Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics
文献类型：期刊论文
| 作者 | Zheng, Mo1,2; Li, Xiaoxia1; Guo, Li1 |
| 刊名 | JOURNAL OF MOLECULAR GRAPHICS & MODELLING
 |
| 出版日期 | 2013-04-01 |
| 卷号 | 41期号:0页码:1-11 |
| 关键词 | ReaxFF GPU computing GMD-Reax Reactive molecular dynamics Lammps |
| ISSN号 | 1093-3263 |
| 英文摘要 | Reactive force field (ReaxFF), a recent and novel bond order potential, allows for reactive molecular dynamics (ReaxFF MD) simulations for modeling larger and more complex molecular systems involving chemical reactions when compared with computation intensive quantum mechanical methods. However, ReaxFF MD can be approximately 10-50 times slower than classical MD due to its explicit modeling of bond forming and breaking, the dynamic charge equilibration at each time-step, and its one order smaller time-step than the classical MD, all of which pose significant computational challenges in simulation capability to reach spatio-temporal scales of nanometers and nanoseconds. The very recent advances of graphics processing unit (GPU) provide not only highly favorable performance for GPU enabled MD programs compared with CPU implementations but also an opportunity to manage with the computing power and memory demanding nature imposed on computer hardware by ReaxFF MD. In this paper, we present the algorithms of GMD-Reax, the first GPU enabled ReaxFF MD program with significantly improved performance surpassing CPU implementations on desktop workstations. The performance of GMD-Reax has been benchmarked on a PC equipped with a NVIDIA C2050 GPU for coal pyrolysis simulation systems with atoms ranging from 1378 to 27,283. GMD-Reax achieved speedups as high as 12 times faster than Duin et al.'s FORTRAN codes in Lammps on 8 CPU cores and 6 times faster than the Lammps' C codes based on PuReMD in terms of the simulation time per time-step averaged over 100 steps. GMD-Reax could be used as a new and efficient computational tool for exploiting very complex molecular reactions via ReaxFF MD simulation on desktop workstations. (C) 2013 Elsevier Inc. All rights reserved. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine ; Technology ; Physical Sciences |
| 类目[WOS] | Biochemical Research Methods ; Biochemistry & Molecular Biology ; Computer Science, Interdisciplinary Applications ; Crystallography ; Mathematical & Computational Biology |
| 研究领域[WOS] | Biochemistry & Molecular Biology ; Computer Science ; Crystallography ; Mathematical & Computational Biology |
| 关键词[WOS] | MATRIX VECTOR PRODUCT ; SIMULATIONS ; DECOMPOSITION ; OXIDE |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000317795900001 |
| 公开日期 | 2015-05-27 |
| 源URL | [http://ir.ipe.ac.cn/handle/122111/13348]  |
| 专题 | 过程工程研究所_研究所（批量导入） |
| 作者单位 | 1.Chinese Acad Sci, Inst Proc Engn, State Key Lab Multiphase Complex Syst, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zheng, Mo,Li, Xiaoxia,Guo, Li. Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics[J]. JOURNAL OF MOLECULAR GRAPHICS & MODELLING,2013,41(0):1-11. |
| APA | Zheng, Mo,Li, Xiaoxia,&Guo, Li.(2013).Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics.JOURNAL OF MOLECULAR GRAPHICS & MODELLING,41(0),1-11. |
| MLA | Zheng, Mo,et al."Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics".JOURNAL OF MOLECULAR GRAPHICS & MODELLING 41.0(2013):1-11. |
入库方式： OAI收割
来源：过程工程研究所
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