences Periodic boundary conditions Statistical physics Time complexity Physics Chemical Physics (physics.chem-ph) Condensed Matter - Materials Science Mesoscopic physics 010304 chemical physics Materials Science (cond-mat.mtrl-sci) General Chemistry Computational Physics (physics.comp-ph) Electrostatics 0104 chemical sciences Computational Mathematics Soft Condensed Matter (cond-mat.soft) Physics - Computational Physics |
| Zdroj: | Journal of computational chemistryREFERENCES. 41(27) |
| ISSN: | 1096-987X |
| Popis: | Computer simulations of model systems are widely used to explore striking phenomena in promising applications spanning from physics, chemistry, biology, to materials science and engineering. The long range electrostatic interactions between charged particles constitute a prominent factor in determining structures and states of model systems. How to efficiently calculate electrostatic interactions in model systems subjected to partial or full periodic boundary conditions has been a grand challenging task. In the past decades, a large variety of computational schemes have been proposed, among which the Ewald summation method is the most reliable route to accurately deal with electrostatic interactions in model systems. In addition, extensive effort has been done to improve computational efficiency of the Ewald summation based methods. Representative examples are approaches based on cutoffs, reaction fields, multi-poles, multi-grids, and particle-mesh schemes. We sketched an ENUF method, an abbreviation for the Ewald summation method based on Non-Uniform fast Fourier transform technique, and have implemented this method in particle-based simulation packages to calculate electrostatic energies and forces at micro- and mesoscopic levels. Extensive computational studies of conformational properties of polyelectrolytes, dendrimer-membrane complexes, and ionic fluids demonstrated that the ENUF method and its derivatives conserve both energy and momentum to floating point accuracy, and exhibit a computational complexity of $\mathcal{O}(N\log N)$ with optimal physical parameters. These ENUF based methods are attractive alternatives in molecular simulations where high accuracy and efficiency of simulation methods are needed to accelerate calculations of electrostatic interactions at extended spatiotemporal scales. Comment: 46 pages, 8 figures |
| Databáze: | OpenAIRE |
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